ALBERT

Beschreibung: The Aegean water masses and circulation structure are studied via two large-scale surveys performed during the late winters of 1988 and 1990 by the R/V Yakov Gakkel of the former Soviet Union. The analysis of these data sheds light on the mechanisms of water mass formation in the Aegean Sea that triggered the outflow of Cretan Deep Water (CDW) from the Cretan Sea into the abyssal basins of the eastern Mediterranean Sea (the so-called Eastern Mediterranean Transient). It is found that the central Aegean Basin is the site of the formation of Aegean Intermediate Water, which slides southward and, depending on their density, renews either the intermediate or the deep water of the Cretan Sea. During the winter of 1988, the Cretan Sea waters were renewed mainly at intermediate levels, while during the winter of 1990 it was mainly the volume of CDW that increased. This Aegean water mass redistribution and formation process in 1990 differed from that in 1988 in two major aspects: (i) during the winter of 1990 the position of the front between the Black Sea Water and the Levantine Surface Water was displaced farther north than during the winter of 1988 and (ii) heavier waters were formed in 1990 as a result of enhanced lateral advection of salty Levantine Surface Water that enriched the intermediate waters with salt. In 1990 the 29.2 isopycnal rose to the surface of the central basin and a large volume of CDW filled the Cretan Basin. It is found that, already in 1988, the 29.2 isopycnal surface, which we assume is the lowest density of the CDW, was shallower than the Kassos Strait sill and thus CDW egressed into the Eastern Mediterranean.

Beschreibung: Published

Beschreibung: 1841-1859

Beschreibung: JCR Journal

Beschreibung: reserved

Beschreibung: In this work, we analyse continuous measurements of microseisms to assess the reliability of the fundamental resonance frequency estimated by means of the horizontal-to-vertical (H/V) spectral ratio within the 0.1–1 Hz frequency range, using short-period sensors (natural period of 1 s). We apply the H/V technique to recordings of stations installed in two alluvial basins with different sedimentary cover thicknesses—the Lower Rhine Embayment (Germany) and the Gubbio Plain (Central Italy). The spectral ratios are estimated over the time–frequency domain, and we discuss the reliability of the results considering both the variability of the microseism activity and the amplitude of the instrumental noise. We show that microseisms measured by short period sensors allow the retrieval of fundamental resonance frequencies greater than about 0.1–0.2 Hz, with this lower frequency bound depending on the relative amplitude of themicroseism signal and the self-noise of the instruments. In particular,we show an examplewhere the considered short-period sensor is connected to instruments characterized by an instrumental noise level which allows detecting only fundamental frequencies greater than about 0.4 Hz. Since the frequency at which the peak of the H/V spectral ratio is biased depends upon the seismic signal-to-instrument noise ratio, the power spectral amplitude of instrumental self-noise should be always considered when interpreting the frequency of the peak as the fundamental resonance frequency of the investigated site.

Beschreibung: Published

Beschreibung: 175-184

Beschreibung: 4.1. Metodologie sismologiche per l'ingegneria sismica

Beschreibung: JCR Journal

Beschreibung: open

Beschreibung: Five non-eddy-resolving oceanic general circulation models driven by atmospheric fluxes derived from the NCEP reanalysis are used to investigate the link between the Gulf Stream (GS) variability, the atmospheric circulation, and the Atlantic meridional overturning circulation (AMOC). Despite the limited model resolution, the temperature at the 200-m depth along the mean GS axis behaves similarly in most models to that observed, and it is also well correlated with the North Atlantic Oscillation (NAO), indicating that a northward (southward) GS shift lags a positive (negative) NAO phase by 0–2 yr. The northward shift is accompanied by an increase in the GS transport, and conversely the southward shift with a decrease in the GS transport. Two dominant time scales appear in the response of the GS transport to the NAO forcing: a fast time scale (less than 1 month) for the barotropic component, and a slower one (about 2 yr) for the baroclinic component. In addition, the two components are weakly coupled. The GS response seems broadly consistent with a linear adjustment to the changes in the wind stress curl, and evidence for baroclinic Rossby wave propagation is found in the southern part of the subtropical gyre. However, the GS shifts are also affected by basin-scale changes in the oceanic conditions, and they are well correlated in most models with the changes in the AMOC. A larger AMOC is found when the GS is stronger and displaced northward, and a higher correlation is found when the observed changes of the GS position are used in the comparison. The relation between the GS and the AMOC could be explained by the inherent coupling between the thermohaline and the wind-driven circulation, or by the NAO variability driving them on similar time scales in the models.

Beschreibung: This research was supported by the PREDICATE project of the European Community, and for M. Bentsen by the Research Council of Norway through RegClim, NOClim, and the Programme of Supercomputing.

Beschreibung: Published

Beschreibung: 2119–2135

Beschreibung: 3.7. Dinamica del clima e dell'oceano

Beschreibung: JCR Journal

Beschreibung: reserved

Beschreibung: A land surface model (LSM) has been included in the ECMWF Hamburg version 4 (ECHAM4) atmospheric general circulation model (AGCM). The LSM is an early version of the Organizing Carbon and Hydrology in Dynamic Ecosystems (ORCHIDEE) and it replaces the simple land surface scheme previously included in ECHAM4. The purpose of this paper is to document how a more exhaustive consideration of the land surface–vegetation processes affects the simulated boreal summer surface climate. To investigate the impacts on the simulated climate, different sets of Atmospheric Model Intercomparison Project (AMIP)-type simulations have been performed with ECHAM4 alone and with the AGCM coupled with ORCHIDEE. Furthermore, to assess the effects of the increase in horizontal resolution the coupling of ECHAM4 with the LSM has been implemented at different horizontal resolutions. The analysis reveals that the LSM has large effects on the simulated boreal summer surface climate of the atmospheric model. Considerable impacts are found in the surface energy balance due to changes in the surface latent heat fluxes over tropical and midlatitude areas covered with vegetation. Rainfall and atmospheric circulation are substantially affected by these changes. In particular, increased precipitation is found over evergreen and summergreen vegetated areas. Because of the socioeconomical relevance, particular attention has been devoted to the Indian summer monsoon (ISM) region. The results of this study indicate that precipitation over the Indian subcontinent is better simulated with the coupled ECHAM4–ORCHIDEE model compared to the atmospheric model alone.

Beschreibung: Published

Beschreibung: 255–278

Beschreibung: 3.7. Dinamica del clima e dell'oceano

Beschreibung: JCR Journal

Beschreibung: partially_open

Beschreibung: In this paper results from the application of an ocean data assimilation (ODA) system, combining a multivariate reduced-order optimal interpolator (OI) scheme with a global ocean general circulation model (OGCM), are described. The present ODA system, designed to assimilate in situ temperature and salinity observations, has been used to produce ocean reanalyses for the 1962–2001 period. The impact of assimilating observed hydrographic data on the ocean mean state and temporal variability is evaluated. A special focus of this work is on the ODA system skill in reproducing a realistic ocean salinity state. Results from a hierarchy of different salinity reanalyses, using varying combinations of assimilated data and background error covariance structures, are described. The impact of the space and time resolution of the background error covariance parameterization on salinity is addressed.

Beschreibung: This work has been funded by the ENACT Project (Contract EVK2-CT2001-00117) for A. Bellucci and P. Di Pietro, and partially by the ENSEMBLES Project (Contract GOCE-CT-2003-505539) for A. Bellucci.

Beschreibung: Published

Beschreibung: 3785-3807

Beschreibung: 3.7. Dinamica del clima e dell'oceano

Beschreibung: JCR Journal

Beschreibung: reserved

Beschreibung: The effect of horizontal resolution on tropical variability is investigated within the modified SINTEX model, SINTEX-F, developed jointly at INGV, IPSL and at the Frontier Research System. The horizontal resolutions T30 and T106 are investigated in terms of the coupling characteristics, frequency and variability of the tropical ocean-atmosphere interactions. It appears that the T106 resolution is generally beneficial even if it does not eliminate all the major systematic errors of the coupled model. There is an excessive shift west of the cold tongue and ENSO variability, and high resolution has also a somewhat negative impact to the variability in the East Indian Ocean. A dominant two-year peak for the NINO3 variabilty in the T30 model is moderated in the T106 as it shifts to longer time scale. At high resolution new processes come into play, as the coupling of tropical instability waves, the resolution of coastal flows at the Pacific Mexican coasts and improved coastal forcing along the coast of South America. The delayed oscillator seems the main mechanism that generates the interannual variability in both models, but the models realize it in different ways. In the T30 model it is confined close to the equator, involving relatively fast equatorial and near-equatorial modes, in the high resolution, it involves a wider latitudinal region and slower waves. It is speculated that the extent of the region that is involved in the interannual variability may be linked to the time scale of the variability itself.

Beschreibung: This research was partially supported by the Italy–USA Cooperation Program of the Italian Ministry of Environment and by the EU projects ENSEMBLES and DYNAMITE.

Beschreibung: Published

Beschreibung: 730-750

Beschreibung: 3.7. Dinamica del clima e dell'oceano

Beschreibung: JCR Journal

Beschreibung: reserved

Beschreibung: Geochemical investigations have shown that there is a considerable inflow of gas into both crater lakes of Monticchio, Southern Italy. These lakes are located in two maars that formed 140 000 years ago during Mt. Vulture volcano s last eruptive activity. Isotopic analyses suggest that CO2 and helium are of magmatic origin; the latter displays 3He ⁄ 4He isotope ratios similar to those measured in olivines of the maar ejecta. In spite of the fact that the amount of dissolved gases in the water is less than that found in Lake Nyos (Cameroon), both the results obtained and the historical reports studied indicate that these crater lakes could be highly hazardous sites, even though they are located in a region currently considered inactive. This could be of special significance in very popular tourist areas such as the Monticchio lakes, which are visited by about 30 000 people throughout the summer, for the most part on Sundays.

Beschreibung: Published

Beschreibung: 83-87

Beschreibung: 2.4. TTC - Laboratori di geochimica dei fluidi

Beschreibung: JCR Journal

Beschreibung: reserved

Beschreibung: On 2009 April 6, the Central Apennines were hit by an Mw = 6.3 earthquake. The region had been shaken since 2008 October by seismic activity that culminated in two foreshocks with Mw 〉 4, 1 week and a few hours before the main shock. We computed seismic moment tensors for 26 events with Mw between 3.9 and 6.3, using the Regional Centroid Moment Tensor (RCMT) scheme. Most of these source parameters have been computed within 1 hr after the earthquake and rapidly revised successively. The focal mechanisms are all extensional, with a variable and sometimes significant strike-slip component. This geometry agrees with the NE–SW extensional deformation of the Apennines, known from previous seismic and geodetic observations. Events group into three clusters. Those located in the southern area have larger centroid depths and a wider distribution of T-axis directions. These differences suggest that towards south a different fault systemwas activated with respect to the SW-dipping normal faults beneath L’Aquila and more to the north.

Beschreibung: In press

Beschreibung: 1.1. TTC - Monitoraggio sismico del territorio nazionale

Beschreibung: JCR Journal

Beschreibung: open

Beschreibung: The Indian Summer Monsoon (ISM) is one of the main components of the Asian summer monsoon. It is well known that one of the starting mechanisms of a summer monsoon is the thermal contrast between land and ocean and that sea surface temperature (SST) and moisture are crucial factors for its evolution and intensity. The Indian Ocean, therefore, may play a very important role in the generation and evolution of the ISM itself. A coupled general circulation model, implemented with a high resolution atmospheric component, appears to be able to simulate the Indian summer monsoon in a realistic way. In particular, the features of the simulated ISM variability are similar to the observations. In this study, the relationships between ISM and Tropical Indian Ocean (TIO) SST anomalies are investigated, as well as the ability of the coupled model to capture those connections. The recent discovery of the Indian Ocean Dipole Mode (IODM) may suggest new perspectives in the relationship between ISM and TIO SST. A new statistical technique, the Coupled Manifold, is used to investigate the TIO SST variability and its relation with the Tropical Pacific Ocean (TPO). The analysis shows that the SST variability in the TIO contains a significant portion that is independent from the TPO variability. The same technique is used to estimate the amount of Indian rainfall variability that can be explained by the Tropical Indian Ocean SST. Indian Ocean SST anomalies are separated in a part remotely forced from the Tropical Pacific Ocean variability and a part independent from that. The relationships between the two SSTA components and the Indian monsoon variability are then investigated in detail.

Beschreibung: Published

Beschreibung: 3083-3105

Beschreibung: 3.7. Dinamica del clima e dell'oceano

Beschreibung: JCR Journal

Beschreibung: reserved

Beschreibung: An assessment of the present European operational marine monitoring and forecasting systems shows how observations, atmospheric forcing fields and ocean models combine to make useful oceanographic products possible.

Beschreibung: Published

Beschreibung: 1081-1090

Beschreibung: open

Beschreibung: Ensemble experiments are performed with five coupled atmosphere–ocean models to investigate the potential for initial-value climate forecasts on interannual to decadal time scales. Experiments are started from similar model-generated initial states, and common diagnostics of predictability are used. We find that variations in the ocean meridional overturning circulation (MOC) are potentially predictable on interannual to decadal time scales, a more consistent picture of the surface temperature impact of decadal variations in the MOC is now apparent, and variations of surface air temperatures in the North Atlantic Ocean are also potentially predictable on interannual to decadal time scales, albeit with potential skill levels that are less than those seen for MOC variations. This intercomparison represents a step forward in assessing the robustness of model estimates of potential skill and is a prerequisite for the development of any operational forecasting system.

Beschreibung: Published

Beschreibung: 1195-1203

Beschreibung: JCR Journal

Beschreibung: reserved

Beschreibung: The strong motion data of 2009 April 6 L’Aquila (Central Italy) earthquake (Mw = 6.3) and of 12 aftershocks (4.1 ≤ Mw ≤ 5.6) recorded by 56 stations of the Italian strong motion network are spectrally analysed to estimate the source parameters, the seismic attenuation, and the site amplification effects. The obtained source spectra for S wave have stress drop values ranging from 2.4 to 16.8 MPa, being the stress drop of the main shock equal to 9.2 MPa. The spectral curves describing the attenuation with distance show the presence of shoulders and bumps, mainly around 50 and 150 km, as consequence of significant reflected and refracted arrivals from crustal interfaces. The attenuation in the first 50 km is well described by a quality factor equal to Q( f ) = 59 f 0.56 obtained by fixing the geometrical spreading exponent to 1. Finally, the horizontal-to-vertical spectral ratio provides unreliable estimates of local site effects for those stations showing large amplifications over the vertical component of motion.

Beschreibung: Published

Beschreibung: 1573–1579

Beschreibung: 4.1. Metodologie sismologiche per l'ingegneria sismica

Beschreibung: JCR Journal

Beschreibung: open

Beschreibung: The accuracy of all types of Vaisala radiosondes and two types of Snow White chilled-mirror hygrosondes was assessed in an intensive in situ comparison with reference hygrometers. Fourteen nighttime reference comparisons were performed to determine a working reference for the radiosonde comparisons. These showed that the night version of the Snow White agreed best with the references [i.e., the NOAA frost-point hygrometer (FPH) and University of Colorado cryogenic frost-point hygrometer (CFH)], but that the daytime version had severe problems with contamination in the humid upper troposphere. Since the RS92 performance was superior to the other radiosondes and to the day version of the Snow White, it was selected to be the working reference. According to the reference comparison, the RS92 has no bias in the mid- and lower troposphere, with deviations 〈±5% in relative humidity (RH). In the upper troposphere, the RS92 has a 5% RH wet bias, which is partly due to the RS92 time lag error and the termination of the heating cycle. It was shown that the time lag effects relating to Vaisala radiosondes can be corrected. Because these were nighttime comparisons, they can be considered to be free from solar radiation effects. Neither the radiosondes nor the Snow White succeeded in reproducing reference class hygrometer profiles in the stratosphere. According to the 29 radiosonde intercomparisons, the RS92 and the modified RS90 (FN) had the best mutual agreement and no bias. The disagreement is largest (〈±10% RH) at low temperatures (T ≪ −30°C), where the FN underestimated (overestimated) in high (low) ambient RH. In comparison with the RS92, the RS90 had a semilinearly increasing wet bias with decreasing temperature, where the bias was 10% RH at −60°C. The RS80-A suffers from a large temperature-dependent dry bias in high RH conditions, being over 30% RH at −60°C and 5% RH near 0°C. The RS80-A dry bias can be almost totally removed with the correction algorithm by Leiterer et al., which was chosen as the best available. The other approach tested tends to overcorrect in high RH conditions when T 〈 −50°C. For T 〉 −30°C it is ineffective and does not correct the RS80-A dry bias in high ambient RH.

Beschreibung: In this study we show a teleconnection pattern relating Outgoing Longwave Radiation (OLR) anomalies over the western Pacific Ocean and sea surface temperature anomalies (SSTA) over the western Indian Ocean over two seasons (Sept-Oct-Nov and Dec-Jan-Feb) at zero lag from observations and atmospheric general circulation model (AGCM) integrations. This teleconnection pattern suggests that a positive SSTA in Sept-Oct-Nov (SON) and Dec-Jan-Feb (DJF) seasons over the western Indian Ocean increases the contemporaneous positive OLR anomalies over the western Pacific Ocean. This teleconnection pattern is also simulated by the Center for Ocean-Land- Atmosphere studies (COLA) AGCM forced with observed SST’s. From the experimental COLA AGCM runs (wherein the Pacific Ocean SST variability is suppressed except for the climatological annual cycle) it is diagnosed that the interannual variability of OLR over the western Pacific Ocean persists because of this teleconnection. In relation to this teleconnection pattern it is shown that there is a significant linear response of the SON and DJF equatorial zonal wind anomaly over the Pacific Ocean to contemporaneous SSTA over the western Indian Ocean which is comparable to that of the eastern and western Pacific Oceans. The experimental AGCM runs clearly show that this response of the equatorial zonal wind anomaly to the western Indian Ocean forcing shifts westward towards the Indian Ocean in the absence of Pacific SST variability.

Beschreibung: Published

Beschreibung: Skill in ensemble-mean dynamical seasonal climate hindcasts with a coupled land-atmosphere model and specified observed sea surface temperature is compared to that for long multi-decade integrations of the same model where the initial conditions are far removed from the seasons of validation. The evaluations are performed for surface temperature and compared among all seasons. Skill is found to be higher in the seasonal simulations than the multi-decadal integrations except during boreal winter. The higher skill is prominent even beyond the first month when the direct influence of the atmospheric initial state elevates model skill. Skill is generally found to be lowest during the winter season for the dynamical seasonal forecasts, equal to that of the long integrations, which show some of the highest skill during winter. The reason for the differences in skill during the non-winter months is attributed to the severe climate drift in the long simulations, manifest through errors in downward fluxes of water and energy over land and evident in soil wetness. The drift presses the land surface to extreme dry or wet states over much of the globe, into a range where there is little sensitivity of evaporation to fluctuations in soil moisture. Thus, the land-atmosphere feedback is suppressed, which appears to lessen the model’s ability to respond correctly over land to remote ocean temperature anomalies.

Beschreibung: Center for Ocean-Land-Atmosphere Studies

Beschreibung: Published

Beschreibung: In this paper, the circulations driven by deep heating and shallow heating are investigated through analytically solving a set of linear equations and examining circulations simulated by a dry primitive equation model. Special emphasis is placed on the low-level mass (moisture) convergence associated with the forced circulation and the maintenance of the shallow and deep heat sources. It is found that the forced circulation driven by shallow heating is more likely to be trapped horizontally near the heating area but relatively extended in the vertical. As a consequence, diabatic heating can not balance adiabatic cooling due to upward motion. At the levels slightly above the top of the heating, a negative vertical gradient of temperature perturbation appears. For the atmosphere driven by deep heating, however, the temperature perturbation cannot accumulate because the heating signals propagate away very fast, allowing an approximate equilibrium between the convective diabatic heating and adiabatic cooling due to upward motion. The converged moisture associated with circulation driven by shallow heating exceeds the amount needed to maintain the heat source. However, the circulation driven by deep heating does not feed back effectively to the moisture convergence, and thus can not be self-sustaining.

Beschreibung: Center for Ocean-Land-Atmosphere Studies - Calverton

Beschreibung: Published

Beschreibung: Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 72 (2006): 1452-1458, doi:10.1128/AEM.72.2.1452-1458.2006.

Beschreibung: Through the fixation of atmospheric nitrogen and photosynthesis, marine diazotrophs play a critical role in the global cycling of nitrogen and carbon. Crocosphaera watsonii is a recently described unicellular diazotroph that may significantly contribute to marine nitrogen fixation in tropical environments. One of the many factors that can constrain the growth and nitrogen fixation rates of marine diazotrophs is phosphorus bioavailability. Using genomic and physiological approaches, we examined phosphorus scavenging mechanisms in strains of C. watsonii from both the Atlantic and the Pacific. Observations from the C. watsonii WH8501 genome suggest that this organism has the capacity for high-affinity phosphate transport (e.g., homologs of pstSCAB) in low-phosphate, oligotrophic systems. The pstS gene (high-affinity phosphate binding) is present in strains isolated from both the Atlantic and the Pacific, and its expression was regulated by the exogenous phosphate supply in strain WH8501. Genomic observation also indicated a broad capacity for phosphomonoester hydrolysis (e.g., a putative alkaline phosphatase). In contrast, no clear homologs of genes for phosphonate transport and hydrolysis could be identified. Consistent with these genomic observations, C. watsonii WH8501 is able to grow on phosphomonoesters as a sole source of added phosphorus but not on the phosphonates tested to date. Taken together these data suggest that C. watsonii has a robust capacity for scavenging phosphorus in oligotrophic systems, although this capacity differs from that of other marine cyanobacterial genera, such as Synechococcus, Prochlorococcus, and Trichodesmium.

Beschreibung: Funding for this research was provided by the NSF OCE Biological Oceanography Program and the Woods Hole Oceanographic Institution Ocean Life Institute.

Beschreibung: Author Posting. © American Society for Microbiology, 2003. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Molecular and Cellular Biology 23 (2003): 9061-9072, doi:10.1128/MCB.23.24.9061-9072.2003.

Beschreibung: Trypanosoma brucei lacks mitochondrial genes encoding tRNAs and must import nuclearly encoded tRNAs from the cytosol. The mechanism and specificity of this process remain unclear. We have identified a unique sequence motif, YGG(C/A)RRC, upstream of the genes encoding mitochondrially localized tRNAs in T. brucei. Both in vitro import studies and in vivo transfection studies indicate that deletion of the YGG(C/A)RRC sequence alters mitochondrial localization of tRNALeu, and in vivo studies also show a decrease in the cellular abundance of tRNALeu. These studies provide direct evidence for cis-acting RNA motifs within precursor tRNAs that facilitate the selection of tRNAs for mitochondrial import in trypanosomes. Furthermore, we found that mutations to the YGG(C/A)RRC sequence also altered the intracellular distribution of other endogenous tRNAs, suggesting a general role for this sequence in tRNA trafficking in trypanosomes.

Beschreibung: This work was supported by the National Institutes of Health grant AI21401 (to S.L.H.).

Beschreibung: Author Posting. © American Society for Microbiology, 2003. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 69 (2003): 2906-2913, doi:10.1128/AEM.69.5.2906-2913.2003.

Beschreibung: We report the isolation and physiological characterization of novel, psychrophilic, iron-oxidizing bacteria (FeOB) from low-temperature weathering habitats in the vicinity of the Juan de Fuca deep-sea hydrothermal area. The FeOB were cultured from the surfaces of weathered rock and metalliferous sediments. They are capable of growth on a variety of natural and synthetic solid rock and mineral substrates, such as pyrite (FeS2), basalt glass (~10 wt% FeO), and siderite (FeCO3), as their sole energy source, as well as numerous aqueous Fe substrates. Growth temperature characteristics correspond to the in situ environmental conditions of sample origin; the FeOB grow optimally at 3 to 10°C and at generation times ranging from 57 to 74 h. They are obligate chemolithoautotrophs and grow optimally under microaerobic conditions in the presence of an oxygen gradient or anaerobically in the presence of nitrate. None of the strains are capable of using any organic or alternate inorganic substrates tested. The bacteria are phylogenetically diverse and have no close Fe-oxidizing or autotrophic relatives represented in pure culture. One group of isolates are γ-Proteobacteria most closely related to the heterotrophic bacterium Marinobacter aquaeolei (87 to 94% sequence similarity). A second group of isolates are α-Proteobacteria most closely related to the deep-sea heterotrophic bacterium Hyphomonas jannaschiana (81 to 89% sequence similarity). This study provides further evidence for the evolutionarily widespread capacity for Fe oxidation among bacteria and suggests that FeOB may play an unrecognized geomicrobiological role in rock weathering in the deep sea.

Beschreibung: Funding for this work was provided by NSF grant OCE-0096992 to K.J.E. We thank J. Seewald for inviting our participation in the cruise that allowed this work to be initiated (sponsored by NSF; OCE-9906752).

Beschreibung: Author Posting. © American Society for Microbiology, 2000. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 66 (2000): 1987-1993, doi:10.1128/AEM.66.5.1987-1993.2000.

Beschreibung: Unicellular protozoan grazers represent a size class of organisms where a transition in the mechanism of chlorobiphenyl (CB) introduction, from diffusion through surface membranes to ingestion of contaminated prey, could occur. This study compares the relative importance of these two processes in the overall uptake of polychlorinated biphenyls by protists. Uptake rates and steady-state concentrations were compared in laboratory cultures of grazing and nongrazing protozoa. These experiments were conducted with a 10-µm marine scuticociliate (Uronema sp.), bacterial prey (Halomonas halodurans), and a suite of 21 CB congeners spanning a range of aqueous solubilities. The dominant pathway of CB uptake by both grazing and nongrazing protozoa was diffusion. Organic-carbon-normalized CB concentrations (in the protozoan cell) were equivalent in grazing and nongrazing protozoa for all congeners studied. Rate constants for uptake into and loss from the protozoan cell were independently determined by using [3,3',4,4'-14C]tetrachlorobiphenyl (IUPAC no. 77), 0.38 ± 0.03 min-1 and (1.1 ± 0.1) × 10-5 (g of organic carbon)-1 min-1, respectively. Magnitudes of the uptake and loss processes were calculated and compared by using a numerical model. The model result was consistent with data from the bioaccumulation experiment and supported the hypothesis that diffusive uptake is faster than ingestive uptake in phagotrophic unicellular protozoa.

Beschreibung: The work described herein was supported by NSF contract no. OCE-9523910 and ONR contract no. N00014-97-1-0718.

Beschreibung: Author Posting. © American Society for Microbiology, 2000. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Journal of Bacteriology 182 (2000): 3867-3869, doi:10.1128/JB.182.13.3867-3869.2000.

Beschreibung: In contrast to genome size variation in most bacterial taxa, the small genome size of Buchnera sp. was shown to be highly conserved across genetically diverse isolates (630 to 643 kb). This exceptional size conservation may reflect the inability of this obligate mutualist to acquire foreign DNA and reduced selection for genetic novelty within a static intracellular environment.

Beschreibung: Financial support was provided by a National Institute of Health postdoctoral training grant to J.J.W. (Center for Insect Science, University of Arizona) and a National Science Foundation grant (DEB- 9815413) to N.A.M.

Beschreibung: Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 72 (2006): 2918-2924, doi:10.1128/AEM.72.4.2918-2924.2006.

Beschreibung: Although the role of iron in marine productivity has received a great deal of attention, no iron storage protein has been isolated from a marine microorganism previously. We describe an Fe-binding protein belonging to the Dps family (DNA binding protein from starved cells) in the N2-fixing marine cyanobacterium Trichodesmium erythraeum. A dps gene encoding a protein with significant levels of identity to members of the Dps family was identified in the genome of T. erythraeum. This gene codes for a putative DpsT. erythraeurm protein (Dpstery) with 69% primary amino acid sequence similarity to Synechococcus DpsA. We expressed and purified Dpstery, and we found that Dpstery, like other Dps proteins, is able to bind Fe and DNA and protect DNA from degradation by DNase. We also found that Dpstery binds phosphate, like other ferritin family proteins. Fe K near-edge X-ray absorption of Dpstery indicated that it has an iron core that resembles that of horse spleen ferritin.

Beschreibung: This work was supported by the Center for Environmental Bioinorganic Chemistry (CHE 0221978).

Beschreibung: Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 72 (2006): 1966-1973, doi:10.1128/AEM.72.3.1966-1973.2006.

Beschreibung: The species diversity, phylogenetic affiliations, and physiological activity rates of carbon monoxide-oxidizing microorganisms were investigated, using new isolates from surface waters collected from the coast of New England and type strains from established collections. A direct isolation method allowed the simultaneous recovery of organisms with different growth rates and nutritional requirements and the identification of marine microorganisms that oxidize CO at an environmentally relevant concentration (42 nM CO). Isolates that oxidized CO at environmentally relevant rates (〉4.5 x 10–11 nmol CO oxidized cell–1 h–1) were taxonomically diverse, with representatives in the alpha and gamma subclasses of the Proteobacteria and the phylum Bacteroidetes, and represent a hitherto unreported metabolic function for several diverse microbial types. Isolates and type strains having the greatest specific rates of CO metabolism (1.1 x 10–10 to 2.3 x 10–10 nmol CO oxidized cell–1 h–1) belonged to the Roseobacter-associated clade (RAC) of the alpha subclass of the Proteobacteria. By using triple-labeled slide preparations, differential counts of active CO-oxidizing RAC cells, total RAC cells, and total bacterial cell counts in environmental samples were obtained. RAC organisms were a major component of total cell numbers (36%). Based on the density of active CO-oxidizing RAC cells in natural samples and RAC-specific metabolic activities determined for pure cultures, active CO-oxidizing RAC cells may contribute up to 15% of the total CO oxidation occurring in coastal waters.

Beschreibung: Funding was provided by National Science Foundation grant OCE-0136876, Coastal Ocean Institute and Rinehart Coastal Research Center grant BI10918, and the Woods Hole Oceanographic Institution Academic Programs Office.

Beschreibung: Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Eukaryotic Cell 5 (2006): 132-139, doi:10.1128/EC.5.1.132-139.2006.

Beschreibung: Trypanosoma brucei brucei is the causative agent of nagana in cattle and can infect a wide range of mammals but is unable to infect humans because it is susceptible to the innate cytotoxic activity of normal human serum. A minor subfraction of human high-density lipoprotein (HDL) containing apolipoprotein A-I (apoA-I), apolipoprotein L-I (apoL-I), and haptoglobin-related protein (Hpr) provides this innate protection against T. b. brucei infection. This HDL subfraction, called trypanosome lytic factor (TLF), kills T. b. brucei following receptor binding, endocytosis, and lysosomal localization. Trypanosoma brucei rhodesiense, which is morphologically and physiologically indistinguishable from T. b. brucei, is resistant to TLF-mediated killing and causes human African sleeping sickness. Human infectivity by T. b. rhodesiense correlates with the evolution of a resistance-associated protein (SRA) that is able to ablate TLF killing. To examine the mechanism of TLF resistance, we transfected T. b. brucei with an epitope-tagged SRA gene. Transfected T. b. brucei expressed SRA mRNA at levels comparable to those in T. b. rhodesiense and was highly resistant to TLF. In the SRA-transfected cells, intracellular trafficking of TLF was altered, with TLF being mainly localized to a subset of SRA-containing cytoplasmic vesicles but not to the lysosome. These results indicate that the cellular distribution of TLF is influenced by SRA expression and may directly determine the organism's susceptibility to TLF.

Beschreibung: This research was supported by a grant from the NIH (AI39033) and support from the Ellison Medical Foundation.

Beschreibung: Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 72 (2006): 5742-5749, doi:10.1128/AEM.00332-06.

Beschreibung: Harmful algal blooms (HABs) are a serious threat to coastal resources, causing a variety of impacts on public health, regional economies, and ecosystems. Plankton analysis is a valuable component of many HAB monitoring and research programs, but the diversity of plankton poses a problem in discriminating toxic from nontoxic species using conventional detection methods. Here we describe a sensitive and specific sandwich hybridization assay that combines fiber-optic microarrays with oligonucleotide probes to detect and enumerate the HAB species Alexandrium fundyense, Alexandrium ostenfeldii, and Pseudo-nitzschia australis. Microarrays were prepared by loading oligonucleotide probe-coupled microspheres (diameter, 3 μm) onto the distal ends of chemically etched imaging fiber bundles. Hybridization of target rRNA from HAB cells to immobilized probes on the microspheres was visualized using Cy3-labeled secondary probes in a sandwich-type assay format. We applied these microarrays to the detection and enumeration of HAB cells in both cultured and field samples. Our study demonstrated a detection limit of approximately 5 cells for all three target organisms within 45 min, without a separate amplification step, in both sample types. We also developed a multiplexed microarray to detect the three HAB species simultaneously, which successfully detected the target organisms, alone and in combination, without cross-reactivity. Our study suggests that fiber-optic microarrays can be used for rapid and sensitive detection and potential enumeration of HAB species in the environment.

Beschreibung: This work was funded by the Sea Grant Technology Program (NA16RG2273).

Beschreibung: Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Eukaryotic Cell 5 (2006): 2062-2071, doi:10.1128/EC.00205-06.

Beschreibung: Trichomonas vaginalis is a unicellular eukaryote that lacks mitochondria and contains a specialized organelle, the hydrogenosome, involved in carbohydrate metabolism and iron-sulfur cluster assembly. We report the identification of two glycine cleavage H proteins and a dihydrolipoamide dehydrogenase (L protein) of the glycine decarboxylase complex in T. vaginalis with predicted N-terminal hydrogenosomal presequences. Immunofluorescence analyses reveal that both H and L proteins are localized in hydrogenosomes, providing the first evidence for amino acid metabolism in this organelle. All three proteins were expressed in Escherichia coli and purified to homogeneity. The experimental Km of L protein for the two H proteins were 2.6 µM and 3.7 µM, consistent with both H proteins serving as substrates of L protein. Analyses using purified hydrogenosomes showed that endogenous H proteins exist as monomers and endogenous L protein as a homodimer in their native states. Phylogenetic analyses of L proteins revealed that the T. vaginalis homologue shares a common ancestry with dihydrolipoamide dehydrogenases from the firmicute bacteria, indicating its acquisition via a horizontal gene transfer event independent of the origins of mitochondria and hydrogenosomes.

Beschreibung: This work was supported by National Institutes of Health (NIH) grants to P.J.J., a Burroughs-Wellcome Molecular Parasitology Award to P.J.J., and an NIH Microbial Pathogenesis Training Grant (2-T32-AI-07323) to M.T.B. A.G.M. was supported by the Marine Biological Laboratory's Program in Global Infectious Disease, funded by the Ellison Medical Foundation.

Beschreibung: Author Posting. © American Society for Microbiology, 2004. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 70 (2004): 1494-1505, doi:10.1128/AEM.70.3.1494-1505.2004.

Beschreibung: Shifts in bacterioplankton community composition along the salinity gradient of the Parker River estuary and Plum Island Sound, in northeastern Massachusetts, were related to residence time and bacterial community doubling time in spring, summer, and fall seasons. Bacterial community composition was characterized with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA. Average community doubling time was calculated from bacterial production ([14C]leucine incorporation) and bacterial abundance (direct counts). Freshwater and marine populations advected into the estuary represented a large fraction of the bacterioplankton community in all seasons. However, a unique estuarine community formed at intermediate salinities in summer and fall, when average doubling time was much shorter than water residence time, but not in spring, when doubling time was similar to residence time. Sequencing of DNA in DGGE bands demonstrated that most bands represented single phylotypes and that matching bands from different samples represented identical phylotypes. Most river and coastal ocean bacterioplankton were members of common freshwater and marine phylogenetic clusters within the phyla Proteobacteria, Bacteroidetes, and Actinobacteria. Estuarine bacterioplankton also belonged to these phyla but were related to clones and isolates from several different environments, including marine water columns, freshwater sediments, and soil.

Beschreibung: This work was supported by two grants from the National Science Foundation (LTER grant OCE-9726921 and Microbial Observatory grant MCB-9977897) and the NASA Astrobiology Institute (cooperative agreement NCC2-1054 to M.L.S.).

Beschreibung: Author Posting. © American Society for Microbiology, 2004. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 70 (2004): 4103-4110, doi:10.1128/AEM.70.7.4103-4110.2004.

Beschreibung: Vibrios are ubiquitous marine bacteria that have long served as models for heterotrophic processes and have received renewed attention because of the discovery of increasing numbers of facultatively pathogenic strains. Because the occurrence of specific vibrios has frequently been linked to the temperature, salinity, and nutrient status of water, we hypothesized that seasonal changes in coastal water bodies lead to distinct vibrio communities and sought to characterize their level of differentiation. A novel technique was used to quantify shifts in 16S rRNA gene abundance in samples from Barnegat Bay, N.J., collected over a 15-month period. Quantitative PCR (QPCR) with primers specific for the genus Vibrio was combined with separation and quantification of amplicons by constant denaturant capillary electrophoresis (CDCE). Vibrio populations identified by QPCR-CDCE varied between summer and winter samples, suggesting distinct warm-water and year-round populations. Identification of the CDCE populations by cloning and sequencing of 16S rRNA genes from two summer and two winter samples confirmed this distinction. It further showed that CDCE populations corresponded in most cases to ~98% rRNA similarity groups and suggested that the abundance of these follows temperature trends. Phylogenetic comparison yielded closely related cultured and often pathogenic representatives for most sequences, and the temperature ranges of these isolates confirmed the trends seen in the environmental samples. Overall, this suggests that temperature is a good predictor of the occurrence of closely related vibrios but that considerable microdiversity of unknown significance coexists within this trend.

Beschreibung: Funding was for this study was provided by grants from Seagrant and NOAA to M.F.P. and graduate fellowships from the National Science Foundation, the Switzer Environmental Science Foundation, and the Whittaker Health Sciences Foundation to J.R.T.

Beschreibung: Author Posting. © American Society for Microbiology, 2005. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 71 (2005): 6383-6387, doi:10.1128/AEM.71.10.6383-6387.2005.

Beschreibung: The ability of metabolically diverse hyperthermophilic archaea to withstand high temperatures, low pHs, high sulfide concentrations, and the absence of carbon and energy sources was investigated. Close relatives of our study organisms, Methanocaldococcus jannaschii, Archaeoglobus profundus, Thermococcus fumicolans, and Pyrococcus sp. strain GB-D, are commonly found in hydrothermal vent chimney walls and hot sediments and possibly deeper in the subsurface, where highly dynamic hydrothermal flow patterns and steep chemical and temperature gradients provide an ever-changing mosaic of microhabitats. These organisms (with the possible exception of Pyrococcus strain GB-D) tolerated greater extremes of low pH, high sulfide concentration, and high temperature when actively growing and metabolizing than when starved of carbon sources and electron donors/acceptors. Therefore these organisms must be actively metabolizing in the hydrothermal vent chimneys, sediments, and subsurface in order to withstand at least 24 h of exposure to extremes of pH, sulfide, and temperature that occur in these environments.

Beschreibung: This study was supported by the NSF (Life in Extreme Environments grant OCE-0085534 to A.T., S.J.M., S.B., K.G.L., S.B., and C.O.W.), the MBL (Environmental Genomes, S/C NCC2-1054) and URI (Subsurface Biospheres) NASA Astrobiology Institute Teams (A.T. and S.J.M.), an NSF Postdoctoral Fellowship in Microbial Biology (M.S.A.), and an NRC Astrobiology postdoctoral fellowship (V.P.E.).

Beschreibung: Author Posting. © American Society for Microbiology, 2002. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in [citation], doi:10.1128/AEM.68.12.6292-6299.2002.

Beschreibung: Wood-boring bivalves of the family Teredinidae (commonly called shipworms) are known to harbor dense populations of gram-negative bacteria within specialized cells (bacteriocytes) in their gills. These symbionts are thought to provide enzymes, e.g., cellulase and dinitrogenase, which assist the host in utilizing wood as a primary food source. A cellulolytic, dinitrogen-fixing bacterium, Teredinibacter turnerae, has been isolated from the gill tissues of numerous teredinid bivalves and has been proposed to constitute the sole or predominant symbiont of this bivalve family. Here we demonstrate that one teredinid species, Lyrodus pedicellatus, contains at least four distinct bacterial 16S rRNA types within its gill bacteriocytes, one of which is identical to that of T. turnerae. Phylogenetic analyses indicate that the three newly detected ribotypes are derived from gamma proteobacteria that are related to but distinct (〉6.5% sequence divergence) from T. turnerae. In situ hybridizations with 16S rRNA-directed probes demonstrated that the pattern of occurrence of symbiont ribotypes within bacteriocytes was predictable and specific, with some bacteriocytes containing two symbiont ribotypes. However, only two of the six possible pairwise combinations of the four ribotypes were observed to cooccur within the same host cells. The results presented here are consistent with the existence of a complex multiple symbiosis in this shipworm species.

Beschreibung: This work was supported by grants from the National Science Foundation (DEB-9420051 and IBN-9982982), the Maine Science and Technology Foundation’s Center for Innovation in Biotechnology, and the University of Maine’s Faculty Research program.

Beschreibung: Author Posting. © American Society for Microbiology, 2000. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 66 (2000): 3125-3133, doi:10.1128/AEM.66.8.3125-3133.2000.

Beschreibung: Species diversity, phylogenetic affiliations, and environmental occurrence patterns of thiosulfate-oxidizing marine bacteria were investigated by using new isolates from serially diluted continental slope and deep-sea abyssal plain sediments collected off the coast of New England and strains cultured previously from Galapagos hydrothermal vent samples. The most frequently obtained new isolates, mostly from 103- and 104-fold dilutions of the continental slope sediment, oxidized thiosulfate to sulfate and fell into a distinct phylogenetic cluster of marine alpha-Proteobacteria. Phylogenetically and physiologically, these sediment strains resembled the sulfate-producing thiosulfate oxidizers from the Galapagos hydrothermal vents while showing habitat-related differences in growth temperature, rate and extent of thiosulfate utilization, and carbon substrate patterns. The abyssal deep-sea sediments yielded predominantly base-producing thiosulfate-oxidizing isolates related to Antarctic marine Psychroflexus species and other cold-water marine strains of the Cytophaga-Flavobacterium-Bacteroides phylum, in addition to gamma-proteobacterial isolates of the genera Pseudoalteromonas and Halomonas-Deleya. Bacterial thiosulfate oxidation is found in a wide phylogenetic spectrum of Flavobacteria and Proteobacteria.

Beschreibung: Andreas Teske was supported by DFG postdoctoral fellowship 262-1/1 and a subsequent WHOI postdoctoral fellowship.

Beschreibung: Author Posting. © American Society for Microbiology, 2007. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Journal of Bacteriology 189 (2007): 7436-7441, doi:10.1128/JB.00524-07.

Beschreibung: Transposition (the movement of discrete segments of DNA, resulting in rearrangement of genomic DNA) initiates when transposase forms a dimeric DNA-protein synaptic complex with transposon DNA end sequences. The synaptic complex is a prerequisite for catalytic reactions that occur during the transposition process. The transposase-DNA interactions involved in the synaptic complex have been of great interest. Here we undertook a study to verify the protein-DNA interactions that lead to synapsis in the Tn5 system. Specifically, we studied (i) Arg342, Glu344, and Asn348 and (ii) Ser438, Lys439, and Ser445, which, based on the previously published cocrystal structure of Tn5 transposase bound to a precleaved transposon end sequence, make cis and trans contacts with transposon end sequence DNA, respectively. By using genetic and biochemical assays, we showed that in all cases except one, each of these residues plays an important role in synaptic complex formation, as predicted by the cocrystal structure.

Beschreibung: This work was supported by NIH grant GM 50692.

Beschreibung: Author Posting. © American Society for Microbiology, 2008. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Journal of Bacteriology 190 (2008): 1484-1487, doi:10.1128/JB.01488-07.

Beschreibung: A series of Tn5 transposases (Tnp's) with mutations at the conserved amino acid position W450, which was structurally predicted to be important for synapsis, have been generated and characterized. This study demonstrates that W450 is involved in hydrophobic (and possibly aromatic) contacts within the Tnp monomer that negatively regulate synaptic complex formation.

Beschreibung: This work was supported by the NIH (grant no. GM50693) and the University of Wisconsin—Madison (grant no. WIS04792) and through the Evelyn Mercer Professorship in Biochemistry and Molecular Biology.

Beschreibung: Author Posting. © American Society for Microbiology, 2004. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 70 (2004): 6230-6239, doi:10.1128/AEM.70.10.6230-6239.2004.

Beschreibung: The occurrence and distribution of magnetotactic bacteria (MB) were studied as a function of the physical and chemical conditions in meromictic Salt Pond, Falmouth, Mass., throughout summer 2002. Three dominant MB morphotypes were observed to occur within the chemocline. Small microaerophilic magnetite-producing cocci were present at the top of the chemocline, while a greigite-producing packet-forming bacterium occurred at the base of the chemocline. The distributions of these groups displayed sharp changes in abundance over small length scales within the water column as well as strong seasonal fluctuations in population abundance. We identified a novel, greigite-producing rod in the sulfidic hypolimnion that was present in relatively constant abundance over the course of the season. This rod is the first MB that appears to belong to the {gamma}-Proteobacteria, which may suggest an iron- rather than sulfur-based respiratory metabolism. Its distribution and phylogenetic identity suggest that an alternative model for the ecological and physiological role of magnetotaxis is needed for greigite-producing MB.

Beschreibung: This work was partially funded by a grant from the Woods Hole Oceanographic Institution Reinhart Coastal Research Center to S.L.S. and K.J.E. S.L.S. was supported by a National Defense Science and Engineering graduate fellowship. D.A.B. was supported by National Science Foundation grant EAR-0311950 and National Aeronautics and Space Administration (NASA) Johnson Space Center grant NAG 9-1115.

Beschreibung: Author Posting. © American Society for Microbiology, 2001. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 67 (2001): 4726-4733, doi:10.1128/AEM.67.10.4726-4733.2001.

Beschreibung: Methanotrophic bacteria play a major role in the global carbon cycle, degrade xenobiotic pollutants, and have the potential for a variety of biotechnological applications. To facilitate ecological studies of these important organisms, we developed a suite of oligonucleotide probes for quantitative analysis of methanotroph-specific 16S rRNA from environmental samples. Two probes target methanotrophs in the family Methylocystaceae (type II methanotrophs) as a group. No oligonucleotide signatures that distinguish between the two genera in this family, Methylocystis and Methylosinus, were identified. Two other probes target, as a single group, a majority of the known methanotrophs belonging to the family Methylococcaceae (type I/X methanotrophs). The remaining probes target members of individual genera of the Methylococcaceae, including Methylobacter, Methylomonas, Methylomicrobium, Methylococcus, and Methylocaldum. One of the family-level probes also covers all methanotrophic endosymbionts of marine mollusks for which 16S rRNA sequences have been published. The two known species of the newly described genus Methylosarcina gen. nov. are covered by a probe that otherwise targets only members of the closely related genus Methylomicrobium. None of the probes covers strains of the newly proposed genera Methylocella and "Methylothermus," which are polyphyletic with respect to the recognized methanotrophic families. Empirically determined midpoint dissociation temperatures were 49 to 57°C for all probes. In dot blot screening against RNA from positive- and negative-control strains, the probes were specific to their intended targets. The broad coverage and high degree of specificity of this new suite of probes will provide more detailed, quantitative information about the community structure of methanotrophs in environmental samples than was previously available.

Beschreibung: This work was supported by the U.S. National Science Foundation (award DEB9708092).

Beschreibung: This paper is not subject to U.S. copyright. The definitive version was published in Journal of Atmospheric and Oceanic Technology 21 (2004): 1448–1461, doi:10.1175/1520-0426(2004)021〈1448:AOAPAD〉2.0.CO;2.

Beschreibung: The accuracy of velocities measured by a pulse-coherent acoustic Doppler profiler (PCADP) in the bottom boundary layer of a wave-dominated inner-shelf environment is evaluated. The downward-looking PCADP measured velocities in eight 10-cm cells at 1 Hz. Velocities measured by the PCADP are compared to those measured by an acoustic Doppler velocimeter for wave orbital velocities up to 95 cm s−1 and currents up to 40 cm s−1. An algorithm for correcting ambiguity errors using the resolution velocities was developed. Instrument bias, measured as the average error in burst mean speed, is −0.4 cm s−1 (standard deviation = 0.8). The accuracy (root-mean-square error) of instantaneous velocities has a mean of 8.6 cm s−1 (standard deviation = 6.5) for eastward velocities (the predominant direction of waves), 6.5 cm s−1 (standard deviation = 4.4) for northward velocities, and 2.4 cm s−1 (standard deviation = 1.6) for vertical velocities. Both burst mean and root-mean-square errors are greater for bursts with ub ≥ 50 cm s−1. Profiles of burst mean speeds from the bottom five cells were fit to logarithmic curves: 92% of bursts with mean speed ≥ 5 cm s−1 have a correlation coefficient R2 〉 0.96. In cells close to the transducer, instantaneous velocities are noisy, burst mean velocities are biased low, and bottom orbital velocities are biased high. With adequate blanking distances for both the profile and resolution velocities, the PCADP provides sufficient accuracy to measure velocities in the bottom boundary layer under moderately energetic inner-shelf conditions.

Beschreibung: This work was funded by the U.S. Geological Survey as part of the Southwest Washington Coastal Erosion Study

Beschreibung: Author Posting. © American Society for Microbiology, 2008. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 74 (2008): 4454-4462, doi:10.1128/AEM.02799-07.

Beschreibung: A novel, soluble cytochrome with an unusual visible spectral signature at 579 nm (Cyt579) has been characterized after isolation from several different microbial biofilms collected in an extremely acidic ecosystem. Previous proteogenomic studies of an Fe(II)-oxidizing community indicated that this abundant red cytochrome could be extracted from the biofilms with dilute sulfuric acid. Here, we found that the Fe(II)-dependent reduction of Cyt579 was thermodynamically favorable at a pH of 〉3, raising the possibility that Cyt579 acts as an accessory protein for electron transfer. The results of transmission electron microscopy of immunogold-labeled biofilm indicated that Cyt579 is localized near the bacterial cell surface, consistent with periplasmic localization. The results of further protein analysis of Cyt579, using preparative chromatofocusing and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, revealed three forms of the protein that correspond to different N-terminal truncations of the amino acid sequence. The results of intact-protein analysis corroborated the posttranslational modifications of these forms and identified a genomically uncharacterized Cyt579 variant. Homology modeling was used to predict the overall cytochrome structure and heme binding site; the positions of nine amino acid substitutions found in three Cyt579 variants all map to the surface of the protein and away from the heme group. Based on this detailed characterization of Cyt579, we propose that Cyt579 acts as an electron transfer protein, shuttling electrons derived from Fe(II) oxidation to support critical metabolic functions in the acidophilic microbial community.

Beschreibung: Funding was provided by the U.S. Department of Energy, Office of Science, from the Genomics: GTL Program, grant DE-FG02-05ER64134, to J.F.B., R.L.H., and M.P.T. Work at LLNL was performed under the auspices of the U.S. Department of Energy under contract DE-AC52-07NA27344.

Beschreibung: Author Posting. © American Society for Microbiology, 2001. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Journal of Bacteriology 183 (2001): 785-790, doi:10.1128/JB.183.2.785-790.2001.

Beschreibung: This study tested for horizontal transfer of plasmids among Buchnera aphidicola strains associated with ecologically and phylogenetically related aphid hosts (Uroleucon species). Phylogenetic congruence of Buchnera plasmid (trpEG and leuABC) and chromosomal (dnaN and trpB) genes supports strictly vertical long-term transmission of plasmids, which persist due to their contributions to host nutrition rather than capacity for infectious transfer. Synonymous divergences indicate elevated mutation on plasmids relative to chromosomal genes.

Beschreibung: This work was supported by a National Institutes of Health postdoctoral training grant in Molecular Insect Science (Center for Insect Science, University of Arizona) to J.J.W. and a National Science Foundation grant (DEB-9815413) to N.A.M.

Beschreibung: Author Posting. © American Society for Microbiology, 2001. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 67 (2001): 5444-5452, doi:10.1128/AEM.67.12.5444-5452.2001.

Beschreibung: Cyanobacteria are prominent constituents of the marine biosphere that account for a significant percentage of oceanic primary productivity. In an effort to resolve how open-ocean cyanobacteria persist in regions where the Fe concentration is thought to be limiting their productivity, we performed a number of Fe stress experiments on axenic cultures of marine Synechococcus spp., Crocosphaera sp., and Trichodesmium sp. Through this work, we determined that all of these marine cyanobacteria mount adaptive responses to Fe stress, which resulted in the induction and/or repression of several proteins. We have identified one of the Fe stress-induced proteins as an IdiA homologue. Genomic observations and laboratory data presented herein from open-ocean Synechococcus spp. are consistent with IdiA having a role in cellular Fe scavenging. Our data indicate that IdiA may make an excellent marker for Fe stress in open-ocean cyanobacterial field populations. By determining how these microorganisms respond to Fe stress, we will gain insight into how and when this important trace element can limit their growth in situ. This knowledge will greatly increase our understanding of how marine Fe cycling impacts oceanic processes, such as carbon and nitrogen fixation.

Beschreibung: This work was partially funded by the Woods Hole Oceanographic Institution postdoctoral scholarship and a subcontract from the Center for Bioinorganic Chemistry at Princeton University (grant no. CHE-9810248) to E.A.W. Additional funds were supplied by the Seaver Institute to J.W.M.

Beschreibung: Author Posting. © American Society for Microbiology, 2002. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 68 (2002): 401-404, doi:10.1128/AEM.68.1.401-404.2002.

Beschreibung: The marine autotroph Aureococcus anophagefferens (Pelagophyceae) was rendered axenic in order to investigate hydrolysis rates of peptides, chitobiose, acetamide, and urea as indicators of the ability to support growth on dissolved organic nitrogen. Specific rates of hydrolysis varied between 8 and 700% of rates observed in associated heterotrophic marine bacteria.

Beschreibung: This work was supported by grants from the Suffolk County Department of Health Services, Office of Ecology, the Alexander Von Humboldt Foundation, and the Deutsche Forschungsgemeinschaft.

Beschreibung: Author Posting. © American Society for Microbiology, 2003. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology, 69 (2003): 2253-2268, doi:10.1128/AEM.69.4.2253-2268.2003.

Beschreibung: Seasonal shifts in bacterioplankton community composition in Toolik Lake, a tundra lake on the North Slope of Alaska, were related to shifts in the source (terrestrial versus phytoplankton) and lability of dissolved organic matter (DOM). A shift in community composition, measured by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes, occurred at 4°C in near-surface waters beneath seasonal ice and snow cover in spring. This shift was associated with an annual peak in bacterial productivity ([14C]leucine incorporation) driven by the large influx of labile terrestrial DOM associated with snow meltwater. A second shift occurred after the flux of terrestrial DOM had ended in early summer as ice left the lake and as the phytoplankton community developed. Bacterioplankton communities were composed of persistent populations present throughout the year and transient populations that appeared and disappeared. Most of the transient populations could be divided into those that were advected into the lake with terrestrial DOM in spring and those that grew up from low concentrations during the development of the phytoplankton community in early summer. Sequencing of DNA in DGGE bands demonstrated that most bands represented single ribotypes and that matching bands from different samples represented identical ribotypes. Bacteria were identified as members of globally distributed freshwater phylogenetic clusters within the {alpha}- and ß-Proteobacteria, the Cytophaga-Flavobacteria-Bacteroides group, and the Actinobacteria.

Beschreibung: This work was supported by National Science Foundation LTER grant no. 9810222.

Beschreibung: Author Posting. © American Society for Microbiology, 2004. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 70 (2004): 4840-4847, doi:10.1128/AEM.70.8.4840-4847.2004.

Beschreibung: The high-temperature limit for growth of microorganisms differs greatly depending on their species and habitat. The importance of an organism's ability to manage thermal stress is reflected in the ubiquitous distribution of the heat shock chaperones. Although many chaperones function to reduce protein folding defects, it has been difficult to identify the specific protein folding pathways that set the high-temperature limit of growth for a given microorganism. We have investigated this for a simple system, phage P22 infection of Salmonella enterica serovar Typhimurium. Production of infectious particles exhibited a broad maximum of 150 phage per cell when host cells were grown at between 30 and 39°C in minimal medium. Production of infectious phage declined sharply in the range of 40 to 41°C, and at 42°C, production had fallen to less than 1% of the maximum rate. The host cells maintained optimal division rates at these temperatures. The decrease in phage infectivity was steeper than the loss of physical particles, suggesting that noninfectious particles were formed at higher temperatures. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a decrease in the tailspike adhesins assembled on phage particles purified from cultures incubated at higher temperatures. The infectivity of these particles was restored by in vitro incubation with soluble tailspike trimers. Examination of tailspike folding and assembly in lysates of phage-infected cells confirmed that the fraction of polypeptide chains able to reach the native state in vivo decreased with increasing temperature, indicating a thermal folding defect rather than a particle assembly defect. Thus, we believe that the folding pathway of the tailspike adhesin sets the high-temperature limit for P22 formation in Salmonella serovar Typhimurium.

Beschreibung: This work was funded by NIH grant GM17980 and NSF grant EIA0225609 to J.K.

Beschreibung: Author Posting. © American Society for Microbiology, 2005. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Journal of Clinical Microbiology 43 (2005): 348-355, doi:10.1128/JCM.43.1.348-355.2005.

Beschreibung: Small-subunit (SSU) rRNA gene sequences were obtained by PCR from 12 Blastocystis isolates from humans, rats, and reptiles for which elongation factor 1{alpha} (EF-1{alpha}) gene sequences are already available. These new sequences were analyzed by the Bayesian method in a broad phylogeny including, for the first time, all Blastocystis sequences available in the databases. Phylogenetic trees identified seven well-resolved groups plus several discrete lineages that could represent newly defined clades. Comparative analysis of SSU rRNA- and EF-1{alpha}-based trees obtained by maximum-likelihood methods from a restricted sampling (13 isolates) revealed overall agreement between the two phylogenies. In spite of their morphological similarity, sequence divergence among Blastocystis isolates reflected considerable genetic diversity that could be correlated with the existence of potentially ≥12 different species within the genus. Based on this analysis and previous PCR-based genotype classification data, six of these major groups might consist of Blastocystis isolates from both humans and other animal hosts, confirming the low host specificity of Blastocystis. Our results also strongly suggest the existence of numerous zoonotic isolates with frequent animal-to-human and human-to-animal transmissions and of a large potential reservoir in animals for infections in humans.

Beschreibung: This work was supported by the Institut Pasteur de Lille, the Institut National de la Sante´ et de la Recherche Me´dicale, the Centre National de la Recherche Scientifique, the Institut National de la Recherche Agronomique, the Ecole Ve´te´rinaire de Lyon, and the “Programme Trans-Zoonoses 2002–2004” (INRA—De´partement de Sante´ Animale).

Beschreibung: Author Posting. © American Society for Microbiology, 2002. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 68 (2002): 1994-2007, doi:10.1128/AEM.68.4.1994-2007.2002.

Beschreibung: Microbial communities in hydrothermally active sediments of the Guaymas Basin (Gulf of California, Mexico) were studied by using 16S rRNA sequencing and carbon isotopic analysis of archaeal and bacterial lipids. The Guaymas sediments harbored uncultured euryarchaeota of two distinct phylogenetic lineages within the anaerobic methane oxidation 1 (ANME-1) group, ANME-1a and ANME-1b, and of the ANME-2c lineage within the Methanosarcinales, both previously assigned to the methanotrophic archaea. The archaeal lipids in the Guaymas Basin sediments included archaeol, diagnostic for nonthermophilic euryarchaeota, and sn-2-hydroxyarchaeol, with the latter compound being particularly abundant in cultured members of the Methanosarcinales. The concentrations of these compounds were among the highest observed so far in studies of methane seep environments. The δ-13C values of these lipids (δ-13C = -89 to -58%) indicate an origin from anaerobic methanotrophic archaea. This molecular-isotopic signature was found not only in samples that yielded predominantly ANME-2 clones but also in samples that yielded exclusively ANME-1 clones. ANME-1 archaea therefore remain strong candidates for mediation of the anaerobic oxidation of methane. Based on 16S rRNA data, the Guaymas sediments harbor phylogenetically diverse bacterial populations, which show considerable overlap with bacterial populations of geothermal habitats and natural or anthropogenic hydrocarbon-rich sites. Consistent with earlier observations, our combined evidence from bacterial phylogeny and molecular-isotopic data indicates an important role of some novel deeply branching bacteria in anaerobic methanotrophy. Anaerobic methane oxidation likely represents a significant and widely occurring process in the trophic ecology of methane-rich hydrothermal vents. This study stresses a high diversity among communities capable of anaerobic oxidation of methane.

Beschreibung: Andreas Teske was supported by DFG postdoctoral fellowship 262-1/1 and a subsequent WHOI postdoctoral fellowship.

Beschreibung: Author Posting. © American Society for Microbiology, 2003. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 69 (2003): 5492-5502, doi:10.1128/AEM.69.9.5492-5502.2003.

Beschreibung: A method was developed for the rapid detection and enumeration of Aureococcus anophagefferens, the cause of harmful algal blooms called "brown tides" in estuaries of the Mid-Atlantic United States. The method employs a monoclonal antibody (MAb) and a colorimetric, enzyme-linked immunosorbent assay format. The MAb obtained exhibits high reactivity with A. anophagefferens and very low cross-reactivities with a phylogenetically diverse array of other protists and bacteria. Standard curves are constructed for each 96-well microtiter plate by using known amounts of a preserved culture of A. anophagefferens. This approach allows estimation of the abundance of the alga in natural samples. The MAb method was compared to an existing method that employs polyclonal antibodies and epifluorescence microscopy and to direct microscopic counts of A. anophagefferens in samples with high abundances of the alga. The MAb method provided increased quantitative accuracy and greatly reduced sample processing time. A spatial survey of several Long Island estuaries in May 2000 using this new approach documented a range of abundances of A. anophagefferens in these bays spanning nearly 3 orders of magnitude.

Beschreibung: This work was supported by a grant from The Seaver Institute.

Beschreibung: Author Posting. © American Society for Microbiology, 2005. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 71 (2005): 7401-7413, doi:10.1128/AEM.71.11.7401-7413.2005.

Beschreibung: Natural products are a functionally diverse class of biochemically synthesized compounds, which include antibiotics, toxins, and siderophores. In this paper, we describe both the detection of natural product activities and the sequence identification of gene fragments from two molecular systems that have previously been implicated in natural product production, i.e., nonribosomal peptide synthetases (NRPSs) and modular polyketide synthases (PKSs), in diverse marine and freshwater cyanobacterial cultures. Using degenerate PCR and the sequencing of cloned products, we show that NRPSs and PKSs are common among the cyanobacteria tested. Our molecular data, when combined with genomic searches of finished and progressing cyanobacterial genomes, demonstrate that not all cyanobacteria contain NRPS and PKS genes and that the filamentous and heterocystous cyanobacteria are the richest sources of these genes and the most likely sources of novel natural products within the phylum. In addition to validating the use of degenerate primers for the identification of PKS and NRPS genes in cyanobacteria, this study also defines numerous gene fragments that will be useful as probes for future studies of the synthesis of natural products in cyanobacteria. Phylogenetic analyses of the cyanobacterial NRPS and PKS fragments sequenced in this study, as well as those from the cyanobacterial genome projects, demonstrate that there is remarkable diversity and likely novelty of these genes within the cyanobacteria. These results underscore the potential variety of novel products being produced by these ubiquitous organisms.

Beschreibung: I.M.E. was partially supported through a Woods Hole Oceanographic Institution Summer Fellowship. This work was funded by a WHOI internal grant, Woods Hole Center for Oceans and Human Health (OCE-0430724), and an NSF grant (OCE-0352241) to E.A.W.

Beschreibung: Author Posting. © American Society for Microbiology, 2003. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 69 (2003): 2765-2772, doi:10.1128/AEM.69.5.2765-2772.2003.

Beschreibung: The Guaymas Basin (Gulf of California) is a hydrothermal vent site where thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material which supports diverse sulfate-reducing bacteria. We explored the phylogenetic and functional diversity of the sulfate-reducing bacteria by characterizing PCR-amplified dissimilatory sulfite reductase (dsrAB) and 16S rRNA genes from the upper 4 cm of the Guaymas sediment. The dsrAB sequences revealed that there was a major clade closely related to the acetate-oxidizing delta-proteobacterial genus Desulfobacter and a clade of novel, deeply branching dsr sequences related to environmental dsr sequences from marine sediments in Aarhus Bay and Kysing Fjord (Denmark). Other dsr clones were affiliated with gram-positive thermophilic sulfate reducers (genus Desulfotomaculum) and the delta-proteobacterial species Desulforhabdus amnigena and Thermodesulforhabdus norvegica. Phylogenetic analysis of 16S rRNAs from the same environmental samples resulted in identification of four clones affiliated with Desulfobacterium niacini, a member of the acetate-oxidizing, nutritionally versatile genus Desulfobacterium, and one clone related to Desulfobacula toluolica and Desulfotignum balticum. Other bacterial 16S rRNA bacterial phylotypes were represented by non-sulfate reducers and uncultured lineages with unknown physiology, like OP9, OP8, as well as a group with no clear affiliation. In summary, analyses of both 16S rRNA and dsrAB clone libraries resulted in identification of members of the Desulfobacteriales in the Guaymas sediments. In addition, the dsrAB sequencing approach revealed a novel group of sulfate-reducing prokaryotes that could not be identified by 16S rRNA sequencing.

Beschreibung: This study was supported by the NASA Astrobiology Institute (grant CAN NCC2-1054) and by the G. Unger Vetlesen Foundation. Sampling at the Guaymas Basin was made possible by NSF Life in Extreme Environments grant OCE 9714195 to A.T.

Beschreibung: Author Posting. © American Society for Microbiology, 2001. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 67 (2001): 1922-1934, doi:10.1128/AEM.67.4.1922-1934.2001.

Beschreibung: The oxidation of methane in anoxic marine sediments is thought to be mediated by a consortium of methane-consuming archaea and sulfate-reducing bacteria. In this study, we compared results of rRNA gene (rDNA) surveys and lipid analyses of archaea and bacteria associated with methane seep sediments from several different sites on the Californian continental margin. Two distinct archaeal lineages (ANME-1 and ANME-2), peripherally related to the order Methanosarcinales, were consistently associated with methane seep marine sediments. The same sediments contained abundant 13C-depleted archaeal lipids, indicating that one or both of these archaeal groups are members of anaerobic methane-oxidizing consortia. 13C-depleted lipids and the signature 16S rDNAs for these archaeal groups were absent in nearby control sediments. Concurrent surveys of bacterial rDNAs revealed a predominance of delta -proteobacteria, in particular, close relatives of Desulfosarcina variabilis. Biomarker analyses of the same sediments showed bacterial fatty acids with strong 13C depletion that are likely products of these sulfate-reducing bacteria. Consistent with these observations, whole-cell fluorescent in situ hybridization revealed aggregations of ANME-2 archaea and sulfate-reducing Desulfosarcina and Desulfococcus species. Additionally, the presence of abundant 13C-depleted ether lipids, presumed to be of bacterial origin but unrelated to ether lipids of members of the order Desulfosarcinales, suggests the participation of additional bacterial groups in the methane-oxidizing process. Although the Desulfosarcinales and ANME-2 consortia appear to participate in the anaerobic oxidation of methane in marine sediments, our data suggest that other bacteria and archaea are also involved in methane oxidation in these environments.

Beschreibung: Funding for this project was provided by the David and Lucile Packard Foundation and a NASA isotopic biogeochemistry grant, NAG5-9422, to J.M.H.

Beschreibung: Author Posting. © American Society for Microbiology, 2004. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 70 (2004): 2028-2037, doi:10.1128/AEM.70.4.2028-2037.2004.

Beschreibung: The diversity of protistan assemblages has traditionally been studied using microscopy and morphological characterization, but these methods are often inadequate for ecological studies of these communities because most small protists inherently lack adequate taxonomic characters to facilitate their identification at the species level and many protistan species also do not preserve well. We have therefore used a culture-independent approach (denaturing gradient gel electrophoresis [DGGE]) to obtain an assessment of the genetic composition and distribution of protists within different microhabitats (seawater, meltwater or slush on sea-ice floes, and ice) of the Ross Sea, Antarctica. Samples of the same type (e.g., water) shared more of the same bands than samples of different types (e.g., ice versus water), despite being collected from different sites. These findings imply that samples from the same environment have a similar protistan species composition and that the type of microenvironment significantly influences the protistan species composition of these Antarctic assemblages. It should be noted that a large number of bands among the samples within each microhabitat were distinct, indicating the potential presence of significant genetic diversity within each microenvironment. Sequence analysis of selected DGGE bands revealed sequences that represent diatoms, dinoflagellates, ciliates, flagellates, and several unidentified eukaryotes.

Beschreibung: This work was supported by National Science Foundation grants OPP-9714299 and OPP-0125437.

Beschreibung: Author Posting. © American Society for Microbiology, 2002. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 68 (2002): 6392-6398, doi:10.1128/AEM.68.12.6392-6398.2002.

Beschreibung: Group II introns are catalytic RNAs and mobile retrotransposable elements known to be present in the genomes of some nonmarine bacteria and eukaryotic organelles. Here we report the discovery of group II introns in a bacterial mat sample collected from a deep-sea hydrothermal vent near 9°N on the East Pacific Rise. One of the introns was shown to self-splice in vitro. This is the first example of marine bacterial introns from molecular population structure studies of microorganisms that live in the proximity of hydrothermal vents. These types of mobile genetic elements may prove useful in improving our understanding of bacterial genome evolution and may serve as valuable markers in comparative studies of bacterial communities.

Beschreibung: This research was supported by a WHOI Townsend postdoctoral scholarship to M.P., by National Science Foundation grant OCE-9712233 to L.M., by NIH grant GM31480 and grant I-1211 from the Robert A. Welch Foundation to P.S.P., and by NASA Astrobiology Cooperative Agreement NCC2-1054 and continuing support from the Unger G. Vetlesen Foundation to M.L.S.

Beschreibung: Author Posting. © American Society for Microbiology, 2000. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Journal of Bacteriology 182 (2000): 5180-5187, doi:10.1128/JB.182.18.5180-5187.2000.

Beschreibung: Thiamine pyrophosphate is an essential cofactor that is synthesized de novo in Salmonella enterica serovar Typhimurium and other bacteria. In addition to genes encoding enzymes in the biosynthetic pathway, mutations in other metabolic loci have been shown to prevent thiamine synthesis. The latter loci identify the integration of the thiamine biosynthetic pathway with other metabolic processes and can be uncovered when thiamine biosynthesis is challenged. Mutations in gshA, encoding gamma -L-glutamyl-L-cysteine synthetase, prevent the synthesis of glutathione, the major free thiol in the cell, and are shown here to result in a thiamine auxotrophy in some of the strains tested, including S. enterica LT2. Phenotypic characterization of the gshA mutants indicated they were similar enough to apbC and apbE mutants to warrant the definition of a class of mutants unified by (i) a requirement for both the hydroxymethyl pyrimidine (HMP) and thiazole (THZ) moiety of thiamine, (ii) the ability of L-tryosine to satisfy the THZ requirement, (iii) suppression of the thiamine requirement by anaerobic growth, and (iv) suppression by a second-site mutation at a single locus. Genetic data indicated that a defective ThiH generates the THZ requirement in these strains, and we suggest this defect is due to a reduced ability to repair a critical [Fe-S] cluster.

Beschreibung: This work was supported by competitive grant MCB9723830 from the National Science Foundation, GM47296 from the National Institutes of Health, and a Shaw Scientists Award from the Milwaukee Foundation.

Beschreibung: Author Posting. © American Society for Microbiology, 2002. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 68 (2002): 2236-2245, doi:10.1128/AEM.68.5.2236-2245.2002.

Beschreibung: The genetic diversity of Trichodesmium spp. from natural populations (off Bermuda in the Sargasso Sea and off North Australia in the Arafura and Coral Seas) and of culture isolates from two regions (Sargasso Sea and Indian Ocean) was investigated. Three independent techniques were used, including a DNA fingerprinting method based on a highly iterated palindrome (HIP1), denaturing gradient gel electrophoresis of a hetR fragment, and sequencing of the internal transcribed spacer (ITS) of the 16S-23S rDNA region. Low genetic diversity was observed in natural populations of Trichodesmium spp. from the two hemispheres. Culture isolates of Trichodesmium thiebautii, Trichodesmium hildebrandtii, Trichodesmium tenue, and Katagnymene spiralis displayed remarkable similarity when these techniques were used, suggesting that K. spiralis is very closely related to the genus Trichodesmium. The largest genetic variation was found between Trichodesmium erythraeum and all other species of Trichodesmium, including a species of Katagnymene. Our data obtained with all three techniques suggest that there are two major clades of Trichodesmium spp. The HIP1 fingerprinting and ITS sequence analyses allowed the closely related species to be distinguished. This is the first report of the presence of HIP1 in marine cyanobacteria.

Beschreibung: This work was funded by the Swedish Foundation for International Co-operation in Research and Higher Education (STINT) (B.B.), the Swedish Natural Science Research Council (B.B.), and the Swedish Institute (K.M.O.).

Beschreibung: Author Posting. © American Society for Microbiology, 2003. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 69 (2003): 390-398, doi:10.1128/AEM.69.1.390-398.2003.

Beschreibung: Filamentous, gliding, sulfide-oxidizing bacteria of the genus Thioploca were found on sediments in profundal areas of Lake Biwa, a Japanese freshwater mesotrophic lake, and were characterized morphologically and phylogenetically. The Lake Biwa Thioploca resembled morphologically Thioploca ingrica, a brackish water species from a Danish fjord. The diameters of individual trichomes were 3 to 5.6 µm; the diameters of complete Thioploca filaments ranged from 18 to 75 µm. The cell lengths ranged from 1.2 to 3.8 µm. In transmission electron microscope specimens stained with uranyl acetate, dense intracellular particles were found, which did not show any positive signals for phosphorus and sulfur in an X-ray analysis. The 16S rRNA gene of the Thioploca from Lake Biwa was amplified by using newly designed Thioploca-specific primers (706-Thioploca, Biwa160F, and Biwa829R) in combination with general bacterial primers in order to avoid nonspecific amplification of contaminating bacterial DNA. Denaturing gradient gel electrophoresis (DGGE) analysis of the three overlapping PCR products resulted in single DGGE bands, indicating that a single 16S rRNA gene had been amplified. With the same method, the Thioploca from Lake Constance was examined. The 16S rRNA sequence was verified by performing fluorescence in situ hybridization targeted at specific motifs of the Lake Biwa Thioploca. Positive signals were obtained with the bacterial probe EUB-338, the {gamma}-proteobacterial probe GAM42a, and probe Biwa829 targeting the Lake Biwa Thioploca. Based on the nearly complete 16S rRNA sequence and on morphological similarities, the Thioploca from Lake Biwa and the Thioploca from Lake Constance are closely related to T. ingrica and to each other.

Beschreibung: This work was supported by grant 12440219 from the Ministry of Education, Culture, Sports, Science and Technology, Japan, to Manabu Fukui. Andreas Teske was supported by an Independent Studies Award from the Mellon Foundation.

Beschreibung: Author Posting. © American Society for Microbiology, 2005. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Journal of Bacteriology 187 (2005): 3020-3027, doi:10.1128/JB.187.9.3020-3027.2005.

Beschreibung: Based on 16S rRNA gene surveys, bacteria of the ε subdivision of proteobacteria have been identified to be important members of microbial communities in a variety of environments, and quite a few have been demonstrated to grow autotrophically. However, no information exists on what pathway of autotrophic carbon fixation these bacteria might use. In this study, Thiomicrospira denitrificans and Candidatus Arcobacter sulfidicus, two chemolithoautotrophic sulfur oxidizers of the ε subdivision of proteobacteria, were examined for activities of the key enzymes of the known autotrophic CO2 fixation pathways. Both organisms contained activities of the key enzymes of the reductive tricarboxylic acid cycle, ATP citrate lyase, 2-oxoglutarate:ferredoxin oxidoreductase, and pyruvate:ferredoxin oxidoreductase. Furthermore, no activities of key enzymes of other CO2 fixation pathways, such as the Calvin cycle, the reductive acetyl coenzyme A pathway, and the 3-hydroxypropionate cycle, could be detected. In addition to the key enzymes, the activities of the other enzymes involved in the reductive tricarboxylic acid cycle could be measured. Sections of the genes encoding the {alpha}- and ß-subunits of ATP citrate lyase could be amplified from both organisms. These findings represent the first direct evidence for the operation of the reductive tricarboxylic acid cycle for autotrophic CO2 fixation in {varepsilon}-proteobacteria. Since {varepsilon}-proteobacteria closely related to these two organisms are important in many habitats, such as hydrothermal vents, oxic-sulfidic interfaces, or oilfields, these results suggest that autotrophic CO2 fixation via the reductive tricarboxylic acid cycle might be more important than previously considered.

Beschreibung: This study was supported by the National Science Foundation “Ecological and Evolutionary Physiology” program (grant IBN-0131557) and the NASA Astrobiology Institute (“From Early Biospheric Metabolism to the Evolution of Complex Systems”; grant NNA04CC04A).

Beschreibung: Author Posting. © American Society for Microbiology, 2004. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Journal of Bacteriology 186 (2004): 8240-8247, doi:10.1128/JB.186.24.8240-8247.2004.

Beschreibung: Comparative sequence analysis of IS50 transposase-related protein sequences in conjunction with known structural, biochemical, and genetic data was used to determine domains and residues that play key roles in IS50 transposase function. BLAST and ClustalW analyses have been used to find and analyze six complete protein sequences that are related to the IS50 transposase. The protein sequence identity of these six homologs ranged from 25 to 55% in comparison to the IS50 transposase. Homologous motifs were found associated with each of the three catalytic residues. Residues that play roles in transposase-DNA binding, protein autoregulation, and DNA hairpin formation were also found to be conserved in addition to other residues of unknown function. On the other hand, some homologous sequences did not appear to be competent to encode the inhibitor regulatory protein. The results were also used to compare the IS50 transposase with the more distantly related transposase encoded by IS10.

Beschreibung: J.A. was supported by a grant from the National Science Foundation (MCB0084089) administered by W.S.R. S.R.B. held a National Research Council Research Associateship Award. W.S.R. is the Evelyn Mercer Professor of Biochemistry and Molecular Biology. Additional thanks are given to the NASA Astrobiology Institute (Cooperative Agreement NNA04CC04A to Mitchell L. Sogin) and the W. M. Keck Ecological and Evolutionary Genetics Facility within the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution at the M.B.L. Molecular graphics images were produced by using the UCSF Chimera package from the Computer Graphics Laboratory, University of California, San Francisco (supported by NIH grant P41 RR-01081).

Beschreibung: Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Eukaryotic Cell 5 (2006): 1276-1286, doi:10.1128/EC.00116-06.

Beschreibung: The host range of African trypanosomes is influenced by innate protective molecules in the blood of primates. A subfraction of human high-density lipoprotein (HDL) containing apolipoprotein A-I, apolipoprotein L-I, and haptoglobin-related protein is toxic to Trypanosoma brucei brucei but not the human sleeping sickness parasite Trypanosoma brucei rhodesiense. It is thought that T. b. rhodesiense evolved from a T. b. brucei-like ancestor and expresses a defense protein that ablates the antitrypanosomal activity of human HDL. To directly investigate this possibility, we developed an in vitro selection to generate human HDL-resistant T. b. brucei. Here we show that conversion of T. b. brucei from human HDL sensitive to resistant correlates with changes in the expression of the variant surface glycoprotein (VSG) and abolished uptake of the cytotoxic human HDLs. Complete transcriptome analysis of the HDL-susceptible and -resistant trypanosomes confirmed that VSG switching had occurred but failed to reveal the expression of other genes specifically associated with human HDL resistance, including the serum resistance-associated gene (SRA) of T. b. rhodesiense. In addition, we found that while the original active expression site was still utilized, expression of three expression site-associated genes (ESAG) was altered in the HDL-resistant trypanosomes. These findings demonstrate that resistance to human HDLs can be acquired by T. b. brucei.

Beschreibung: These studies were supported by grants AI39033 and AI054596 from the National Institutes of Health and the Ellison Medical Foundation. Mass spectrometry was supported by NIH P20 RR17695 from the Institutional Development Award (IDeA) Program of the National Center for Research Resources. Computational resources were provided by the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution (MBL) through funds provided by the W. M. Keck Foundation and the G. Unger Vetlesen Foundation.

Beschreibung: Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Journal of Bacteriology 188 (2006): 4601-4609, doi:10.1128/JB.01787-05.

Beschreibung: Genomic sequences have been used to find the genetic foundation for carbon source metabolism in Shewanella oneidensis MR-1. Annotated S. oneidensis MR-1 gene products were examined for their sequence similarity to enzymes participating in pathways for utilization of carbon and energy as described in the BioCyc database (http://www.biocyc.org/) or in the primary literature. A picture emerges that relegates five- and six-carbon sugars to minor roles as carbon sources, whereas multiple pathways for utilization of up to three-carbon carbohydrates seem to be present. Capacity to utilize amino acids for carbon and energy is also present. A few contradictions emerged in which enzymes appear to be present by annotations but are not active in the cell according to physiological experiments. Annotations are based on close sequence similarity and will not reveal inactivity due to deleterious mutations or due to lack of coordination of regulation and transport. Genes for a few enzymes known by experiment to be active are not found in the genome. This may be due to extensive divergence after duplication or convergence of function in separate lines in evolution rendering activities undetectable by sequence similarity. To minimize false predictions from protein sequences, we have been conservative in predicting pathways. We did not predict any pathway when, although a partial pathway was seen it was composed largely of enzymes already accounted for in any other complete pathway. This is an example of how a biochemically oriented sequence analysis can generate questions and direct further experimental investigation.

Beschreibung: This work was supported by the Office of Science (BER), U.S. Department of Energy, grant no. DE-FG02-01ER63202.

Beschreibung: Author Posting. © American Society for Microbiology, 2008. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 74 (2008): 1145-1156, doi:10.1128/AEM.01844-07.

Beschreibung: Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. In order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas denitrificans DSM1251 was sequenced. This genome has many features, including a larger size (2.2 Mbp), that suggest a greater degree of metabolic versatility or responsiveness to the environment than seen for most of the other sequenced epsilonproteobacteria. A branched electron transport chain is apparent, with genes encoding complexes for the oxidation of hydrogen, reduced sulfur compounds, and formate and the reduction of nitrate and oxygen. Genes are present for a complete, autotrophic reductive citric acid cycle. Many genes are present that could facilitate growth in the spatially and temporally heterogeneous sediment habitat from where Sulfurimonas denitrificans was originally isolated. Many resistance-nodulation-development family transporter genes (10 total) are present; of these, several are predicted to encode heavy metal efflux transporters. An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress.

Beschreibung: This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory, University of California, under contract W-7405-ENG-48. Genome closure was funded in part by a USF Innovative Teaching Grant (K.M.S.). S.M.S. received partial support through a fellowship from the Hanse Wissenschaftskolleg in Delmenhorst, Germany (http://www.h-w-k.de), and NSF grant OCE-0452333. K.M.S. is grateful for support from NSF grant MCB-0643713. M.H. was supported by a WHOI postdoctoral scholarship. M.G.K. was supported in part by incentive funds provided by the UofL-EVPR office, the KY Science and Engineering Foundation (KSEF-787-RDE-007), and the National Science Foundation (EF-0412129).

Beschreibung: Author Posting. © American Society for Microbiology, 2001. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 67 (2001): 5179-5189, doi:10.1128/AEM.67.11.5179-5189.2001.

Beschreibung: The molecular and isotopic compositions of lipid biomarkers of cultured Aquificales genera have been used to study the community and trophic structure of the hyperthermophilic pink streamers and vent biofilm from Octopus Spring. Thermocrinis ruber, Thermocrinis sp. strain HI 11/12, Hydrogenobacter thermophilus TK-6, Aquifex pyrophilus, and Aquifex aeolicus all contained glycerol-ether phospholipids as well as acyl glycerides. The n-C20:1 and cy-C21 fatty acids dominated all of the Aquificales, while the alkyl glycerol ethers were mainly C18:0. These Aquificales biomarkers were major constituents of the lipid extracts of two Octopus Spring samples, a biofilm associated with the siliceous vent walls, and the well-known pink streamer community (PSC). Both the biofilm and the PSC contained mono- and dialkyl glycerol ethers in which C18 and C20 alkyl groups were prevalent. Phospholipid fatty acids included both the Aquificales n-C20:1 and cy-C21, plus a series of iso-branched fatty acids (i-C15:0 to i-C21:0), indicating an additional bacterial component. Biomass and lipids from the PSC were depleted in 13C relative to source water CO2 by 10.9 and 17.2per thousand , respectively. The C20-21 fatty acids of the PSC were less depleted than the iso-branched fatty acids, 18.4 and 22.6per thousand , respectively. The biomass of T. ruber grown on CO2 was depleted in 13C by only 3.3per thousand relative to C source. In contrast, biomass was depleted by 19.7per thousand when formate was the C source. Independent of carbon source, T. ruber lipids were heavier than biomass (+1.3per thousand ). The depletion in the C20-21 fatty acids from the PSC indicates that Thermocrinis biomass must be similarly depleted and too light to be explained by growth on CO2. Accordingly, Thermocrinis in the PSC is likely to have utilized formate, presumably generated in the spring source region.

Beschreibung: The work of Linda Jahnke and David Des Marais was supported by grants from NASA’s Exobiology Program and the NASA Astrobiology Institute. The work of Wolfgang Eder was supported by the Fonds der Chemischen Industrie (to K.O.S.). Work by Sherry Cady was supported by the NASA Exobiology and the NSF Life in Extreme Environments Programs.

Beschreibung: Author Posting. © American Society for Microbiology, 2003. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 69 (2003): 5875-5883, doi:10.1128/AEM.69.10.5875-5883.2003.

Beschreibung: The identification of phylogenetic clusters of bacteria that are common in freshwater has provided a basis for probe design to target important freshwater groups. We present a set of 16S ribosomal RNA gene-based oligonucleotide probes specific for 15 of these freshwater clusters. The probes were applied in reverse line blot hybridization, a simple method that enables the rapid screening of PCR products from many samples against an array of probes. The optimized assay was made stringent to discriminate at approximately the single-mismatch level. This made 10 of the probes highly specific, with at least two mismatches to the closest noncluster member in the global database. Screening of PCR products from bacterioplankton of 81 diverse lakes from Belgium, The Netherlands, Denmark, Sweden, and Norway showed that the respective probes were reactive against 5 to 100% of the lake samples. Positive reactivity of six highly specific probes showed that bacteria from actinobacterial clusters ACK-M1 and Sta2-30 and from verrucomicrobial cluster CLO-14 occurred in at least 90% of the investigated lakes. Furthermore, bacteria from alpha-proteobacterial cluster LD12 (closely related to the marine SAR11 cluster), beta-proteobacterial cluster LD28 and cyanobacterial cluster Synechococcus 6b occurred in more than 70% of the lakes. Reverse line blot hybridization is a new tool in microbial ecology that will facilitate research on distribution and habitat specificity of target species at relatively low costs.

Beschreibung: This work was supported by EC project BIOMAN EVK2-1999-00046.

Beschreibung: Author Posting. © American Society for Microbiology, 2002. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 68 (2002): 316-325, doi:10.1128/AEM.68.1.316-325.2002.

Beschreibung: A coastal marine sulfide-oxidizing autotrophic bacterium produces hydrophilic filamentous sulfur as a novel metabolic end product. Phylogenetic analysis placed the organism in the genus Arcobacter in the epsilon subdivision of the Proteobacteria. This motile vibrioid organism can be considered difficult to grow, preferring to grow under microaerophilic conditions in flowing systems in which a sulfide-oxygen gradient has been established. Purified cell cultures were maintained by using this approach. Essentially all 4',6-diamidino-2-phenylindole dihydrochloride-stained cells in a flowing reactor system hybridized with Arcobacter-specific probes as well as with a probe specific for the sequence obtained from reactor-grown cells. The proposed provisional name for the coastal isolate is "Candidatus Arcobacter sulfidicus." For cells cultured in a flowing reactor system, the sulfide optimum was higher than and the CO2 fixation activity was as high as or higher than those reported for other sulfur oxidizers, such as Thiomicrospira spp. Cells associated with filamentous sulfur material demonstrated nitrogen fixation capability. No ribulose 1,5-bisphosphate carboxylase/oxygenase could be detected on the basis of radioisotopic activity or by Western blotting techniques, suggesting an alternative pathway of CO2 fixation. The process of microbial filamentous sulfur formation has been documented in a number of marine environments where both sulfide and oxygen are available. Filamentous sulfur formation by "Candidatus Arcobacter sulfidicus" or similar strains may be an ecologically important process, contributing significantly to primary production in such environments.

Beschreibung: This work was supported by National Science Foundation grant IBN-9630054.

Beschreibung: Author Posting. © American Society for Microbiology, 2002. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 68 (2002): 1728-1734, doi:10.1128/AEM.68.4.1728-1734.2002.

Beschreibung: The strain Burkholderia cepacia G4 aerobically mineralized trichloroethene (TCE) to CO2 over a time period of ~20 h. Three biodegradation experiments were conducted with different bacterial optical densities at 540 nm (OD540s) in order to test whether isotope fractionation was consistent. The resulting TCE degradation was 93, 83.8, and 57.2% (i.e., 7.0, 16.2, and 42.8% TCE remaining) at OD540s of 2.0, 1.1, and 0.6, respectively. ODs also correlated linearly with zero-order degradation rates (1.99, 1.11, and 0.64 µmol h-1). While initial nonequilibrium mass losses of TCE produced only minor carbon isotope shifts (expressed in per mille {delta}13CVPDB), they were 57.2, 39.6, and 17.0{per thousand} between the initial and final TCE levels for the three experiments, in decreasing order of their OD540s. Despite these strong isotope shifts, we found a largely uniform isotope fractionation. The latter is expressed with a Rayleigh enrichment factor, {varepsilon}, and was -18.2 when all experiments were grouped to a common point of 42.8% TCE remaining. Although, decreases of {varepsilon} to -20.7 were observed near complete degradation, our enrichment factors were significantly more negative than those reported for anaerobic dehalogenation of TCE. This indicates typical isotope fractionation for specific enzymatic mechanisms that can help to differentiate between degradation pathways.

Beschreibung: This work was conducted with finances from the German Academic Exchange Service (DAAD), the Swiss National Science Foundation, and EPSRC grants (GR/M26374 and GR/L85183), as well as support of the Department of Education (Northern Ireland) and the QUESTOR Industrial Board.

Beschreibung: Author Posting. © American Society for Microbiology, 2002. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Eukaryotic Cell 1 (2002): 181-190, doi:10.1128/EC.1.2.181-190.2002.

Beschreibung: Giardia lamblia and Entamoeba histolytica are amitochondriate, microaerophilic protists which use fermentation enzymes like those of bacteria to survive anaerobic conditions within the intestinal lumen. Genes encoding fermentation enzymes and related electron transport peptides (e.g., ferredoxins) in giardia organisms and amebae are hypothesized to be derived from either an ancient anaerobic eukaryote (amitochondriate fossil hypothesis), a mitochondrial endosymbiont (hydrogen hypothesis), or anaerobic bacteria (lateral transfer hypothesis). The goals here were to complete the molecular characterization of giardial and amebic fermentation enzymes and to determine the origins of the genes encoding them, when possible. A putative giardia [2Fe-2S]ferredoxin which had a hypothetical organelle-targeting sequence at its N terminus showed similarity to mitochondrial ferredoxins and the hydrogenosomal ferredoxin of Trichomonas vaginalis (another luminal protist). However, phylogenetic trees were star shaped, with weak bootstrap support, so we were unable to confirm or rule out the endosymbiotic origin of the giardia [2Fe-2S]ferredoxin gene. Putative giardial and amebic 6-kDa ferredoxins, ferredoxin-nitroreductase fusion proteins, and oxygen-insensitive nitroreductases each tentatively supported the lateral transfer hypothesis. Although there were not enough sequences to perform meaningful phylogenetic analyses, the unique common occurrence of these peptides and enzymes in giardia organisms, amebae, and the few anaerobic prokaryotes suggests the possibility of lateral transfer. In contrast, there was more robust phylogenetic evidence for the lateral transfer of G. lamblia genes encoding an NADH oxidase from a gram-positive coccus and a microbial group 3 alcohol dehydrogenase from thermoanaerobic prokaryotes. In further support of lateral transfer, the G. lamblia NADH oxidase and adh3 genes appeared to have an evolutionary history distinct from those of E. histolytica.

Beschreibung: This work was supported by NIH grants (AI33492 to J.S., AI43273 to M.L.S., and AI46516 to B.J.L.). Additional support was provided by the G. Unger Vetlesen Foundation and LI-COR Biotechnology.

Beschreibung: Author Posting. © American Society for Microbiology, 2002. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 68 (2002): 1180-1191, doi:10.1128/AEM.68.3.1180-1191.2002.

Beschreibung: Cultured isolates of the marine cyanobacteria Prochlorococcus and Synechococcus vary widely in their pigment compositions and growth responses to light and nutrients, yet show greater than 96% identity in their 16S ribosomal DNA (rDNA) sequences. In order to better define the genetic variation that accompanies their physiological diversity, sequences for the 16S-23S rDNA internal transcribed spacer (ITS) region were determined in 32 Prochlorococcus isolates and 25 Synechococcus isolates from around the globe. Each strain examined yielded one ITS sequence that contained two tRNA genes. Dramatic variations in the length and G+C content of the spacer were observed among the strains, particularly among Prochlorococcus strains. Secondary-structure models of the ITS were predicted in order to facilitate alignment of the sequences for phylogenetic analyses. The previously observed division of Prochlorococcus into two ecotypes (called high and low-B/A after their differences in chlorophyll content) were supported, as was the subdivision of the high-B/A ecotype into four genetically distinct clades. ITS-based phylogenies partitioned marine cluster A Synechococcus into six clades, three of which can be associated with a particular phenotype (motility, chromatic adaptation, and lack of phycourobilin). The pattern of sequence divergence within and between clades is suggestive of a mode of evolution driven by adaptive sweeps and implies that each clade represents an ecologically distinct population. Furthermore, many of the clades consist of strains isolated from disparate regions of the world's oceans, implying that they are geographically widely distributed. These results provide further evidence that natural populations of Prochlorococcus and Synechococcus consist of multiple coexisting ecotypes, genetically closely related but physiologically distinct, which may vary in relative abundance with changing environmental conditions.

Beschreibung: This work was supported by an NSF graduate fellowship to G.R., by NASA grant NAG5-3727 and NSF grant OCE9820035 to S.W.C., and by NSF grant OCE9315895 to D.L.D. and J.B.W.

Beschreibung: Author Posting. © American Society for Microbiology, 2000. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 66 (2000): 2105-2112, doi:10.1128/AEM.66.5.2105-2112.2000.

Beschreibung: Genes showing differential expression related to the early G1 phase of the cell cycle during synchronized circadian growth of the toxic dinoflagellate Alexandrium fundyense were identified and characterized by differential display (DD). The determination in our previous work that toxin production in Alexandrium is relegated to a narrow time frame in early G1 led to the hypothesis that transcriptionally up- or downregulated genes during this subphase of the cell cycle might be related to toxin biosynthesis. Three genes, encoding S-adenosylhomocysteine hydrolase (Sahh), methionine aminopeptidase (Map), and a histone-like protein (HAf), were isolated. Sahh was downregulated, while Map and HAf were upregulated, during the early G1 phase of the cell cycle. Sahh and Map encoded amino acid sequences with about 90 and 70% similarity to those encoded by several eukaryotic and prokaryotic Sahh and Map genes, respectively. The partial Map sequence also contained three cobalt binding motifs characteristic of all Map genes. HAf encoded an amino acid sequence with 60% similarity to those of two histone-like proteins from the dinoflagellate Crypthecodinium cohnii Biecheler. This study documents the potential of applying DD to the identification of genes that are related to physiological processes or cell cycle events in phytoplankton under conditions where small sample volumes represent an experimental constraint. The identification of an additional 21 genes with various cell cycle-related DD patterns also provides evidence for the importance of pretranslational or transcriptional regulation in dinoflagellates, contrary to previous reports suggesting the possibility that translational mechanisms are the primary means of circadian regulation in this group of organisms.

Beschreibung: This work was supported by a grant from the National Science Foundation (OCE 94-15536).

Beschreibung: Author Posting. © American Society for Microbiology, 2000. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 66 (2000): 5013-5018, doi:10.1128/AEM.66.11.5013-5018.2000.

Beschreibung: A chemostat coculture of the sulfate-reducing bacterium Desulfovibrio oxyclinae together with a facultative aerobe heterotroph tentatively identified as Marinobacter sp. strain MB was grown under anaerobic conditions and then exposed to a stepwise-increasing oxygen influx (0 to 20% O2 in the incoming gas phase). The coculture consumed oxygen efficiently, and no residual oxygen was detected with an oxygen supply of up to 5%. Sulfate reduction persisted at all levels of oxygen input, even at the maximal level, when residual oxygen in the growth vessel was 87 µM. The portion of D. oxyclinae cells in the coculture decreased gradually from 92% under anaerobic conditions to 27% under aeration. Both absolute cell numbers and viable cell counts of the organism were the same as or even higher than those observed in the absence of oxygen input. The patterns of consumption of electron donors and acceptors suggest that aerobic incomplete oxidation of lactate to acetate is performed by D. oxyclinae under high oxygen input. Both organisms were isolated from the same oxic zone of a cyanobacterial mat where they have to adapt to daily shifts from oxic to anoxic conditions. This type of syntrophic association may occur in natural habitats, enabling sulfate-reducing bacteria to cope with periodic exposure to oxygen.

Beschreibung: This research was financially sponsored by grants from the German Israel Science Foundation (I-252-131.09), The Red Sea Program for Marine Sciences of the German Federal Ministry of Education and Research (03F0151A), and Deutsche Forschungsgemeinschaft, Bonn, Germany (Ru 458/18).

Beschreibung: Author Posting. © American Society for Microbiology, 2004. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 70 (2004): 2551-2555, doi:10.1128/AEM.70.4.2551-2555.2004.

Beschreibung: The chemical stress factors for microbial life at deep-sea hydrothermal vents include high concentrations of heavy metals and sulfide. Three hyperthermophilic vent archaea, the sulfur-reducing heterotrophs Thermococcus fumicolans and Pyrococcus strain GB-D and the chemolithoautotrophic methanogen Methanocaldococcus jannaschii, were tested for survival tolerance to heavy metals (Zn, Co, and Cu) and sulfide. The sulfide addition consistently ameliorated the high toxicity of free metal cations by the formation of dissolved metal-sulfide complexes as well as solid precipitates. Thus, chemical speciation of heavy metals with sulfide allows hydrothermal vent archaea to tolerate otherwise toxic metal concentrations in their natural environment.

Beschreibung: This work was supported by the National Science Foundation (Life in Extreme Environments [LExEn] grant OCE-0085534 to A.T., S.J.M., K.L, S.B., and C.O.W.), an NSF Postdoctoral Fellowship in Microbial Biology (M.S.A.), the MBL (Environmental Genomes, S/C NCC2-1054) and URI (Subsurface Biospheres) NASA Astrobiology Institute Teams (A.T. and S.J.M.), an NRC Astrobiology postdoctoral fellowship (V.P.E.), and a Princeton Harry Hess postdoctoral fellowship (M.A.S.).

Beschreibung: Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 72 (2006): 252-260, doi:10.1128/AEM.72.1.252-260.2006.

Beschreibung: The abundant and widespread coccolithophore Emiliania huxleyi plays an important role in mediating CO2 exchange between the ocean and the atmosphere through its impact on marine photosynthesis and calcification. Here, we use long serial analysis of gene expression (SAGE) to identify E. huxleyi genes responsive to nitrogen (N) or phosphorus (P) starvation. Long SAGE is an elegant approach for examining quantitative and comprehensive gene expression patterns without a priori knowledge of gene sequences via the detection of 21-bp nucleotide sequence tags. E. huxleyi appears to have a robust transcriptional-level response to macronutrient deficiency, with 42 tags uniquely present or up-regulated twofold or greater in the N-starved library and 128 tags uniquely present or up-regulated twofold or greater in the P-starved library. The expression patterns of several tags were validated with reverse transcriptase PCR. Roughly 48% of these differentially expressed tags could be mapped to publicly available genomic or expressed sequence tag (EST) sequence data. For example, in the P-starved library a number of the tags mapped to genes with a role in P scavenging, including a putative phosphate-repressible permease and a putative polyphosphate synthetase. In short, the long SAGE analyses have (i) identified many new differentially regulated gene sequences, (ii) assigned regulation data to EST sequences with no database homology and unknown function, and (iii) highlighted previously uncharacterized aspects of E. huxleyi N and P physiology. To this end, our long SAGE libraries provide a new public resource for gene discovery and transcriptional analysis in this biogeochemically important marine organism.

Beschreibung: This work was supported by the Woods Hole Oceanographic Institution Ocean Life Institute, the J. Lamar Worzel Assistant Scientist Fund, and the Frank and Lisina Hoch Endowed Fund. A.G.M., S.R.B., and M.J.C. were supported in part by the Marine Biological Laboratory's Program in Global Infectious Diseases, funded by the Ellison Medical Foundation. Computational resources were provided by the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution (Marine Biological Laboratory) through funds provided by the W. M. Keck Foundation and the G. Unger Vetlesen Foundation.

Beschreibung: Author Posting. © American Society for Microbiology, 2005. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 71 (2005): 8411-8418, doi:10.1128/AEM.71.12.8411-8418.2005.

Beschreibung: Obligate lithotrophs (e.g., ammonia oxidizers) and facultative lithotrophs (e.g., CO and hydrogen oxidizers) collectively comprise a phylogenetically diverse functional group that contributes significantly to carbon and nitrogen cycles in soils and plays important roles in trace gas dynamics (e.g., carbon monoxide and nitrous and nitric oxides) that affect tropospheric chemistry and radiative forcing. In spite of their diverse physiologies, facultative and obligate lithotrophs typically possess the Calvin-Benson-Bassham cycle enzyme, ribulose-1,5- bisphosphate carboxylase/oxygenase (rubisCO). In an effort designed to understand the structure of lithotrophic communities in soil, genomic DNA extracts from surface (0 to 2 cm) and subsurface (5 to 7 cm) soils have been obtained from two sites in a Georgia agroecosystem (peanut and cotton plots) and an unmanaged pine stand (〉50 years old). The extracts have been used in PCR amplifications of the cbbL gene for the rubisCO large subunit protein. cbbL PCR products were cloned, sequenced, and subjected to phylogenetic and statistical analyses. Numerous novel lineages affiliated with the form IC clade (one of four form I rubisCO clades), which is typified by facultative lithotrophs, comprised lithotrophic communities from all soils. One of the form IC clone sequences clustered with a form IC clade of ammonia-oxidizing Nitrosospira. Distinct assemblages were obtained from each of the sites and from surface and subsurface soils. The results suggest that lithotrophic populations respond differentially to plant type and land use, perhaps forming characteristic associations. The paucity of clone sequences attributed to ammonia-oxidizing bacteria indicates that even though ammonia oxidation occurs in the various soils, the relevant populations are small compared to those of facultative lithotrophs.

Beschreibung: This study was supported in part by NSF grant DEB-0089900.

Beschreibung: Advances in computer power, new forecasting challenges, and new diagnostic techniques have brought about changes in the way atmospheric development and vertical motion are diagnosed in an operational setting. Many of these changes, such as improved model skill, model resolution, and ensemble forecasting, have arguably been detrimental to the ability of forecasters to understand and respond to the evolving atmosphere. The use of nondivergent wind in place of geostrophic wind would be a step in the right direction, but the advantages of potential vorticity suggest that its widespread adoption as a diagnostic tool on the west side of the Atlantic is overdue. Ertel potential vorticity (PV), when scaled to be compatible with pseudopotential vorticity, is generally similar to pseudopotential vorticity, so forecasters accustomed to quasigeostrophic reasoning through the height tendency equation can transfer some of their intuition into the Ertel-PV framework. Indeed, many of the differences between pseudopotential vorticity and Ertel potential vorticity are consequences of the choice of definition of quasigeostrophic PV and are not fundamental to the quasigeostrophic system. Thus, at its core, PV thinking is consistent with commonly used quasigeostrophic diagnostic techniques.

Beschreibung: Synoptic and mesoscale meteorology underwent a revolution in the 1940s and 1950s with the widespread deployment of novel weather observations, such as the radiosonde network and the advent of weather radar. These observations provoked a rapid increase in our understanding of the structure and dynamics of the atmosphere by pioneering analysts such as Fred Sanders. The authors argue that we may be approaching an analogous revolution in our ability to study the structure and dynamics of atmospheric phenomena with the advent of probabilistic objective analyses. These probabilistic analyses provide not only best estimates of the state of the atmosphere (e.g., the expected value) and the uncertainty about this state (e.g., the variance), but also the relationships between all locations and all variables at that instant in time. Up until now, these relationships have been determined by sampling in time by, for example, case studies, composites, and time-series analysis. Here the authors propose a new approach, ensemble synoptic analysis, which exploits the information contained in probabilistic samples of analyses at one or more instants in time. One source of probabilistic analyses is ensemble-based state-estimation methods, such as ensemble-based Kalman filters. Analyses from such a filter may be used to study atmospheric phenomena and the relationships between fields and locations at one or more instants in time. After a brief overview of a research-based ensemble Kalman filter, illustrative examples of ensemble synoptic analysis are given for an extratropical cyclone, including relationships between the cyclone minimum sea level pressure and other synoptic features, statistically determined operators for potential-vorticity inversion, and ensemble-based sensitivity analysis.

Beschreibung: The pioneering large-scale studies of cyclone frequency, location, and intensity conducted by Fred Sanders prompt similar questions about lesser-studied anticyclone development. The results of a climatology of closed anticyclones (CAs) at 200, 500, and 850 hPa, with an emphasis on the subtropics and midlatitudes, is presented to assess the seasonally varying distribution and hemispheric differences of these features. To construct the CA climatology, a counting program was applied to twice-daily 2.5° NCEP–NCAR reanalysis 200-, 500-, and 850-hPa geopotential height fields for the period 1950–2003. Stationary CAs, defined as those CAs that were located at a particular location for consecutive time periods, were counted only once. The climatology results show that 200-hPa CAs occur preferentially during summer over subtropical continental regions, while 500-hPa CAs occur preferentially over subtropical oceans in all seasons and over subtropical continents in summer. Conversely, 850-hPa CAs occur preferentially over oceanic regions beneath upper-level midocean troughs, and are most prominent in the Northern Hemisphere, and over midlatitude continents in winter. Three case studies of objectively identified CAs that produced heal waves over the United States, Europe, and Australia in 1995, 2003, and 2004, respectively, are presented to supplement the climatological results. The case studies, examining the subset of CAs than can produce heat waves, illustrate how climatologically hot continental tropical air masses produced over arid and semiarid regions of the subtropics and lower midlatitudes can become abnormally hot in conjunction with dynamically driven upper-level ridge amplification. Subsequently, these abnormally hot air masses are advected downstream away from their source regions in conjunction with transient disturbances embedded in anomalously strong westerly jets.

Beschreibung: Oklahoma Mesonetwork data are used to illustrate important atmospheric features that are not well shown by the usual synoptic data. For example, some shifts of wind from south to north that are shown as cold fronts on synoptic charts are not cold fronts by any plausible definition. As previously discussed by Fred Sanders and others, such errors in analysis can be reduced by knowledge of the wide variety of weather phenomena that actually exists, and by more attention to temperatures at the earth's surface as revealed by conventional synoptic data. Mesoscale data for four cases reinforce previous discussions of the ephemeral nature of fronts and deficiencies in the usual analyses of cold fronts. One type of misanalyzed case involves post-cold-frontal boundary layer air that is warmer than the prefrontal air. A second type is usually nocturnal, with a rise of local temperature during disruption of an inversion and a wind shift with later cooling that accompanies advection of a climatological gradient of temperature.

Beschreibung: The advent of the polar front theory of cyclones in Norway early in the last century held that the development of fronts and air masses is central to understanding midlatitude weather phenomena. While work on fronts continues to this day, the concept of air masses has been largely forgotten, superseded by the idea of a continuum. The Norwegians placed equal emphasis on the thermodynamics of airmass formation and on the dynamical processes that moved air masses around; today, almost all the emphasis is on dynamics, with little published literature on diabatic processes acting on a large scale. In this essay, the author argues that a lack of understanding of large-scale diabatic processes leads to an incomplete picture of the atmosphere and contributes to systematic errors in medium- and long-range weather forecasts. At the same time, modern concepts centered around potential vorticity conservation and inversion lead one to a redefinition of the term "air mass" that may have some utility in conceptualizing atmospheric physics and in weather forecasting.

Beschreibung: Historically, the atmospheric sciences have tended to treat problems of weather and climate separately. The real physical system, however, is a continuum, with short-term (minutes to days) “weather” fluctuations influencing climate variations and change, and, conversely, more slowly varying aspects of the system (typical time scales of a season or longer) affecting the weather that is experienced. While this past approach has served important purposes, it is becoming increasingly apparent that in order to make progress in addressing many socially important problems, an improved understanding of the connections between weather and climate is required. This overview summarizes the progress over the last few decades in the understanding of the phenomena and mechanisms linking weather and climate variations. The principal emphasis is on developments in understanding key phenomena and processes that bridge the time scales between synoptic-scale weather variability (periods of approximately 1 week) and climate variations of a season or longer. Advances in the ability to identify synoptic features, improve physical understanding, and develop forecast skill within this time range are reviewed, focusing on a subset of major, recurrent phenomena that impact extratropical wintertime weather and climate variations over the Pacific–North American region. While progress has been impressive, research has also illuminated areas where future gains are possible. This article concludes with suggestions on near-term directions for advancing the understanding and capabilities to predict the connections between weather and climate variations.

Beschreibung: Fred Sanders' career extended over 55 yr, touching upon many of the revolutionary transformations in the field of meteorology during that period. In this paper, his contributions to the transformation of synoptic meteorology, his research into the nature of explosive cyclogenesis, and related advances in the ability to predict these storms are reviewed. In addition to this review, the current status of forecasting oceanic cyclones 4.5 days in advance is presented, illustrating the progress that has been made and the challenges that persist, especially for forecasting those extreme extratropical cyclones that are marked by surface wind speeds exceeding hurricane force. Last, Fred Sanders' participation in a forecast for the historic 1947 snowstorm (that produced snowfall amounts in the New York City area that set records at that time) is reviewed along with an attempt to use today's operational global model to simulate this storm using data that were available at the time. The study reveals the predictive limitations involved with this case based on the scarcity of upper-air data in 1947, while confirming Fred Sanders' forecasting skills when dealing with these types of major storm events, even as a young aviation forecaster at New York's LaGuardia Airport.

Beschreibung: A case study of a double dryline on 22 May 2002 is presented. Mobile, 3-mm-wavelength Doppler radars from the University of Massachusetts and the University of Wyoming (Wyoming cloud radar) were used to collect very fine resolution vertical-velocity data in the vicinity of each of the moisture gradients associated with the drylines. Very narrow (50–100 m wide) channels of strong upward vertical velocity (up to 8 m s–1) were measured in the convergence zone of the easternmost dryline, larger in magnitude than reported with previous drylines. Distinct areas of descending motion were evident to the east and west of both drylines. Radar data are interpreted in the context of other observational platforms available during the International H2O Project (IHOP-2002). a variational ground-based mobile radar data processing technique was developed and applied to pseudo-dual-Doppler data collected during a rolling range-height indicator deployment. It was found that there was a secondary (vertical) circulation normal to the easternmost moisture gradient; the circulation comprised an easterly component near-surface flow to the east, a strong upward vertical component in the convergence zone, a westerly return, flow above the convective boundary layer, and numerous regions of descending motion, the most prominent approximately 3–5 km to the east of the surface convergence zone.

Beschreibung: Fred Sanders' teaching and research contributions in the area of quasigeostrophic theory are highlighted in this paper. The application of these contributions is made to the topic of extreme cold-season precipitation events in the Saint Lawrence valley in the northeastern United States and southern Quebec. This research focuses on analyses of Saint Lawrence valley heavy precipitation events. Synoptic- and planetary-scale circulation anomaly precursors are typically identified several days prior to these events. These precursors include transient upper-level troughs, strong moisture transports into the region, and anomalously large precipitable water amounts. The physical insight of Fred Sanders' work is used in the analysis of these composite results. Further details of this insight are provided in analyses of one case of heavy precipitation.

Beschreibung: Sanders designed a barotropic tropical cyclone (TC) track prediction model for the North Atlantic TC basin that became known as the Sanders barotropic (SANBAR) model. It predicted the streamfunction of the deeplayer mean winds (tropical circulation vertically averaged from 1000 to 100 hPa) that represents the vertically averaged tropical circulations. Originally, the wind input for the operational objective analysis (OA) consisted of winds measured by radiosondes and 44 bogus winds provided by analysis at the National Hurricane Center (NHC), which corresponded to the vertically averaged flow over sparsely observed tropical, subtropical, and midlatitude oceanic regions. The model covered a fixed regional area and had a grid size of ~ 154 km. It estimated the initial storm motion solely on the basis of the large-scale flow from the OA, not taking into account the observed storm motion. During 1970, the SANBAR model became the first dynamical TC track model to be run operationally at NHC. Track forecasts of SANBAR were verified from the 1971 TC season when track model verifications began at NHC until its retirement after the 1989 Atlantic TC season. The average annual SANBAR forecast track errors were verified relative to Climatology and Persistence (CLIPER), the standard no-skill track forecast. Comparison with CLIPER determines the skill of track forecast methods. Verifications are presented for two different versions of the SANBAR model system used operationally during 1973–84 and 1985–89. In homogeneous comparisons (i.e., includes only forecasts for the same initial times) for the former period, SANBAR's track forecasts were slightly better than CLIPER at 24–48-h forecast intervals; however, from 1985 to 1989 the average SANBAR track forecast errors from 24–72 h were ~10% more skillful than homogeneous CLIPER track forecasts.

Beschreibung: In the last decade, Fred Sanders was often critical of current surface analysis techniques. This led to his promoting the use of surface potential temperatures to distinguish between fronts, baroclinic troughs, and non-frontal baroclinic zones, and to the development of a climatology of surface baroclinic zones. In this paper, criticisms of current surface analysis techniques and the usefulness of surface potential temperature analyses are discussed. Case examples are used to compare potential temperature analyses and current National Centers for Environmental Prediction analyses. The 1-yr climatology of Sanders and Hoffman is reconstructed using a composite technique. Annual and seasonal mean potential temperature analyses over the continental United States, southern Canada, northern Mexico, and adjacent coastal waters are presented. In addition, gridpoint frequencies of moderate and strong potential temperature gradients are calculated. The results of the mean potential temperature analyses show that moderate and strong surface baroclinic zones are favored along the coastlines and the slopes of the North American cordillera. Additional subsynoptic details, not found in Sanders and Hoffman, are identified. The availability of the composite results allows for the calculation of potential temperature gradient anomalies. It is shown that these anomalies can be used to identify significant frontal baroclinic zones that are associated with weak potential temperature gradients. Together the results and reviews in this paper show that surface potential temperature analyses are a valuable forecasting and analysis tool allowing analysts to distinguish and identify fronts, baroclinic troughs, and nonfrontal baroclinic zones.

Beschreibung: The nature of the different types of surface boundaries that appear in the southern plains of the United States during the convectively active season is reviewed. The following boundaries are discussed: fronts, the dryline, troughs, and outflow boundaries, The boundaries are related to their environment and to local topography. The role these boundaries might play in the initiation of convective storms is emphasized. The various types of boundary-related vertical circulations and their dynamics are discussed. In particular, quasigeostrophic and semigeostrophic dynamics, and the dynamics of solenoidal circulations, density currents, boundary layers, and gravity waves are considered. Miscellaneous topics pertinent to convective storms and their relationship to surface boundaries such as along-the-boundary variability, boundary collisions, and the role of vertical shear are also discussed. Although some cases of storm initiation along surface boundaries have been well documented using research datasets collected during comprehensive field experiments, much of what we know is based only on empirical forecasting and nowcasting experience. It is suggested that many problems relating to convective-storm formation need to be explored in detail using real datasets with new observing systems and techniques, in conjunction with numerical simulation studies, and through climatological studies.

Beschreibung: This paper begins with a review of basic surface frontogenesis concepts with an emphasis on fronts located over sloping terrain adjacent to mountain barriers and fronts located in large-scale baroclinic zones close to coastlines. The impact of cold-air damming and differential diabatic heating and cooling on frontogenesis is considered through two detailed case studies of intense surface fronts. The first case, from 17 to 18 April 2002, featured the westward passage of a cold (side-door) front across coastal eastern New England in which 15°–20°C temperature decreases were observed in less than one hour. The second case, from 28 February to 4 March 1972, featured a long-lived front that affected most of the United States from the Rockies to the Atlantic coast and was noteworthy for a 50°C temperature contrast between Kansas and southern Manitoba, Canada. In the April 2002 case most of New England was initially covered by an unusually warm, dry air mass. Dynamical anticyclogenesis over eastern Canada set the stage for a favorable pressure gradient to allow chilly marine air to approach coastal New England from the east. Diabatic cooling over the chilly (5°–8°C) waters of the Gulf of Maine allowed surface pressures to remain relatively high offshore while diabatic heating over the land (31°–33°C temperatures) enabled surface pressures to fall relative to over the ocean. The resulting higher pressures offshore resulted in an onshore cold push. Frontal intensity was likely enhanced prior to leaf out and grass green-up as virtually all of the available insolation went into sensible heating. The large-scale environment in the February–March 1972 case favored the accumulation of bitterly cold arctic air in Canada. Frontal formation occurred over northern Montana and North Dakota as the arctic air moved slowly southward in conjunction with surface pressure rises east of the Canadian Rockies. The arctic air accelerated southward subsequent to lee cyclogenesis–induced pressure falls ahead of an upstream trough that crossed the Rockies. The southward acceleration of the arctic air was also facilitated by dynamic anticyclogenesis in southern Canada beneath a poleward jet-entrance region. Frontal intensity varied diurnally in response to differential diabatic heating. Three types of cyclogenesis events were observed over the lifetime of the event: 1) low-amplitude frontal waves with no upper-level support, 2) low-amplitude frontal waves that formed in a jet-entrance region, and 3) cyclones that formed ahead of advancing upper-level troughs. All cyclones were either nondeveloping or weak developments despite extreme baroclinicity, likely the result of large atmospheric static stability in the arctic frontal zone and unfavorable alongfront stretching deformation. Significant frontal–mountain interactions were observed over the Rockies and the Appalachians.

Beschreibung: Over 50 yr have passed since the publication of Sanders' 1955 study, the first quantitative study of the structure and dynamics of a surface cold front. The purpose of this chapter is to reexamine some of the results of that study in light of modern methods of numerical weather prediction and diagnosis. A simulation with a resolution as high as 6-km horizontal grid spacing was performed with the fifth-generation-Pennsylvania State University-National Center for Atmospheric Research (PSU-NCAR) Mesoscale Model (MM5), given initial and lateral boundary conditions from the National Centers for Environmental Precipitation-National Center for Atmospheric Research (NCEP-NCAR) reanalysis project data from 17 to 18 April 1953. The MM5 produced a reasonable simulation af the front, albeit its strength was not as intense and its movement was not as fast as was analyzed by Sanders. The vertical structure of the front differed from that analyzed by Sanders in several significant ways. First, the strongest horizontal temperature gradient associated with the cold front in the simulation occurred above a surface-based inversion, not at the earth's surface. Second, the ascent plume at the leading edge of the front was deeper and more intense than that analyzed by Sanders. The reason was an elevated mixed layer that had moved over the surface cold front in the simulation, allowing a much deeper vertical circulation than was analyzed by Sanders. This structure is similar to that of Australian cold fronts with their deep, well-mixed, prefrontal surface layer. These two differences between the model simulation and the analysis by Sanders may be because upper-air data from Fort Worth, Texas, was unavailable to Sanders. Third, the elevated mixed layer also meant that isentropes along the leading edge of the front extended vertically. Fourth, the field of frontogenesis of the horizontal temperature gradient calculated from the three-dimensional wind differed in that the magnitude of the maximum of the deformation term was larger than the magnitude of the maximum of the tilting term in the simulation, in contrast to Sanders' analysis and other previously published cases. These two discrepancies may be attributable to the limited horizontal resolution of the data that Sanders used in constructing his cross section. Last, a deficiency of the model simulation was that the postfrontal surface superadiabatic layer in the model did not match the observed well-mixed boundary layer. This result raises the question of the origin of the well-mixed postfrontal boundary layer behind cold fronts. To address this question, an additional model simulation without surface fluxes was performed, producing a well-mixed, not superadiabatic, layer. This result suggests that surface fluxes were not necessary for the development of the well-mixed layer, in agreement with previous research. Analysis of this event also amplifies two research themes that Sanders returned to later in his career, First, a prefrontal wind shift occurred in both the observations and model simulation at stations in western Oklahoma. This prefrontal wind shift was caused by a lee cyclone departing the leeward slopes of the Rockies slightly equatorward of the cold front, rather than along the front as was the case farther eastward. Sanders' later research showed how the occurrence of these prefrontal wind shifts leads to the weakening of fronts. Second, this study shows the advantage of using surface potential temperature, rather than surface temperature, for determining the locations of the surface fronts on sloping terrain.

Beschreibung: Today, even with state-of-the-art observational, data assimilation, and modeling systems run routinely on supercomputers, there are often surprises in the prediction of snowstorms, especially the “big ones,” affecting coastal regions of the mid-Atlantic and northeastern United States. Little did the author know that lessons from Fred Sanders' synoptic meteorology class at the Massachusetts Institute of Technology (1967) would later (late 1980s) inspire him to pursue practical issues of predictability in the context of the development of ensemble prediction systems, strategies, and applications for providing information on the inevitable case-dependent uncertainties in forecasts. This paper is a brief qualitative and somewhat colloquial overview, based upon this author's personal involvement and experiences, intended to highlight some basic aspects of the source and nature of uncertainties in forecasts and to illustrate the sort of value added information ensembles can provide in dealing with uncertainties in predictions of East Coast snowstorms.

Beschreibung: One characteristic of Fred Sanders' research is his ability to take a topic that is believed to be well understood by the research community and show that interesting research problems still exist. Among Sanders' considerable contributions to synoptic meteorology, those concerned with surface cold fronts have been especially influential. After a brief historical review of fronts and frontal analysis, this chapter presents three stages in Sanders' career when he performed research on the structure, dynamics, and analysis of surface cold fronts. First, his 1955 paper, "An investigation of the structure and dynamics of an intense surface frontal zone," was the first study to discuss quantitatively the dynamics of a surface cold front. In the 1960s, Sanders and his students further examined the structure of cold fronts, resulting in the unpublished 1967 report to the National Science Foundation, "Frontal structure and the dynamics of frontogenesis." For a third lime in his career, Sanders published several papers (1995–2005) revisiting the structure and dynamics of cold fronts. His 1967 and 1995–2005 work raises the question of the origin and dynamics of the surface pressure trough and/or wind shift that sometimes precedes the temperature gradient (hereafter called a prefrontal trough or prefrontal wind shift, respectively). Sanders showed that the relationship between this prefrontal feature and the temperature gradient is fundamental to the strength of the front. When the wind shift is coincident with the temperature gradient, frontogenesis (strengthening of the front) results; when the wind shift lies ahead of the temperature gradient, frontolysis (weakening of the front) results. a number of proposed mechanisms for the formation of prefrontal troughs and prefrontal wind shifts exist. Consequently, much research remains to be performed on these topics.

Beschreibung: When a forecast is assessed, a single value for a verification measure is often quoted. This is of limited use, as it needs to be complemented by some idea of the uncertainty associated with the value. If this uncertainty can be quantified, it is then possible to make statistical inferences based on the value observed. There are two main types of inference: confidence intervals can be constructed for an underlying “population” value of the measure, or hypotheses can be tested regarding the underlying value. This paper will review the main ideas of confidence intervals and hypothesis tests, together with the less well known “prediction intervals,” concentrating on aspects that are often poorly understood. Comparisons will be made between different methods of constructing confidence intervals—exact, asymptotic, bootstrap, and Bayesian—and the difference between prediction intervals and confidence intervals will be explained. For hypothesis testing, multiple testing will be briefly discussed, together with connections between hypothesis testing, prediction intervals, and confidence intervals.

Beschreibung: Studies using International Satellite Cloud Climatology Project (ISCCP) data have reported decreases in cloud optical depth with increasing temperature, thereby suggesting a positive feedback in cloud optical depth as climate warms. The negative cloud optical depth and temperature relationships are questioned because ISCCP employs threshold assumptions to identify cloudy pixels that have included partly cloudy pixels. This study applies the spatial coherence technique to one month of Advanced Very High Resolution Radiometer (AVHRR) data over the Pacific Ocean to differentiate overcast pixels from the partly cloudy pixels and to reexamine the cloud optical depth–temperature relationships. For low-level marine stratus clouds studied here, retrievals from partly cloudy pixels showed 30%–50% smaller optical depths, 1°–4°C higher cloud temperatures, and slightly larger droplet effective radii, when they were compared to retrievals from the overcast pixels. Despite these biases, retrievals for the overcast and partly cloudy pixels show similar negative cloud optical depth–temperature relationships and their magnitudes agree with the ISCCP results for the midlatitude and subtropical regions. There were slightly negative droplet effective radius–temperature relationships, and considerable positive cloud liquid water content–temperature relationships indicated by aircraft measurements. However, cloud thickness decreases appear to be the main reason why cloud optical depth decreases with increasing temperature. Overall, cloud thickness thinning may explain why similar negative cloud optical depth–temperature relationships are found in both overcast and partly cloudy pixels. In addition, comparing the cloud-top temperature to the air temperature at 740 hPa indicates that cloud-top height generally rises with warming. This suggests that the cloud thinning is mainly due to the ascending of cloud base. The results presented in this study are confined to the midlatitude and subtropical Pacific and may not be applicable to the Tropics or other regions.

Beschreibung: A statistical model to analyze different time scales of the variability of extreme high sea levels is presented. This model uses a time-dependent generalized extreme value (GEV) distribution to fit monthly maxima series and is applied to a large historical tidal gauge record (San Francisco, California). The model allows the identification and estimation of the effects of several time scales—such as seasonality, interdecadal variability, and secular trends—in the location, scale, and shape parameters of the probability distribution of extreme sea levels. The inclusion of seasonal effects explains a large amount of data variability, thereby allowing a more efficient estimation of the processes involved. Significant correlation with the Southern Oscillation index and the nodal cycle, as well as an increase of about 20% for the secular variability of the scale parameter have been detected for the particular dataset analyzed. Results show that the model is adequate for a complete analysis of seasonal-to-interannual sea level extremes providing time-dependent quantiles and confidence intervals.

Beschreibung: The interannual and intraseasonal variability of West African vegetation over the period 1982–2002 is studied using the normalized difference vegetation index (NDVI) from the Advanced Very High Resolution Radiometer (AVHRR).The novel independent component analysis (ICA) technique is applied to extract the main modes of the interannual variability of the vegetation, among which two modes are worth describing. The first component (IC1) describes NDVI variability over the Sahel from August to October. A strong photosynthetic activity over the Sahel is related to above-normal convection and rainfall within the intertropical convergence zone (ITCZ) in summertime and is partly associated with colder (warmer) SST in the eastern tropical Pacific (the Mediterranean). The second component (IC2) depicts a dipole pattern between the Sahelian and Guinean regions during the northern summer followed by a southward-propagating signal from October to December. It is associated with a north–south dipole in convection and rainfall induced by variations in the latitudinal location of the ITCZ as a response to the occurrence of the tropical Atlantic dipole.The analysis of the intraseasonal variability of the Sahelian vegetation relies on the analysis of the seasonal marches and their main phenological stages. Green-up usually starts in early July and shows a very low year-to-year variability, while senescence ends by mid-November and is prone to larger interannual variability. Six types of vegetative seasonal marches are discriminated according to variations in the timing of phenological stages as well as in the greening intensity. These types appear to be strongly dependent on rainfall distribution and amount, particularly those recorded in late August. Finally, year-to-year memory effects are highlighted: NDVI recorded during the green-up phase in year j appears to be strongly related to the maximum NDVI value recorded at year j − 1.

Beschreibung: Based on the data of optimum interpolation sea surface temperature (OISST), the temporal correlations of the sea surface temperature anomaly (SSTA) in the South China Sea (SCS) are studied by using the rescaled range analysis (R/S) and detrended fluctuation analysis (DFA). The results show that the scaling exponents of SSTAs are larger than 0.8. This finding indicates that the SSTAs in the SCS exhibit persistent long-range time correlation of the fluctuations and the interval spreads over a wide period, from about 1 month to 4.5 yr (4∼235 weeks). In addition, the “degree” of the correlations depends very much on the geographic locations: near to the coastal regions, the value is small, while far from the coastline, the value is relatively larger. This means that SSTAs in the central SCS are smoother than those of the coastal regions. The persistence of SST in the SCS may be used as a “minimum skill” to assess the ocean models and to evaluate their performance.

Beschreibung: Winds at the Salt Lake City International Airport (SLC) during the April–October period from 1948 to 2003 have been observed to shift to the north (up-valley direction) between late morning and afternoon on over 70% of the days without precipitation. Lake-breeze fronts that develop as a result of the differential heating between the air over the nearby Great Salt Lake and that over the lake’s surroundings are observed at SLC only a few times each month. Fewer lake-breeze fronts are observed during late July–early September than before or after that period. Interannual fluctuations in the areal extent of the shallow Great Salt Lake contribute to year-to-year variations in the number of lake-breeze frontal passages at SLC. Data collected during the Vertical Transport and Mixing Experiment (VTMX) of October 2000 are used to examine the structure and evolution of a lake-breeze front that moved through the Salt Lake Valley on 17 October. The onset of upslope and up-valley winds occurred within the valley prior to the passage of the lake-breeze front. The lake-breeze front moved at roughly 3 m s−1 up the valley and was characterized near the surface by an abrupt increase in wind speed and dewpoint temperature over a distance of 3–4 km. Rapid vertical mixing of aerosols at the top of the 600–800-m-deep boundary layer was evident as the front passed.

Beschreibung: This study combines the experimental measurements with large-eddy simulation (LES) data of a neutral planetary boundary layer (PBL) documented by a 60-m tower instrumented with eight sonic anemometers, and a high-resolution Doppler lidar during the 1999 Cooperative Atmospheric and Surface Exchange Study (CASES-99) experiment. The target of the paper is (i) to investigate the multiscale nature of the turbulent eddies in the surface layer (SL), (ii) to explain the existence of a −1 power law in the velocity fluctuation spectra, and (iii) to investigate the different nature of turbulence in the two sublayers within the SL, which are the eddy surface layer (ESL; lower sublayer of the SL lying between the surface and about 20-m height) and the shear surface layer (SSL; lying between the ESL top and the SL top). The sonic anemometers and Doppler lidar prove to be proper instruments for LES validation, and in particular, the Doppler lidar because of its ability to map near-surface eddies.This study shows the different nature of turbulence in the ESL and the SSL in terms of organized eddies, velocity fluctuation spectra, and second-order moment statistics. If quantitative agreement is found in the SSL between the LES and the measurements, only qualitative similarity is found in the ESL due to the subgrid-scale model, indicating that the LES captures part of the physics of the ESL. The LES helps explain the origin of the −1 power-law spectral subrange evidence in the velocity fluctuation spectra computed in the SL using the CASES-99 dataset: strong interaction between the mean flow and the fluctuating vorticities is found in the SL, and turbulent production is found to be larger than turbulent energy transfer for k1z 〉 1 (k1 being the longitudinal wavenumber and z the height), which is the condition of the −1 power-law existence.