ALBERT

Description: As ecosystem engineers, seagrasses are angiosperms of paramount ecological importance in shallow shoreline habitats around the globe. Furthermore, the ancestors of independent seagrass lineages have secondarily returned into the sea in separate, independent evolutionary events. Thus, understanding the molecular adaptation of this clade not only makes significant contributions to the field of ecology, but also to principles of parallel evolution as well. With the use of Dr. Zompo, the first interactive seagrass sequence database presented here, new insights into the molecular adaptation of marine environments can be inferred. The database is based on a total of 14 597 ESTs obtained from two seagrass species, Zostera marina and Posidonia oceanica, which have been processed, assembled and comprehensively annotated. Dr. Zompo provides experimentalists with a broad foundation to build experiments and consider challenges associated with the investigation of this class of non-domesticated monocotyledon systems. Our database, based on the Ruby on Rails framework, is rich in features including the retrieval of experimentally determined heat-responsive transcripts, mining for molecular markers (SSRs and SNPs), and weighted key word searches that allow access to annotation gathered on several levels including Pfam domains, GeneOntology and KEGG pathways. Well established plant genome sites such as The Arabidopsis Information Resource (TAIR) and the Rice Genome Annotation Project are interfaced by Dr. Zompo. With this project, we have initialized a valuable resource for plant biologists in general and the seagrass community in particular. The database is expected to grow together with more data to come in the near future, particularly with the recent initiation of the Zostera genome sequencing project. The Dr. Zompo database is available at http://drzompo.uni-muenster.de/

Description: The taxonomy of two sympatric surf clams Donax marincovichi Coan, 1983 and Donax obesulus Reeve, 1854, inhabiting the coastal Humboldt Current Upwelling System is revisited. Because both species are exploited by artisanal fisheries, it is essential to verify that they are indeed distinct species that have to be managed separately. In this study, both taxa were sampled across their shared distributional area and specimens were indentified according to their respective morphological characteristics. Although width/height and height/length ratios revealed significant differences within sampling areas, the two morphotypes were frequently incongruent for taxonomically important morphometric parameters. In addition, they showed no significant mitochondrial genetic differentiation within or among populations and exhibited indistinguishable sperm ultrastructure. We conclude that the two morphotypes do not represent distinct species and should be included together under D. obesulus.

Description: The diversity of Cyanobacteria in water and sediment samples from four representative sites of the Salar de Huasco was examined using denaturing gradient gel electrophoresis and analysis of clone libraries of 16S rRNA gene PCR products. Salar de Huasco is a high altitude (3800 m altitude) saline wetland located in the Chilean Altiplano. We analyzed samples from a tributary stream (H0) and three shallow lagoons (H1, H4, H6) that contrasted in their physicochemical conditions and associated biota. Seventy-eight phylotypes were identified in a total of 268 clonal sequences deriving from seven clone libraries of water and sediment samples. Oscillatoriales were frequently found in water samples from sites H0, H1 and H4 and in sediment samples from sites H1 and H4. Pleurocapsales were found only at site H0, while Chroococcales were recovered from sediment samples of sites H0 and H1, and from water samples of site H1. Nostocales were found in sediment samples from sites H1 and H4, and water samples from site H1 and were largely represented by sequences highly similar to Nodularia spumigena. We suggest that cyanobacterial communities from Salar de Huasco are unique - they include sequences related to others previously described from the Antarctic, along with others from diverse, but less extreme environments.

Description: The functional gene amoA was used to compare the diversity of ammonia-oxidizing bacteria (AOB) in the water column and sediment-water interface of the two freshwater lakes Plusssee and Schöhsee and the Baltic Sea. Nested amplifications were used to increase the sensitivity of amoA detection, and to amplify a 789-bp fragment from which clone libraries were prepared. The larger part of the sequences was only distantly related to any of the cultured AOB and is considered to represent new clusters of AOB within the Nitrosomonas/Nitrosospira group. Almost all sequences from the water column of the Baltic Sea and from 1-m depth of Schöhsee were related to different Nitrosospira clusters 0 and 2, respectively. The majority of sequences from Plusssee and Schöhsee were associated with sequences from Chesapeake Bay, from a previous study of Plusssee and from rice roots in Nitrosospira-like cluster A, which lacks sequences from Baltic Sea. Two groups of sequences from Baltic Sea sediment were related to clonal sequences from other brackish/marine habitats in the purely environmental Nitrosospira-like cluster B and the Nitrosomonas-like cluster. This confirms previous results from 16S rRNA gene libraries that indicated the existence of hitherto uncultivated AOB in lake and Baltic Sea samples, and showed a differential distribution of AOB along the water column and sediment of these environments

Description: Bacterial communities associated with the brown alga Laminaria saccharina from the Baltic Sea and from the North Sea were investigated using denaturing gradient gel electrophoresis and 16S rRNA gene clone libraries. The rhizoid, cauloid, meristem and phyloid revealed different 16S rRNA gene denaturing gradient gel electrophoresis banding patterns indicating a specific association of bacterial communities with different parts of the alga. Associations with cauloid and meristem were more specific, while less specific associations were obtained from the old phyloid. In addition, seasonal and geographical differences in the associated communities were observed. Results from 16S rRNA gene libraries supported these findings. Bacterial phylotypes associated with the alga were affiliated with the Alphaproteobacteria (nine phylotypes), Gammaproteobacteria (nine phylotypes) and the Bacteroidetes group (four phylotypes). A number of bacteria associated with other algae and other marine macroorganisms were among the closest relatives of phylotypes associated with L. saccharina.

Description: Over recent years, several PCR primers have been described to amplify genes encoding the structural subunits of ammonia monooxygenase (AMO) from ammonia-oxidizing bacteria (AOB). Most of them target amoA, while amoB and amoC have been neglected so far. This study compared the nucleotide sequence of 33 primers that have been used to amplify different regions of the amoCAB operon with alignments of all available sequences in public databases. The advantages and disadvantages of these primers are discussed based on the original description and the spectrum of matching sequences obtained. Additionally, new primers to amplify the almost complete amoCAB operon of AOB belonging to Betaproteobacteria (betaproteobacterial AOB), a primer pair for DGGE analysis of amoA and specific primers for gammaproteobacterial AOB, are also described. The specificity of these new primers was also evaluated using the databases of the sequences created during this study.

Description: We studied the effect of the quorum-sensing (QS) blockers 5-hydroxy-3[(1R)-1-hydroxypropyl]-4-methylfuran-2(5H)-one (FUR1), (5R)-3,4-dihydroxy-5-[(1S)-1,2-dihydroxyethyl]furan-2(5H)-one (FUR2) and triclosan (TRI) on the formation of bacterial biofilms, and the effect of these biofilms on the larval attachment of the polychaete Hydroides elegans and the bryozoan Bugula neritina. 14-day-old subtidal biofilms were harvested from artificial substrata and were allowed to develop in the laboratory with and without QS blockers. QS blockers inhibited the production of violacein by the QS reporter strain Chromobacterium violaceum CV026 and did not affect the metabolic activity of bacteria in multispecies biofilms. At a concentration of 10(-3) M all three tested compounds inhibited the establishment of microbial communities, but at one of 10(-4) M only FUR2 inhibited establishment. The tested QS blockers caused changes in bacterial density and bacterial community structure, as revealed by terminal restriction fragment length polymorphism and FISH. The groups most affected by QS blockers were Alphaproteobacteria, Gammaproteobacteria and the Cytophagales. Larvae of H. elegans and B. neritina avoided settling on biofilms that had developed in the presence of QS blockers. Our results suggest that QS blockers directly control the formation of multi-species biofilms, and indirectly - by means of biofilm properties - affect larval attachment on these modified biofilms.

Description: Microbial isolate Z143-1 found to be associated with an unidentified tunicate was characterized due to its significant antimicrobial activity. Z143-1 is similar to Pseudovibrio ascidiaceicola and Pseudovibrio denitrificans in morphological, physiological and biochemical characteristics, except for its ability to ferment glucose and produce a characteristic red pigment. Fatty acid methyl ester analysis revealed a predominance of the fatty acid 18:1 ω7c at 80.55%, at levels slightly lower than the Pseudovibrio denitrificans type strain DN34T (87.7%). The mol% G+C of Z143-1 is 54.02, relatively higher than the Pseudovibrio denitrificans type strain DN34T and Pseudovibrio ascidiaceicola with mol% G+C of 51.7 and 51.4, respectively. However, phylogenetic analysis of the 16S rRNA gene sequence of Z143-1 showed 100% similarity with the Pseudovibrio denitrificans type strain DN34T. In this study, the bacterium Z143-1 is reported as a new strain of Pseudovibrio denitrificans. While there is no report of a secondary metabolite for Pseudovibrio denitrificans, Z143-1 produces the red pigment heptylprodigiosin, also known as 16-methyl-15-heptyl-prodiginine, which shows anti-Staphylococcus aureus activity.

Description: Mechanisms that affect thermal tolerance of ectothermic organisms have recently received much interest, mainly due to global warming and climate-change debates in both the public and in the scientific community. In physiological terms, thermal tolerance of several marine ectothermic taxa can be linked to oxygen availability, with capacity limitations in ventilatory and circulatory systems contributing to oxygen limitation at extreme temperatures. The present review briefly summarizes the processes that define thermal tolerance in a model cephalopod organism, the cuttlefish Sepia officinalis, with a focus on the contribution of the cephalopod oxygen-carrying blood pigment, hemocyanin. When acutely exposed to either extremely high or low temperatures, cuttlefish display a gradual transition to an anaerobic mode of energy production in key muscle tissues once critical temperatures (Tcrit) are reached. At high temperatures, stagnating metabolic rates and a developing hypoxemia can be correlated with a progressive failure of the circulatory system, well before Tcrit is reached. However, at low temperatures, declining metabolic rates cannot be related to ventilatory or circulatory failure. Rather, we propose a role for hemocyanin functional characteristics as a major limiting factor preventing proper tissue oxygenation. Using information on the oxygen binding characteristics of cephalopod hemocyanins, we argue that high oxygen affinities (= low P50 values), as found at low temperatures, allow efficient oxygen shuttling only at very low venous oxygen partial pressures. Low venous PO2s limit rates of oxygen diffusion into cells, thus eventually causing the observed transition to anaerobic metabolism. On the basis of existing blood physiological, molecular, and crystallographical data, the potential to resolve the role of hemocyanin isoforms in thermal adaptation by an integrated molecular physiological approach is discussed.

Description: Recent molecular studies investigating higher-level phylogenetics of coleoid cephalopods (octopuses, squids and cuttlefishes) have produced conflicting results. A wide range of sequence alignment and analysis methods are used in cephalopod phylogenetic studies. The present study investigated the effect of commonly used alignment and analysis methods on higher-level cephalopod phylogenetics. Two sequence homology methods: (1) eye alignment, (2) implied alignment, and three analysis methods: (1) parsimony, (2) maximum likelihood, (3) Bayesian methodologies, were employed on the longest sequence dataset available for the coleoid cephalopods, comprising three mitochondrial and six nuclear loci. The data were also tested for base composition heterogeneity, which was detected in three genes and resolved using RY coding. The Octopoda, Argonautoidea, Oegopsida and Ommastrephidae are monophyletic in the phylogenies resulting from each of the alignment and analysis combinations. Furthermore, the Bathyteuthidae are the sister taxon of the Oegopsida in each case. However many relationships within the Coleoidea differed depending upon the alignment and analysis method used. This study demonstrates how differences in alignment and analysis methods commonly used in cephalopod phylogenetics can lead to different, but often highly supported, relationships.

Description: The basal position of the Mamiellales (Prasinophyceae) within the green lineage makes these unicellular organisms key to elucidating early stages in the evolution of chlorophyll a/b-binding light-harvesting complexes (LHCs). Here, we unveil the complete and unexpected diversity of Lhc proteins in Ostreococcus tauri, a member of the Mamiellales order, based on results from complete genome sequencing. Like Mantoniella squamata, O. tauri possesses a number of genes encoding an unusual prasinophyte-specific Lhc protein type herein designated "Lhcp". Biochemical characterization of the complexes revealed that these polypeptides, which bind chlorophylls a, b, and a chlorophyll c-like pigment (Mg-2,4-divinyl-phaeoporphyrin a 5 monomethyl ester) as well as a number of unusual carotenoids, are likely predominant. They are retrieved to some extent in both reaction center I (RCI)- and RCII-enriched fractions, suggesting a possible association to both photosystems. However, in sharp contrast to previous reports on LHCs of M. squamata, O. tauri also possesses other LHC subpopulations, including LHCI proteins (encoded by five distinct Lhca genes) and the minor LHCII polypeptides, CP26 and CP29. Using an antibody against plant Lhca2, we unambiguously show that LHCI proteins are present not only in O. tauri, in which they are likely associated to RCI, but also in other Mamiellales, including M. squamata. With the exception of Lhcp genes, all the identified Lhc genes are present in single copy only. Overall, the discovery of LHCI proteins in these prasinophytes, combined with the lack of the major LHCII polypeptides found in higher plants or other green algae, supports the hypothesis that the latter proteins appeared subsequent to LHCI proteins. The major LHC of prasinophytes might have arisen prior to the LHCII of other chlorophyll a/b-containing organisms, possibly by divergence of a LHCI gene precursor. However, the discovery in O. tauri of CP26-like proteins, phylogenetically placed at the base of the major LHCII protein clades, yields new insight to the origin of these antenna proteins, which have evolved separately in higher plants and green algae. Its diverse but numerically limited suite of Lhc genes renders O. tauri an exceptional model system for future research on the evolution and function of LHC components. © The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.

Description: We evaluated the effects of self-selected diets on calcium absorption and calculated retention in girls during pre-, early, and late puberty. Dietary calcium absorption was measured in 51 girls aged 4.9–16.7 y by using a dual-tracer stable-isotope technique. We found that calcium intake was similar among girls of all ages and all degrees of pubertal development and was below the recommended dietary allowance (1200 mg/d) for 21 of 25 girls aged ≥ 11 y. The early pubertal period was associated with a higher percent of dietary calcium absorption (34.4 ± 11.9%) than was the prepubertal (27.7 ± 8.2%) or late pubertal periods (25.9 ± 7.8%). Calculated calcium retention averaged 132 ± 83 mg/d in prepubertal girls, 161 ±88 mg/d in early pubertal girls, and 44 ± 91 mg/d in late pubertal girls. Peak calcium retention during early puberty was far below that previously reported after higher calcium intakes. We conclude that peak periods for calcium retention for girls are in the pre- and early pubertal periods. The current calcium intake of American girls during the pubertal growth period may not enable maximal mineral retention; therefore, increased calcium intakes should be considered.

Description: Work on the life histories of common antarctic benthic marine invertebrates over the past several decades demands a revision of several widely held paradigms. First, contrary to expectations derived from work on temperate species, there is little or no evidence for temperature adaptation with respect to reproduction (gametogenesis), devel? opment, and growth. It remains to be determined whether the slow rates of these processes reflect some inherent inability to adapt to low temperatures, or are a response to features of the antarctic marine environment not directly related to low temperature, such as low food resources. Secondly, contrary to the widely accepted opinion designated as "Thor- son's rule," pelagic development is common in many groups of shallow-water marine invertebrates. In fact in some groups, such as asteroids, pelagic development is as prevalent in McMurdo Sound, the southern-most open-water marine environment in the world, as in central California. In other taxonomic groups, especially gastropods, there does seem to be a genuine trend toward non-pelagic development from tropical to antarctic latitudes. Although this trend has been predicted by theoretical models, its underlying causes appear to be group specific rather than general. Thirdly, pelagic lecithotrophic development, often considered to be of negligible importance, occurs in many shallow-water antarctic marine macroinvertebrates. Pelagic lecithotrophy may be an adaptation to a combination of poor food conditions in antarctic waters most ofthe year and slow rates of development. Nevertheless, some of the most abundant and widespread antarctic marine invertebrates have pelagic planktotrophic larvae that take very long times to complete development to metamorphosis. These species are particularly prevalent in productive regions of shallow water (〈 30 m), which are frequently disturbed by anchor ice formation, and the production of numerous pelagic planktotrophic larvae may represent a strategy for colonization. Although planktotrophic larvae tend to be seasonal in occurrence, their production is not linked particularly closely to the mid-summer pulse of phytoplankton production. These larvae show no evidence of starvation, even during times when phytoplankton abundance is very low, and they may depend on unusual sources of food, such as bacteria. How they escape the selective conditions that apparently led to a predominance of non-feeding modes of development in antarctic marine invertebrates remains as a major challenge for antarctic marine biology.

Description: Pelagic aquatic environments differ from terrestrial environments in being three-dimensional and relatively homogeneous, rather than two-dimensional and heterogeneous. The present paper examines the causes and consequences of these differences in the context of their influence on the interactions of animals with environmental light. Particular emphasis is placed on light as a determinant of effective modes of crypsis in the two different habitats. The terrestrial world has selected for the expression of crypticity in the form of superficial color patterns. The heterogeneity of this habitat has resulted in evolutionary divergence of these superficial color patterns, often in very closely-related animals. In contrast, in the homogeneous pelagic aquatic habitats, evolutionary convergence on three main forms of crypsis is evident: (1) transparency; (2) reflection of most, if not all visible wavelengths; and, (3) ventral bioluminescence as counterillumination; thus, to be cryptic most animals in these habitats use one or a combination of these modalities to variously transmit, reflect or mimic environmental light. In the present paper, special attention is given to transparency as the most prevalent, yet least understood, of these mechanisms that are used in predator-prey interactions.