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  • 1
    Electronic Resource
    Electronic Resource
    Allochthonous and autochthonous particulate organic matter in floodplains of the River Danube: the importance of hydrological connectivity (2003)
    Oxford, UK : Blackwell Science Ltd
    Freshwater biology 48 (2003), S. 0 
    Details
    ISSN: 1365-2427
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: SUMMARY 1. The elemental composition, the proportion of living organic carbon and the carbon stable isotope signatures of particulate organic matter (POM) were determined in a large river floodplain system in order to elucidate the major carbon sources in relation to the hydrological conditions over a 13-month period.2. Two floodplain segments and the main channel of the River Danube downstream of Vienna (Austria), were compared on the basis of discharge and water age estimations. The more dynamic floodplain was connected to the main channel for 46% of the study period and drained up to 12% of total discharge at high water.3. The mean C : N ratio and δ13C signature of the POM increased from the floodplain site that was more isolated from the river (6.6; −33‰) to the main channel (8.4; −25‰). At the dynamic floodplain site, the C : N ratio and the δ13C signature of the POM increased with hydrological connectivity (expressed as water age).4. Only during flood events (4% frequency of occurrence), a considerable input of riverine POM was observed. This input was indicated by a C : N ratio of the POM pool of more than 10, the amount of detrital carbon (〉80% of the total POM pool) and a δ13C signature of POM of more than −25‰ in the dynamic floodplain.5. Plankton derived carbon, indicated by C : N ratios less than eight and δ13C values lower than −25‰, dominated the particulate organic carbon (POC) pool at both floodplain sites, emphasising the importance of local (autochthonous) production. Phytoplankton was the major plankton compartment at the dynamic site, with highest biomasses at medium water ages.6. At the dynamic floodplain site, the Danube Restoration Project has enhanced the duration of upstream surface connection with the main channel from 4 to 46% frequency of occurrence. Therefore, the export of living POC to the main channel is now established during phases of maximum phytoplankton production and doubled the estimated total export of non-refractory POM compared with prerestoration conditions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2427.2003.00981.x
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  • 2
    Electronic Resource
    Electronic Resource
    Bacterial metabolism in the River Danube: parameters influencing bacterial production (1995)
    Oxford, UK : Blackwell Publishing Ltd
    Freshwater biology 34 (1995), S. 0 
    Details
    ISSN: 1365-2427
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: 1. Microbial parameters were determined at five sampling sites in the River Danube up-and downstream of Vienna, Austria, twice monthly over an annual cycle. Bacterial production (BP) was estimated from thymidine and leucine incorporations; additionally, the effect of turbulence on BP and the conversion factors for converting incorporation rates into bacterial cell production were determined using the cumulative approach.2. BP under turbulent conditions was not significantly different from that under stagnant conditions. For thymidine, a mean annual conversion factor of 3.2 ± 1018 cells mol−1 thymidine incorporated was calculated. For leucine, the corresponding factor was 0.07 ± 1018 cells mol−1 leucine. Average annual BP calculated by thymidine incorporation was significantly higher than BP calculated from leucine incorporation and ranged from 47.2 to 77.5 μg C 1-−1 day−1 depending on the tracer and the conversion factor used.3. Bacterial growth rates ranged from 0.1 day−1 during winter to 1.7 day−1 in the summer. A strong correlation was found between temperature as well as chlorophyll a and bacterial growth when temperature was greater than 5 °C; a major spring phytoplankton bloom at a temperature below 5 °C did not increase BP.4. Dissolved organic carbon (DOC) concentrations varied between 2 and 7.2 mg C 1-−1 and comprised between 50 and 92% of the total organic carbon pool in the River Danube, Based on the DOC concentration and an assumed bacterial growth yield of 20% we calculated mean DOC turnover times of around 60 days in the winter and less than 8 days during the summer.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2427.1995.tb00916.x
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  • 3
    Electronic Resource
    Electronic Resource
    Seasonal and spatial distribution of dissolved and particulate organic carbon and bacteria in the bank of an impounding reservoir on the Enns River, Austria (2001)
    Oxford UK : Blackwell Science Ltd
    Freshwater biology 46 (2001), S. 0 
    Details
    ISSN: 1365-2427
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: 1. Interstitial bacterial abundance, production and ectoenzyme activity were investigated over an annual cycle in an Austrian river when infiltration of oligotrophic river water into a river-bank was artificially enhanced. These microbial parameters were related to porewater chemistry and the concentration of particulate (POC) and dissolved organic carbon (DOC).2. Porewater chemistry reflected the hydrodynamic mixing of infiltrating river water with riparian groundwater. Seasonal fluctuations in the microbial parameters resulted mainly from changes in temperature and organic matter supply. Seasonal change in porewater chemistry in the river-bank was detectable laterally only within the first metre of the sediment and decreased rapidly with increasing distance from the sediment–water interface.3. The DOC concentration decreased only slightly during lateral transport through the aquifer, while total organic carbon (TOC) concentration as well as abundance and activity of interstitial bacteria were reduced by up to one order of magnitude within the top metre of the sediment. Retention of incoming particulate matter structured the lateral distribution pattern of TOC concentration. The POC and not the DOC pool was the main source of carbon for interstitial bacteria and, therefore, the quality of POC determines the distribution of microbial metabolism within the riparian zone.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2427.2001.00743.x
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  • 4
    Electronic Resource
    Electronic Resource
    A comparison of DNA- and RNA-based clone libraries from the same marine bacterioplankton community (2005)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 51 (2005), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Clones from the same marine bacterioplankton community were sequenced, 100 clones based on DNA (16S rRNA genes) and 100 clones based on RNA (16S rRNA). This bacterioplankton community was dominated by α-Proteobacteria in terms of repetitive DNA clones (52%), but γ-Proteobacteria dominated in terms of repetitive RNA clones (44%). The combined analysis led to a characterization of phylotypes otherwise uncharacterized if only the DNA or RNA libraries would have been analyzed alone. Of the DNA clones, 25.5% were found only in this library and no close relatives were detected in the RNA library. For clones from the RNA library, 21.5% of RNA clones did not indicate close relatives in the DNA library. Based on the comparisons between DNA and RNA libraries, our data indicate that the characterization of the bacterial community based on RNA has the potential to characterize distinct phylotypes from the marine environment, which remain undetected on the DNA level.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2004.09.012
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  • 5
    Electronic Resource
    Electronic Resource
    Dynamics in bacterial surface properties of a natural bacterial community in the coastal North Sea during a spring phytoplankton bloom (2005)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 53 (2005), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The hydrophilic and hydrophobic properties of single cells of natural bacterioplankton communities were determined using a recently developed staining method combined with confocal laser scanning microscopy and advanced image analysis. On an average, about 50% of the bacterial cell area was covered by hydrophobic and only 16% by hydrophilic properties, while about 72% was covered by the genome. However, the size of these properties was independent of the bacterial cell size. Bacterial hydrophobicity was positively correlated with ambient 〈inlineGraphic alt="inline image" href="urn:x-wiley:01686496:FEM285:FEM_285_mu1" location="equation/FEM_285_mu1.gif"/〉 concentrations and negatively correlated with overall bacterial abundance. The expression of hydrophilicity was more dynamic. Over the spring phytoplankton bloom, the bacterioplankton ratiophil/phob repeatedly reached highest values shortly before peaks in bacterioplankton abundance were observed, indicating a direct and fast response of bacterial surface properties, especially hydrophilicity, to changing environmental conditions. Compared to bacterial strains, recently studied with the same method, cells of marine bacterioplankton communities are much smaller and less frequently covered by hydrophobic or hydrophilic properties. While the percentage area covered by the genome is essentially the same, the percentage area covered by hydrophobic or hydrophilic properties is much smaller.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2005.01.015
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  • 6
    Electronic Resource
    Electronic Resource
    Laboratory-made particles as a useful approach to analyse microbial processes in marine macroaggregates (1998)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 26 (1998), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Two kinds of particles were created in the laboratory in rolling tanks to simulate natural macroaggregates. Laboratory-made particles type 1 were formed under sterile conditions from a mixture of cells and extracellular products of four diatom species in artificial seawater, and inoculated with a marine microbial assemblage. Laboratory-made particles type 2 were created directly from natural seawater. These particles were characterised in terms of maximum length, volume and abundance. Chemical composition (carbohydrates, amino acids and total organic carbon) and bacterial and flagellate abundances were measured in the particles and ambient water. We found that both kinds of laboratory-made particles were similar in terms of size, chemical composition and microbial abundance. Moreover, they resembled natural marine aggregates in size and volume. However, laboratory-made particles showed higher concentrations of carbohydrates, amino acids and total organic carbon as well as higher microbial abundance when compared to natural macroaggregates. This difference can be explained by the sampling method, since natural aggregates are frequently collected in the sea with syringes including ambient water, and consequently diluted, whereas in this study the laboratory-made particles were carefully collected without ambient water. Thus, both kinds of laboratory-made particles might be a good alternative for the analysis of microbial processes in marine macroaggregates. Advantages and disadvantages of these two types of laboratory-made particles are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1998.tb00517.x
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  • 7
    Electronic Resource
    Electronic Resource
    A survey on bacteria inhabiting the sea surface microlayer of coastal ecosystems (2005)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 54 (2005), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Bacterial populations inhabiting the sea surface microlayer from two contrasted Mediterranean coastal stations (polluted vs. oligotrophic) were examined by culturing and genetic fingerprinting methods and were compared with those of underlying waters (50 cm depth), for a period of two years. More than 30 samples were examined and 487 strains were isolated and screened. Proteobacteria were consistently more abundant in the collection from the pristine environment whereas Gram-positive bacteria (i.e., Actinobacteria and Firmicutes) were more abundant in the polluted site. Cythophaga-Flavobacter–Bacteroides (CFB) ranged from 8% to 16% of total strains. Overall, 22.5% of the strains showed a 16S rRNA gene sequence similarity only at the genus level with previously reported bacterial species and around 10.5% of the strains showed similarities in 16S rRNA sequence below 93% with reported species. The CFB group contained the highest proportion of unknown species, but these also included Alpha- and Gammaproteobacteria. Such low similarity values showed that we were able to culture new marine genera and possibly new families, indicating that the sea-surface layer is a poorly understood microbial environment and may represent a natural source of new microorganisms. Genetic fingerprinting showed, however, no consistent differences between the predominant bacterial assemblages from surface microlayer and underlying waters, suggesting that the presence of a stable and abundant neustonic bacterial community is not a common trait of coastal marine environments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2005.04.002
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  • 8
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    Towards a better understanding of microbial carbon flux in the sea (2011)
    Inter-Research
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2008. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Aquatic Microbial Ecology 53 (2008): 21-38, doi:10.3354/ame01230.
    Description: We now have a relatively good idea of how bulk microbial processes shape the cycling of organic matter and nutrients in the sea. The advent of the molecular biology era in microbial ecology has resulted in advanced knowledge about the diversity of marine microorganisms, suggesting that we might have reached a high level of understanding of carbon fluxes in the oceans. However, it is becoming increasingly clear that there are large gaps in the understanding of the role of bacteria in regulating carbon fluxes. These gaps may result from methodological as well as conceptual limitations. For example, should bacterial production be measured in the light? Can bacterial production conversion factors be predicted, and how are they affected by loss of tracers through respiration? Is it true that respiration is relatively constant compared to production? How can accurate measures of bacterial growth efficiency be obtained? In this paper, we discuss whether such questions could (or should) be addressed. Ongoing genome analyses are rapidly widening our understanding of possible metabolic pathways and cellular adaptations used by marine bacteria in their quest for resources and struggle for survival (e.g. utilization of light, acquisition of nutrients, predator avoidance, etc.). Further, analyses of the identity of bacteria using molecular markers (e.g. subgroups of Bacteria and Archaea) combined with activity tracers might bring knowledge to a higher level. Since bacterial growth (and thereby consumption of DOC and inorganic nutrients) is likely regulated differently in different bacteria, it will be critical to learn about the life strategies of the key bacterial species to achieve a comprehensive understanding of bacterial regulation of C fluxes. Finally, some processes known to occur in the microbial food web are hardly ever characterized and are not represented in current food web models. We discuss these issues and offer specific comments and advice for future research agendas.
    Description: Our work was supported by the following grants: NSF grant 0217282 (H.D.), Spanish MEC grant MODIVUS (J.M.G.), the Swedish Science Council (J.P.), the IEO time-series RADIALES programme (X.A.G.M.), the Earth and Life Science Division of the Dutch Science Foundation, ARCHIMEDES project, #835.20.023 (G.J.H.).
    Keywords: Carbon flux ; Microbial ecology ; Ocean ; Bacteria ; Protists ; Light ; Genomics ; Chemoautotrophy ; Models
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 9
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    Diversity of Archaea and detection of crenarchaeotal amoA genes in the rivers Rhine and Têt (2011)
    Inter-Research
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © Inter-Research, 2009. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Aquatic Microbial Ecology 55 (2009): 189-201, doi:10.3354/ame01294.
    Description: Pelagic archaeal phylogenetic diversity and the potential for crenarchaeotal nitrification of Group 1.1a were determined in the rivers Rhine and Têt by 16S rRNA sequencing, catalyzed reported deposition-fluorescence in situ hybridization (CARD–FISH) and quantification of 16S rRNA and functional genes. Euryarchaeota were, for the first time, detected in temperate river water even though a net predominance of crenarchaeotal phylotypes was found. Differences in phylogenic distribution were observed between rivers and seasons. Our data suggest that a few archaeal phylotypes (Euryarchaeota Groups RC-V and LDS, Crenarchaeota Group 1.1a) are widely distributed in pelagic riverine environments whilst others (Euryarchaeota Cluster Sagma-1) may only occur seasonally in river water. Crenarchaeota Group 1.1a has recently been identified as a major nitrifier in the marine environment and phylotypes of this group were also present in both rivers, where they represented 0.3% of the total pelagic microbial community. Interestingly, a generally higher abundance of Crenarchaeota Group 1.1a was found in the Rhine than in the Têt, and crenarchaeotal ammonia monooxygenase gene (amoA) was also detected in the Rhine, with higher amoA copy numbers measured in February than in September. This suggests that some of the Crenarchaeota present in river waters have the ability to oxidize ammonia and that riverine crenarchaeotal nitrification of Group 1.1a may vary seasonally.
    Description: The present study is part of the Land–Ocean Interactions in the Coastal Zone (LOICZ) project supported by the Research Council for Earth and Life Science (ALW), with financial aid from the Netherlands Organisation for Scientific Research (NWO) (grant no. 014.27.003 to J.S.S.D.).
    Keywords: Archaea ; River ; Diversity ; Nitrification
    Repository Name: Woods Hole Open Access Server
    Type: Article
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