Genomic content of uncultured <i>Bacteroidetes</i> from contrasting oceanic provinces in the North Atlantic Ocean

Gómez-Pereira, Paola R.; Schüler, Margarete; Fuchs, Bernhard M.; Bennke, Christin M.; Teeling, Hanno; Waldmann, Jost; Richter, Michael; Barbe, Valérie; Bataille, Elodie; Glöckner, Frank Oliver; Amann, Rudolf

doi:10.1111/j.1462-2920.2011.02555.x

Cited by 141 publications

(141 citation statements)

References 86 publications

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“…Different metabolic capabilities to degrade and utilize DOM among bacterial groups is one of the hypotheses that has been developed to explain these observations, an idea that was first supported by results from fluorescence in situ hybridization coupled to microautoradiography (Cottrell & Kirchman 2000, Teira et al 2004, Vila-Costa et al 2007). Single-cell analyses have de monstrated that polymeric substances are preferentially degraded by Bacteroidetes (Cottrell & Kirchman 2000), a finding that was later confirmed by genomic analyses of several members of this group (Bauer et al 2006, Gómez-Pereira et al 2012. Metatranscriptomic analyses of bacterial communities grown on different DOM sources further reveal taxon-specific expression of genes related to carbon metabolism (McCarren et al 2010, Poretsky et al 2010, Rinta-Kanto et al 2012.…”

Section: Introductionmentioning

confidence: 76%

Changes in bacterial diversity in response to dissolved organic matter supply in a continuous culture experiment

Landa¹,

Cottrell²,

Kirchman³

et al. 2013

Aquat. Microb. Ecol.

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Heterotrophic bacterial metabolism is tightly linked to the availability of dissolved organic matter (DOM), but the relationship between substrate supply and bacterial diversity remains unresolved. The objective of the present study was to determine how an increase in the supply of bioavailable DOM affects bacterial metabolism and diversity. We addressed this issue by growing a natural bacterial community over 5 generations in continuous cultures either on seawater (dissolved organic carbon concentration equal to 74 µM) or on seawater amended with 13 µM of diatom-derived DOM. Bacteria markedly responded to the additional DOM supply, as revealed by 1.6-fold higher bacterial abundances and 10-fold higher cell-specific α-and β-gluco sidase activities in the +DOM treatment than in the control throughout the experimental period. Analysis of diversity as determined by tag pyrosequencing of 16S rRNA genes after 3 and 5 bacterial generations showed that the bacterial communities in the +DOM treatment were more similar to each other than to communities in the control. Diversity indices such as richness and phylogenetic distance were higher in the DOM-amended cultures than in the control. Gammaproteobacteria dominated the communities selected in our cultures, representing between 87 and 99% of the sequences. The addition of DOM led to a higher relative abundance of several bacterial groups, in particular Alphaproteobacteria, Bacteroidetes, and Verrucomicrobia, which accounted for up to 14% of the sequences, compared to the control in which they represented < 5% of the sequences. Our results demonstrate that in this experimental context, an increased supply of bioavailable DOM sustained a higher bacterial diversity. KEY WORDS: Bacterial diversity · Dissolved organic matter · Continuous cultures · 454 pyrosequencingResale or republication not permitted without written consent of the publisher

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Section: Introductionmentioning

confidence: 76%

Changes in bacterial diversity in response to dissolved organic matter supply in a continuous culture experiment

Landa¹,

Cottrell²,

Kirchman³

et al. 2013

Aquat. Microb. Ecol.

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“…This agrees with previous observations from field (Crump et al ., 2003; Roiha et al ., 2011) and laboratory experiments (Logue et al ., 2016) showing that rapid shifts in community composition take place upon soil organic matter input. The loss and prevalence of the taxa determined in our study may be explained by their different functional adaptability, including differences in resource affinities (Cottrell & Kirchman, 2000; Salcher et al ., 2011; Heinrich et al ., 2013), physiological characteristics (Hahn & Pöckl, 2005; Šimek et al ., 2006) and genetic composition (Bauer et al ., 2006; Gómez‐Pereira et al ., 2012; Teeling et al ., 2012; Tveit et al ., 2013). Further, changes in lake bacterial community composition have been attributed not only to the differential response of individual bacterial taxa to DOM inputs, but also to the introduction of soil bacteria with allochthonous sources or to incubation effects (Crump et al ., 2003; Logue et al ., 2016).…”

Section: Discussionmentioning

confidence: 99%

Climate‐related changes of soil characteristics affect bacterial community composition and function of high altitude and latitude lakes

Rofner

Peter

Catalán

et al. 2016

Global Change Biology

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Lakes at high altitude and latitude are typically unproductive ecosystems where external factors outweigh the relative importance of in‐lake processes, making them ideal sentinels of climate change. Climate change is inducing upward vegetation shifts at high altitude and latitude regions that translate into changes in the pools of soil organic matter. Upon mobilization, this allochthonous organic matter may rapidly alter the composition and function of lake bacterial communities. Here, we experimentally simulate this potential climate‐change effect by exposing bacterioplankton of two lakes located above the treeline, one in the Alps and one in the subarctic region, to soil organic matter from below and above the treeline. Changes in bacterial community composition, diversity and function were followed for 72 h. In the subarctic lake, soil organic matter from below the treeline reduced bulk and taxon‐specific phosphorus uptake, indicating that bacterial phosphorus limitation was alleviated compared to organic matter from above the treeline. These effects were less pronounced in the alpine lake, suggesting that soil properties (phosphorus and dissolved organic carbon availability) and water temperature further shaped the magnitude of response. The rapid bacterial succession observed in both lakes indicates that certain taxa directly benefited from soil sources. Accordingly, the substrate uptake profiles of initially rare bacteria (copiotrophs) indicated that they are one of the main actors cycling soil‐derived carbon and phosphorus. Our work suggests that climate‐induced changes in soil characteristics affect bacterioplankton community structure and function, and in turn, the cycling of carbon and phosphorus in high altitude and latitude aquatic ecosystems.

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“…Like other Bacteroidetes, this group also possesses a complete repertoire of gliding-motility proteins that have been related to degradation of complex polysaccharides (Gomez-Pereira et al, 2012). In addition, transporters for large biopolymers, glycosyl hydrolases and transferases were detected.…”

Section: Figurementioning

confidence: 99%

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

et al. 2014

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The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to 440%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.

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Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean

Cited by 141 publications

References 86 publications

Changes in bacterial diversity in response to dissolved organic matter supply in a continuous culture experiment

Changes in bacterial diversity in response to dissolved organic matter supply in a continuous culture experiment

Climate‐related changes of soil characteristics affect bacterial community composition and function of high altitude and latitude lakes

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

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