Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean

Gómez-Pereira, Paola R.; Fuchs, Bernhard M.; Alonso, Cecilia; Oliver, Matthew J.; Beusekom, Justus E. E. van; Amann, Rudolf

doi:10.1038/ismej.2009.142

Cited by 142 publications

(147 citation statements)

References 76 publications

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“…The top plume indicator was OTU 9443, a Polaribacter taxon, which is a genus of class Flavobacteria. One study of bacterioplankton communities along a coast to open ocean transect in the North Atlantic Ocean found Polaribacter taxa to be the most prevalent of all Flavobacteria, with higher abundances in coastal samples (Gomez-Pereira et al, 2010). A comparison of all Polaribacter OTUs in the plume to environmental variables showed correlation with temperature, DO, bacterial production rate, DOC, and upwelling (r ¼ 0.576, Table 2).…”

Section: Discussionmentioning

confidence: 99%

Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin

et al. 2013

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Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (q ¼ À 0.664) and residence time (q ¼ 0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments.

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Section: Discussionmentioning

confidence: 99%

Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin

et al. 2013

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“…The percentages of different microbial taxa in the water samples were determined by FISH with horseradish peroxidaselabeled oligonucleotide probes and catalyzed reporter deposition (CARD-FISH) (Pernthaler et al 2002). The following probes were used to characterize the microbial community: EUB338 I-III (most Bacteria) (Daims et al 1999), ALF968 (most Alphaproteobacteria) (Neef 1997), BET42a (most Betaproteobacteria) (Manz et al 1992), GAM42a (most Gammaproteobacteria) (Manz et al 1992), CF319a (many groups of Bacteroidetes) (Manz et al 1996), HGC69a (most Actinobacteria) (Roller et al 1994), PLA46 most Planctomycetes (Neef et al 1998), SAR11-441 (members of the alphaproteobacterial SAR11 clade) (Morris et al 2002), ROS537 (members of the alphaproteobacterial RoseobacterSulfitobacter-Silicibacter clade) (Eilers et al 2001), NOR5-730 (members of the gammaproteobacterial NOR5/OM60 clade) (Eilers et al 2001), SAR86-1245 (members of the gammaproteobacterial SAR86 clade) (Eilers et al 2000), POL740 (members of the genus Polaribacter of Bacteroidetes) (Malmstrom et al 2007), CF6-1267 (members of DE cluster 2 of the Flavobacteria class of the phylum Bacteroidetes) , and VIS1-575 (uncultured marine VIS1 clade of the Flavobacteria class of the phylum Bacteroidetes) (Gomez-Pereira et al 2010).…”

Section: Methodsmentioning

confidence: 99%

Multilevel analysis of the bacterial diversity along the environmental gradient Río de la Plata–South Atlantic Ocean

Alonso¹,

Gómez-Pereira²,

Ramette³

et al. 2010

Aquat. Microb. Ecol.

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The Río de la Plata is the world's largest estuary, draining the second largest basin of South America. In spite of its key significance at the local and global scale, this is the first attempt made so far to characterize the bacterial diversity of this system. We employed a suite of molecular methods to analyze the bacterial diversity at different phylogenetic levels, both in terms of richness and evenness, and we related these findings to physicochemical parameters. A clear environmental gradient was observed with 3 distinctive zones (riverine, frontal, and marine). In turn, the bacterial communities appeared highly diverse and strongly structured by the environment. A high number (324) of different operational taxonomic units (OTUs) were identified by automated ribosomal intergenic spacer analysis (ARISA). The ARISA results suggested that the composition of bacterioplankton communities was strongly related to physicochemical water characteristics, and that the bacterioplankton had little overlap with the bacterial assemblage of the sediments. Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) indicated that Betaproteobacteria and Actinobacteria were more abundant in the riverine zone, whereas Gammaproteobacteria and Planctomycetes preferred the marine waters. The relative abundance of Bacteroidetes peaked in the frontal zone, and Alphaproteobacteria were numerically dominant throughout the estuary. The analysis of about 300 almost full-length 16S rRNA gene sequences pointed to the existence of ubiquitous phylotypes, but also suggested habitat preferences among certain groups. This first look into the bacterial community of the Río de la Plata demonstrated marked diversity patterns, providing further insights into the ecology of globally distributed groups of aquatic bacteria.

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“…As an example, different SAR11 ecotypes have been shown to vary through time and depth in response to physical and chemical variability (Field et al 1997, Morris et al 2005, Carlson et al 2009). Similarly, the presence of different Flavobacteria clades, such as DE2 in polar biomes and the VISION clades in Arctic provinces, suggests that distinct flavobacterial clades have different niches and could present different life strategies (Gómez-Pereira et al 2010).…”

Section: Bacterial Group Biogeographymentioning

confidence: 99%

Global-scale distributions of marine surface bacterioplankton groups along gradients of salinity, temperature, and chlorophyll: a meta-analysis of fluorescence in situ hybridization studies

Lefort

Gasol²

2013

Aquat. Microb. Ecol.

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We used literature data on marine bacterial (sub)group abundances, as determined by fluorescence in situ hybridization, to test whether the ecological variability of the different subgroups was similar to that of the bacterial community as a whole. Patterns of 6 major groups are described (Alpha-, Beta-, Gammaproteobacteria and Bacteroidetes, as well as Rhodobacteraceae and SAR11) and related to environmental variables such as chlorophyll a (chl a) concentration, salinity, and temperature, distinguishing between coastal or open-ocean environments. Coastal ecosystems exhibited higher relative abundances (average % of DAPI counts) of Bacteroidetes (23%), Beta-(11%) and Gammaproteobacteria (10%), and Rhodobacteraceae (6%), while significantly higher contributions of Alphaproteobacteria and SAR11 (32%) were on average enumerated offshore. Multiple regression analyses showed significant explanatory power of chl a and temperature on total and SAR11 absolute abundances (expressed as cells ml −1 ), and of chl a and salinity levels on absolute abundances of Betaproteobacteria and Rhodobacteraceae. Other analyses revealed increasing contribution of Gammaproteobacteria for increasing temperatures and high temperature avoidance for Betaproteobacteria. Significantly different log-log regression slopes were found between bacterial group absolute abundances and chl a concentration at a global scale, ranging from 0.13 ± 0.04 (SE) for SAR11 to 0.53 ± 0.08 for Betaproteobacteria. The different patterns observed for the different groups, in coastal and open-ocean environments, suggest different niche preferences by each group as well as a coherent response to environmental factors.

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Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean

Cited by 142 publications

References 76 publications

Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin

Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin

Multilevel analysis of the bacterial diversity along the environmental gradient Río de la Plata–South Atlantic Ocean

Global-scale distributions of marine surface bacterioplankton groups along gradients of salinity, temperature, and chlorophyll: a meta-analysis of fluorescence in situ hybridization studies

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