Single cell genomics of deep ocean bacteria

Zhao, Weizhou; Andersson, Siv G. E.

doi:10.1016/j.tim.2014.03.002

Cited by 2 publications

(2 citation statements)

References 10 publications

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“…On the contrary, subgroup 3 is more frequently found in coastal or brackish water samples (Brown et al, 2012 ). The lifestyle strategy of SAR11 is that of a K-strategist (slow growing and relatively dominant); in order to deal with oligotrophic conditions, the free-living organisms have streamlined their metabolisms and genomes, and thereby decrease their nutrient requirements (Giovannoni et al, 2005 ; Zhao and Andersson, 2014 ). Another clade that is presumably ecologically and metabolically similar to SAR11 is the SAR116 clade.…”

Section: Resultsmentioning

confidence: 99%

Expanding the World of Marine Bacterial and Archaeal Clades

et al. 2016

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Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies.

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Section: Resultsmentioning

confidence: 99%

Expanding the World of Marine Bacterial and Archaeal Clades

et al. 2016

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“…The life strategy of SAR11 is that of a K-strategist (slow growing and relatively dominant). To cope with oligotrophic conditions, free-living organisms have streamlined their metabolism and genome, thereby reducing their nutrient requirements in poor environments 20 , 21 . The area studied is characterized by low bacterial production and the predominance of LNA bacteria 22 .…”

Section: Discussionmentioning

confidence: 99%

Picoplankton diversity in an oligotrophic and high salinity environment in the central Adriatic Sea

Šantić

Stojan

Matić

et al. 2023

Sci Rep

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By combining qualitative 16S metabarcoding and quantitative CARD-FISH methods with neural gas analysis, different patterns of the picoplankton community were revealed at finer taxonomic levels in response to changing environmental conditions in the Adriatic Sea. We present the results of a one-year study carried out in an oligotrophic environment where increased salinity was recently observed. We have shown that the initial state of community structure changes according to environmental conditions and is expressed as qualitative and quantitative changes. A general pattern of increasing diversity under harsh environmental conditions, particularly under the influence of increasing salinity at the expense of community abundance was observed. Considering the trend of changing seawater characteristics due to climate change, this study helps in understanding a possible structural change in the microbial community of the Adriatic Sea that could affect higher levels of the marine food web.

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Single cell genomics of deep ocean bacteria

Cited by 2 publications

References 10 publications

Expanding the World of Marine Bacterial and Archaeal Clades

Expanding the World of Marine Bacterial and Archaeal Clades

Picoplankton diversity in an oligotrophic and high salinity environment in the central Adriatic Sea

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