Culture-independent and -dependent methods to investigate the diversity of planktonic bacteria in the northern Bering Sea

Zeng, Yangsu; Zou, Yang; Grebmeier, Jacqueline M.; He, Jianfeng; Zheng, Tao

doi:10.1007/s00300-011-1044-8

Cited by 21 publications

(12 citation statements)

References 64 publications

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“…Those mentioned genera are also the most abundant and commonly isolated in all depths of our dataset together with Marinobacter. These genera have been detected in other culture-dependent and culture-independent studies from a wide variety of marine environments, including coastal, shelf, and open ocean waters [4,[38][39][40][41][42][43] corroborating their ubiquity. Alteromonas and Erythrobacter presented the highest number of isolates.…”

Section: Discussionsupporting

confidence: 58%

Diversity and distribution of marine heterotrophic bacteria from a large culture collection

Sanz-Sáez

Salazar

Sánchez

et al. 2020

Preprint

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Background: Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. We described the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along different depths. Results: The partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing all photic, mesopelagic, and bathypelagic isolates sequences retrieved from different stations, 37% of them were 100% identical. This percentage increased up to 59% when mesopelagic and bathypelagic strains were grouped as the aphotic dataset and compared to the photic dataset of isolates, indicating the ubiquity of some bacterial isolates along different ocean depths. Finally, we isolated three strains that represent a new species, and the genome comparison and phenotypic characterization of two of these strains (ISS653 and ISS1889) concluded that they belong to a new species within the genus Mesonia. Conclusions: Overall, this study highlights the relevance of culture-dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of the culturable marine bacteria as part of the total marine microbial diversity.

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Section: Discussionsupporting

confidence: 58%

Diversity and distribution of marine heterotrophic bacteria from a large culture collection

Sanz-Sáez

Salazar

Sánchez

et al. 2020

Preprint

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“…Those mentioned genera are also the most abundant and commonly isolated in all depths of our dataset together with Marinobacter. These genera have been detected in other culture-dependent and culture-independent studies from a wide variety of marine environments, including coastal, shelf, and open ocean waters[4,[33][34][35][36][37][38] corroborating their ubiquity. Alteromonas and Erythrobacter presented the highest number of isolates.…”

supporting

confidence: 58%

Diversity and distribution of marine heterotrophic bacteria from a large culture collection

Sanz-Sáez

Salazar

Lara

et al. 2020

Preprint

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BackgroundIsolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection includes isolates from both photic (817) and aphotic layers (744), including the oxygen minimum zone (OMZ, 362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. With this study, we describe the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along all the water column. ResultsThe partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing photic, OMZ, and bathypelagic isolates sequences, a 37% of them were 100% identical. This percentage increased up to 59% when the comparison was restricted between photic and aphotic sequences (OMZ and bathypelagic together) indicating the ubiquity of some bacterial isolates along the water column. Finally, we isolated three strains related with the genus Mesonia sp. that may represent new species since their whole 16S rRNA gene shared less than 95% sequence similarity with any other culture representative. ConclusionsOverall, this study highlights the relevance of culture dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of marine microbial diversity.

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“…In addition to numerous sequences of terrestrial origin, this clade comprises a marine subclade with sequences from East Pacific Rise vents (e.g. JN874313, Sylvan et al ., database release), or from surface waters in the Northern Bering Sea (Zeng et al ., ) or in the Pacific Ocean off Oregon (Morris et al ., ). Within the class Phycisphaerae , North Sea sequences formed separate clusters or were affiliated mainly with uncultivated clades such as Urania‐1B‐19 (Fig.…”

Section: Resultsmentioning

confidence: 99%

Permeability shapes bacterial communities in sublittoral surface sediments

Probandt

Knittel

Tegetmeyer

et al. 2017

Environmental Microbiology

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The first interaction of water column-derived organic matter with benthic microbial communities takes place in surface sediments which are acting as biological filters catalyzing central steps of elemental cycling. Here we analyzed the bacterial diversity and community structure of sediment top layers at seven sites in the North Sea where sediment properties ranged from coarse-grained and highly permeable to fine-grained and impermeable. Bacterial communities in surface sediments were richer, more even and significantly different from communities in bottom waters as revealed by Illumina tag sequencing of 16S rRNA genes. Sediment permeability had a clear influence on community composition which was confirmed by CARD-FISH. Sulfate-reducing Desulfobacteraceae (2-5% of total cells), Flavobacteriaceae (3-5%) were more abundant in impermeable than in highly permeable sediments where acidobacterial Sva0725 dominated (11-15%). Myxobacterial Sandaracinaceae were most abundant in medium permeable sediments (3-7%). Woeseiaceae/JTB255 and Planctomycetes were major groups in all sediments (4-6%, 8-22%). Planctomycetes were highly diverse and branched throughout the phylum. We propose Planctomycetes as key bacteria for degradation of high molecular weight compounds and recalcitrant material entering surface sediments from the water column. Benthic Flavobacteriaceae likely have restricted capabilities for macromolecule degradation and might profit with Sandaracinaceae and Acidobacteria from low molecular weight compounds.

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Culture-independent and -dependent methods to investigate the diversity of planktonic bacteria in the northern Bering Sea

Cited by 21 publications

References 64 publications

Diversity and distribution of marine heterotrophic bacteria from a large culture collection

Diversity and distribution of marine heterotrophic bacteria from a large culture collection

Diversity and distribution of marine heterotrophic bacteria from a large culture collection

Permeability shapes bacterial communities in sublittoral surface sediments

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