Diversity of culturable Sulphur-oxidising bacteria in the oxygen minimum zones of the northern Indian Ocean

Menezes, Larissa D.; Fernandes, Genevieve L; Mulla, Amara Begum; Meena, Ramavatar; Damare, Samir

doi:10.1016/j.jmarsys.2018.05.007

Cited by 27 publications

(12 citation statements)

References 55 publications

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“…Other taxa at class-level including the Betaproteobacteria, Deltaproteobacteria, Actinobacteria, Nitrospinia, Planctomycetacia, and SAR406 clade were also well-reported however varied along the depths and sites sampled in the Indian Ocean OMZs (Fuchs et al, 2005;Bandekar et al, 2018;Fernandes et al, 2019). Pelagic nitrogen and sulfur cycling in the OMZs of the Indian Ocean have recently revealed presence of nitrate-reducing and sulfur-oxidizing bacteria based on biochemical of culture-dependent studies (Mulla et al, 2017;Menezes et al, 2018;Fernandes et al, 2019). Metagenomic analysis in the AS OMZ have revealed presence of denitrifiers and annamox bacteria (Bandekar et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

“…Microbial activities in the OMZs have shown to contribute 30-50% nitrogen loss in the ocean (Lam and Kuypers, 2011). Although the OMZs are well-studied regions for nitrogen cycling, recent studies, based on metagenomic and biochemical methods, from the Pacific and Indian Oceans investigated the role of microbes in sulfur cycle (Canfield et al, 2010;Menezes et al, 2018). Previous studies, based on culture-based and cultureindependent techniques, from the AS and BoB focused on bacterial and archaeal communities that dominate the coastal and open ocean OMZ and non-OMZ regions.…”

Section: Introductionmentioning

confidence: 99%

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Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing

2020

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The Indian Ocean harbors oxygen minimum zones (OMZs) in the Arabian Sea and Bay of Bengal, with dissolved oxygen < 20 µM, located at the mid-depths of the water column. Till date, high-throughput sequence-data on depth-wise distribution of prokaryotic communities have rarely been reported from these OMZs. The present study aimed to characterize the prokaryotic diversity inhabiting Arabian Sea Time Series (ASTS) and India's Idea 2 (II2) in the Arabian Sea, and Bay of Bengal Time Series (BoBTS) in the Bay of Bengal OMZs based on amplicon sequencing of 16S rRNA gene regions, along six sampled depths in the water column. High prokaryotic richness was observed in the Arabian Sea and Bay of Bengal samples. Operational taxonomic units (OTUs) in the range of 1249-3298 were identified, wherein, less prokaryotic diversity was observed at surface and within oxygen minimum depths. At phylum level, most OTUs were affiliated to Bacteroidetes, Chloroflexi, Cyanobacteria, Marinimicrobia, Planctomycetes, and Proteobacteria. Prokaryotic community differed between ASTS, II2 and BoBTS locations along varying physicochemical conditions. Predictive functional profiling of the bacterial communities suggested the involvement of abundant microbes in nitrogen and sulfur metabolism pathways. Bacterial isolates belonging to genera from the clades, δ-Proteobacteria and γ-Proteobacteria, described previously for their participation in biogeochemical cycling of N-and-S in the OMZs were reported from deoxygenated waters of both the basins. Bacteria involved in anammox such as Candidatus Scalindua were found to be relatively high at ASTS and II2 locations in the Arabian Sea. Further studies are required to ascertain the role of abundant bacteria along the dynamic oceanographic processes in the OMZs.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing

2020

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“…Efforts to culture bacteria from the deep ocean (> 200 m) have focused mostly on isolates from hydrothermal vents [11][12][13], whale carcasses [14], trenches [15], and deep-sea sediments [10,[16][17][18][19]. Thus, very few studies have analyzed the diversity of isolates from mesopelagic (in particular the oxygen minimum zone (OMZ) [20][21][22]), the bathypelagic and abyssopelagic waters [8,[23][24][25], and those available were mainly done at a local or regional scale.…”

Section: Introductionmentioning

confidence: 99%

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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“…Efforts to culture bacteria from the deep ocean (>200 m) have focused mostly on isolates from hydrothermal vents [11][12][13], whale carcasses [14], trenches [15], and deep-sea sediments [10,[16][17][18][19]. Thus, very few studies have analyzed the diversity of isolates from mesopelagic (in particular from regions with oxygen minimum zone areas) [20][21][22][23], the bathypelagic and abyssopelagic waters [8,[24][25][26], and those available were mainly done at a local or regional scale.…”

Section: Introductionmentioning

confidence: 99%

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

Sanz-Sáez

Salazar

Sánchez

et al. 2020

Preprint

View full text Add to dashboard Cite

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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Diversity of culturable Sulphur-oxidising bacteria in the oxygen minimum zones of the northern Indian Ocean

Cited by 27 publications

References 55 publications

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing

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

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

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