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Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island.

Kumbhare SV, Dhotre DP, Dhar SK, Jani K, Apte DA, Shouche YS, Sharma A - PLoS ONE (2015)

Bottom Line: The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well.Significant differences were observed in bacterial diversity within a short region of the continental shelf (1-40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1-20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25-40 meters).By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity.

View Article: PubMed Central - PubMed

Affiliation: Microbial Culture Collection, National Centre for Cell Science, Pune, 411007, Maharashtra, India.

ABSTRACT
Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1-40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1-20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25-40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity.

No MeSH data available.


Related in: MedlinePlus

Spatial distribution of bacterial isolates.The figure depicts the spatial distribution of the representative bacterial isolates across the sampling depths.
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pone.0129864.g001: Spatial distribution of bacterial isolates.The figure depicts the spatial distribution of the representative bacterial isolates across the sampling depths.

Mentions: Spread plate technique used for isolation of bacterial strains from sediment samples resulted in isolation of 28 different bacterial strains from various depths as described in S1 Table. The taxonomic identification was done by 16S rRNA gene sequencing, which demonstrated the presence of 9 different genera (S1 Table). The phylogenetic analysis was carried out using sequences of closely related bacterial type strains from EzTaxon database, which also substantiated the taxonomic identification (See S1 Fig). The Phylogenetic tree analysis showed that most of the isolates formed two major clades of Gamma and Alpha-Proteobacteria, while some of the other bacterial isolates belonging to Firmicutes and Cytophaga-Flavobacterium-Bacteroides (CFB) group of phyla formed distinct clades within the tree, thus indicating the presence of diverse bacterial group in the habitat. Fig 1 depicts the spatial distribution of the bacteria isolated from various depths. Genera with diverse functional capabilities were observed at various depths. The genus Halomonas was observed to be widely distributed across the depth (10, 15, 25, 35 and 40 meters). These bacteria are known to be halophiles or are extremely halotolerant like Halomonas meridiana and thus could be a probable reason for their ubiquity in the marine environment [23]. The xylanase producing bacterium Mesoflavibacter zeaxanthinifaciens was also found ubiquitously in sediment samples (see Fig 1). This bacterium utilizes xylan, which is one of the major polysaccharides in plant cell wall [24,25]. The continental shelves harbor diverse population of marine plants, which may serve as a source of nutrition to such bacteria [26]. Other bacteria isolated like Huaishuia halophila were previously reported to be associated with algal blooms in the coastal regions [27]. Huaishuia produces alginase, which has a specific function of utilizing alginate, a polysaccharide found in the cell wall of the brown algae (Phaeophyceae) [27,28]. Additionally, the bacterium Alteromonas macleodii isolated from sediment samples is known to be widespread in the tropical environments as an opportunistic copiotroph harboring the Na+/H+ antiporters to survive in high salinity environments [29,30]. We also found a novel bacterium Domibacillus indicus, which was isolated from the depth of 5 meters [31]. This bacterium showed 97.6% 16S rRNA gene sequence similarity with the only other species reported, i.e. Domibacillus robiginosus strain WS 4628T, in genus Domibacillus [31]. We were also able to isolate the bacterium Sulfitobacter dubius at the depth of 20 meters. This bacterium is previously reported to be isolated from sea grass (Zostera marina) and most of the species belonging to genera Sulfitobacter are reported to be heterotrophic bacteria residing in hypersaline environments [32]. Furthermore, Sulfitobacter is one of the groups of bacteria which form the Roseobacter clade [33]. The Roseobacter lineage in the marine habitat is known to be conducive to the cycling of oceanic carbon by producing ABC (ATP-binding cassettes) importers and exporters [34]. Additionally, other genera which are ubiquitously found in various ecological niches were also found at various depths as listed in S1 Table.


Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island.

Kumbhare SV, Dhotre DP, Dhar SK, Jani K, Apte DA, Shouche YS, Sharma A - PLoS ONE (2015)

Spatial distribution of bacterial isolates.The figure depicts the spatial distribution of the representative bacterial isolates across the sampling depths.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4465901&req=5

pone.0129864.g001: Spatial distribution of bacterial isolates.The figure depicts the spatial distribution of the representative bacterial isolates across the sampling depths.
Mentions: Spread plate technique used for isolation of bacterial strains from sediment samples resulted in isolation of 28 different bacterial strains from various depths as described in S1 Table. The taxonomic identification was done by 16S rRNA gene sequencing, which demonstrated the presence of 9 different genera (S1 Table). The phylogenetic analysis was carried out using sequences of closely related bacterial type strains from EzTaxon database, which also substantiated the taxonomic identification (See S1 Fig). The Phylogenetic tree analysis showed that most of the isolates formed two major clades of Gamma and Alpha-Proteobacteria, while some of the other bacterial isolates belonging to Firmicutes and Cytophaga-Flavobacterium-Bacteroides (CFB) group of phyla formed distinct clades within the tree, thus indicating the presence of diverse bacterial group in the habitat. Fig 1 depicts the spatial distribution of the bacteria isolated from various depths. Genera with diverse functional capabilities were observed at various depths. The genus Halomonas was observed to be widely distributed across the depth (10, 15, 25, 35 and 40 meters). These bacteria are known to be halophiles or are extremely halotolerant like Halomonas meridiana and thus could be a probable reason for their ubiquity in the marine environment [23]. The xylanase producing bacterium Mesoflavibacter zeaxanthinifaciens was also found ubiquitously in sediment samples (see Fig 1). This bacterium utilizes xylan, which is one of the major polysaccharides in plant cell wall [24,25]. The continental shelves harbor diverse population of marine plants, which may serve as a source of nutrition to such bacteria [26]. Other bacteria isolated like Huaishuia halophila were previously reported to be associated with algal blooms in the coastal regions [27]. Huaishuia produces alginase, which has a specific function of utilizing alginate, a polysaccharide found in the cell wall of the brown algae (Phaeophyceae) [27,28]. Additionally, the bacterium Alteromonas macleodii isolated from sediment samples is known to be widespread in the tropical environments as an opportunistic copiotroph harboring the Na+/H+ antiporters to survive in high salinity environments [29,30]. We also found a novel bacterium Domibacillus indicus, which was isolated from the depth of 5 meters [31]. This bacterium showed 97.6% 16S rRNA gene sequence similarity with the only other species reported, i.e. Domibacillus robiginosus strain WS 4628T, in genus Domibacillus [31]. We were also able to isolate the bacterium Sulfitobacter dubius at the depth of 20 meters. This bacterium is previously reported to be isolated from sea grass (Zostera marina) and most of the species belonging to genera Sulfitobacter are reported to be heterotrophic bacteria residing in hypersaline environments [32]. Furthermore, Sulfitobacter is one of the groups of bacteria which form the Roseobacter clade [33]. The Roseobacter lineage in the marine habitat is known to be conducive to the cycling of oceanic carbon by producing ABC (ATP-binding cassettes) importers and exporters [34]. Additionally, other genera which are ubiquitously found in various ecological niches were also found at various depths as listed in S1 Table.

Bottom Line: The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well.Significant differences were observed in bacterial diversity within a short region of the continental shelf (1-40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1-20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25-40 meters).By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity.

View Article: PubMed Central - PubMed

Affiliation: Microbial Culture Collection, National Centre for Cell Science, Pune, 411007, Maharashtra, India.

ABSTRACT
Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1-40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1-20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25-40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity.

No MeSH data available.


Related in: MedlinePlus