Culture independent molecular analysis of bacterial communities in the mangrove sediment of Sundarban, India

Ghosh, Abhrajyoti; Dey, Nirmalya; Bera, Amit; Tiwari, Anjali; Sathyaniranjan, KB; Chakrabarti, Kalyan; Chattopadhyay, Dhrubajyoti

doi:10.1186/1746-1448-6-1

Cited by 133 publications

(81 citation statements)

References 48 publications

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“…The organisms function in the liberation of CO2, phosphorus and nitrogen, which are the principal elements in the trophic network (Holguin et al, 2001;Hewson & Fuhrman, 2004;Zhang et al, 2008;Ghosh et al, 2010). For example, Desulfotomaculum arcticum (recorded at P3), which survives at high temperatures and is involved in the sulfur cycle.…”

Section: Discussionmentioning

confidence: 99%

Bacterial Diversity in an Amazonian Mangrove Ecosystem

Pureza

Graças

Gonçalves

et al. 2012

AST

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Mangroves form a transition zone among terrestrial, marine, and freshwater environments, and they host a striking diversity of macro-and microorganisms. In recent years, increasing anthropogenic impacts have caused widespread degradation of mangrove environments. To analyze the bacterial diversity of Salina Lake, an artificial body of water located in the mangroves of eastern Amazonia, total DNA was extracted from sediment and water samples that were collected from three sites (P1, P2, P3) located within the lake. The 16S rRNA gene was partially amplified, separated using the Denaturing High Performance Liquid Chromatography (DHPLC) method, and sequenced. The DHPLC profiles were quite distinct for the different aquatic and sedimentary bacterial communities. The most abundant groups (> 70%) at all sampled locations were Proteobacteria and unclassified bacteria, but other phyla were also identified, including Bacteroidetes, Cyanobacteria, Acidobacteria, Firmicutes, Actinobacteria, Chloroflexi, Siprochaetes and TM7. A total of 24, 15, and 23 OTUs (Operational Taxonomic Units) were observed in the water samples from P1, P2, and P3, respectively, whereas the sediment samples returned 29, 34, and 52 OTUs. This is the first analysis performed on the bacterial diversity of Salina Lake, which was created by the construction of a highway within a protected mangrove area.

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Section: Discussionmentioning

confidence: 99%

Bacterial Diversity in an Amazonian Mangrove Ecosystem

Pureza

Graças

Gonçalves

et al. 2012

AST

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“…ValenzuelaEncinas et al (2009) showed that the Acidobacteria was the dominant phylum in medium-saline soils but absent in high and low saline soils. Acidobacteria was found to represent significant proportions of bacterial communities in saline sediments from Qinghai Lake (Dong et al 2006) and mangrove sediments of Sundarban (Ghosh et al 2010).…”

Section: Bacteriamentioning

confidence: 99%

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

Gong

2013

World J Microbiol Biotechnol

102

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An integrated view of bacterial and archaeal diversity in saline soil habitats is essential for understanding the biological and ecological processes and exploiting potential of microbial resources from such environments. This study examined the collective bacterial and archaeal diversity in saline soils using a meta-analysis approach. All available 16S rDNA sequences recovered from saline soils were retrieved from publicly available databases and subjected to phylogenetic and statistical analyses. A total of 9,043 bacterial and 1,039 archaeal sequences, each longer than 250 bp, were examined. The bacterial sequences were assigned into 5,784 operational taxonomic units (OTUs, based on C97 % sequence identity), representing 24 known bacterial phyla, with Proteobacteria (44.9 %), Actinobacteria (12.3 %), Firmicutes (10.4 %), Acidobacteria (9.0 %), Bacteroidetes (6.8 %), and Chloroflexi (5.9 %) being predominant. Lysobacter (12.8 %) was the dominant bacterial genus in saline soils, followed by Sphingomonas (4.5 %), Halomonas (2.5 %), and Gemmatimonas (2.5 %). Archaeal sequences were assigned to 602 OTUs, primarily from the phyla Euryarchaeota (88.7 %) and Crenarchaeota (11.3 %).Halorubrum and Thermofilum were the dominant archaeal genera in saline soils. Rarefaction analysis indicated that less than 25 % of bacterial diversity, and approximately 50 % of archaeal diversity, in saline soil habitats has been sampled. This analysis of the global bacterial and archaeal diversity in saline soil habitats can guide future studies to further examine the microbial diversity of saline soils.

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“…The presence of the high frequency of genes associated with carbohydrate metabolism in this soil metagenome analysis is not surprising because these genes are commonly detected in abundance in most studies of soil metagenomes 8,21 . However, the presence of the high frequency of virulence factor genes in the soil metagenomes is unusual, because they are not commonly reported 8,22 . This leads to the speculation that mangrove soil is a potential reservoir of pathogenic bacteria, but further work is necessary to verify this finding.…”

Section: Discussionmentioning

confidence: 99%

Tropical Mangrove Swamp Metagenome Reveals Unusual Abundance of Ecologically Important Microbes

Ismail¹,

Sam²,

Yin³

et al. 2017

Current Science

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The tropical ecosystem is extremely rich in flora and fauna, but the tropical mangrove soil microbial diversity remains illusive. To address this knowledge gap, we characterized the metagenome of a Malaysian mangrove soil sample and its microbial ecological roles via next-generation sequencing (NGS). Shotgun NGS data analysis revealed high diversity of ecologically important microbes from bacteria and archaea domains. Also, an unusually high number of archaea was detected together with high abundance of Deltaproteobacteria. In a functional study by the SEED classification in MEGAN, virulence factor genes were abundantly present, implying that the mangrove soil is a potential reservoir of pathogens.

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Culture independent molecular analysis of bacterial communities in the mangrove sediment of Sundarban, India

Cited by 133 publications

References 48 publications

Bacterial Diversity in an Amazonian Mangrove Ecosystem

Bacterial Diversity in an Amazonian Mangrove Ecosystem

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

Tropical Mangrove Swamp Metagenome Reveals Unusual Abundance of Ecologically Important Microbes

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