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First insights into the rhizospheric bacterial abundance data of Ceriops tagal (Perr.) C.B.Rob. from Indian Sundarbans.

ABSTRACT: This article reports the analyses of the rhizospheric microbiome of the terrestrial mangrove Ceriops tagal (Perr.) C.B.Rob. from the Indian Sundarbans. Samples were collected using standard protocols and 16S rRNA gene V3-V4 region amplicon sequencing was performed to identify the bacterial communities prevalent in the rhizosphere. A total of 1,74,324 quality checked reads were assembled into contigs and were analyzed using QIIME2 and MetaG server to reveal the abundance of Proteobacteria, Bacteroidetes and Actinobacteria. The data is available at the NCBI - Sequence Read Archive with accession number: SRR15652592. This is the first report of the rhizospheric microbiome belonging to this plant from the Indian Sundarbans.

SUBMITTER: Dhar GA

PROVIDER: S-EPMC9309684 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature

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First insights into the rhizospheric bacterial abundance data of Ceriops tagal (Perr.) C.B.Rob. from Indian Sundarbans.

Dhar Gaurab Aditya GA Ganguli Sayak S Mallick Bidisha B

Data in brief 20220714

This article reports the analyses of the rhizospheric microbiome of the terrestrial mangrove Ceriops tagal (Perr.) C.B.Rob. from the Indian Sundarbans. Samples were collected using standard protocols and 16S rRNA gene V3-V4 region amplicon sequencing was performed to identify the bacterial communities prevalent in the rhizosphere. A total of 1,74,324 quality checked reads were assembled into contigs and were analyzed using QIIME2 and MetaG server to reveal the abundance of Proteobacter ...[more]

PMID: 35898864

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Project description:Identification of genes involved in mangrove species' adaptation to salt stress can provide valuable information for developing salt-tolerant crops and understanding the molecular evolution of salt tolerance in halophiles. Ceriops tagal is a salt-tolerant mangrove tree growing in mudflats and marshes in tropical and subtropical areas, without any prior genome information. In this study, we assessed the biochemical and transcriptional responses of C. tagal to high salt treatment (500 mmol/L NaCl) by hydroponic experiments and RNA-seq. In C. tagal root tissues under salt stress, proline accumulated strongly from 3 to 12 h of treatment; meanwhile, malondialdehyde content progressively increased from 0 to 9 h, then dropped to lower than control levels by 24 h. These implied that C. tagal plants could survive salt stress through biochemical modification. Using the Illumina sequencing platform, approximately 27.39 million RNA-seq reads were obtained from three salt-treated and control (untreated) root samples. These reads were assembled into 47,111 transcripts with an average length of 514 bp and an N50 of 632 bp. Approximately 78% of the transcripts were annotated, and a total of 437 genes were putative transcription factors. Digital gene expression analysis was conducted by comparing transcripts from the untreated control to the three salt treated samples, and 7,330 differentially expressed transcripts were identified. Using k-means clustering, these transcripts were divided into six clusters that differed in their expression patterns across four treatment time points. The genes identified as being up- or downregulated are involved in salt stress responses, signal transduction, and DNA repair. Our study shows the main adaptive pathway of C. tagal in saline environments, under short-term and long-term treatments of salt stress. This provides vital clues as to which genes may be candidates for breeding salt-tolerant crops and clarifying molecular mechanisms of salt tolerance in C. tagal. The expression levels of 20 candidate genes measured by RNA-Seq were validated via qRT-PCR. Eighteen genes showed consistent expression patterns in RNA-Seq and qRT-PCR results, suggesting that the RNA-seq dataset was dependable for gene expression pattern analysis.

Project description:BackgroundAnthropogenic perturbations have strong impact on water quality and ecological health of mangrove areas of Indian Sundarbans. Diversity in microbial community composition is important causes for maintaining the health of the mangrove ecosystem. However, microbial communities of estuarine water in Indian Sundarbans mangrove areas and environmental determinants that contribute to those communities were seldom studied.MethodsNevertheless, this study attempted first to report bacterial and archaeal communities simultaneously in the water from Matla River and Thakuran River of Maipith coastal areas more accurately using 16S rRNA gene-based amplicon approaches. Attempt also been made to assess the capability of the environmental parameters for explaining the variation in microbial community composition.ResultsOur investigation indicates the dominancy of halophilic marine bacteria from families Flavobacteriaceae and OM1 clade in the water with lower nutrient load collected from costal regions of a small Island of Sundarban Mangroves (ISM). At higher eutrophic conditions, changes in bacterial communities in Open Marine Water (OMW) were detected, where some of the marine hydrocarbons degrading bacteria under families Oceanospirillaceae and Spongiibacteraceae were dominated. While most abundant bacterial family Rhodobacteracea almost equally (18% of the total community) dominated in both sites. Minor variation in the composition of archaeal community was also observed between OMW and ISM. Redundancy analysis indicates a combination of total nitrogen and dissolved inorganic nutrients for OMW and for ISM, salinity and total nitrogen was responsible for explaining the changes in their respective microbial community composition.ConclusionsOur study contributes the first conclusive overview on how do multiple environmental/anthropogenic stressors (salinity, pollution, eutrophication, land-use) affect the Sundarban estuary water and consequently the microbial communities in concert. However, systematic approaches with more samples for evaluating the effect of environmental pollutions on mangrove microbial communities are recommended.

Dataset Information

First insights into the rhizospheric bacterial abundance data of Ceriops tagal (Perr.) C.B.Rob. from Indian Sundarbans.

Publications

First insights into the rhizospheric bacterial abundance data of <i>Ceriops tagal</i> (Perr.) C.B.Rob. from Indian Sundarbans.

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