Microbial community structure of surface sediments from a tropical estuarine environment using next generation sequencing

Khandeparker, Lidita; Kuchi, Nishanth; Kale, Dipesh; Anil, Arga Chandrashekar

doi:10.1016/j.ecolind.2016.11.023

Cited by 39 publications

(18 citation statements)

References 75 publications

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“…The coupling of FISH and FCM techniques can detect specific pathogens in the environmental samples and have been used recently for detecting and quantifying Vibrio cholerae populations from different geographic regions (Khandeparker et al 2018). The genetics of uncultured microorganisms, metagenomics, is also emerging as a powerful tool (Khandeparker et al 2017b). Therefore, future studies should integrate both molecular and automated analytical methods allowing quick and specific identification of target microorganisms.…”

Section: Resultsmentioning

confidence: 99%

“…Thus, microbial communities in port environments are influenced by both anthropogenic and shipping activities, and the associated risk to aquatic ecosystems and human health can be effectively determined by quantifying the pathogen pool. Natural phenomena, such as tidal influence and riverine discharge (Khandeparker et al 2017b), also exert pressure on microorganisms and can alter their community structure.…”

Section: Introductionmentioning

confidence: 99%

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Spatio-temporal Variations in Bacterial Abundance with an Emphasis on Fecal Indicator Bacteria and Vibrio spp. in and around Visakhapatnam Port, East Coast of India

Khandeparker

Desai

Sawant

et al. 2020

AJSTD

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The ecological health of port environments, which are dynamic and hotspots of anthropogenic activities, can be analyzed using specific pathogenic bacteria as they provide definite evidence and source of pollution. The influence of seasons and environmental settings on total bacterial count (TBC), distribution of fecal indicators, and Vibrio spp. was explored in Visakhapatnam port, located along the east coast of India. South-west monsoon had a significant influence on TBC, fecal indicators, and Vibrio spp., and the abundance was influenced by the eutrophic environment in the inner harbour. Fecal indicators were one order higher in sub-surface water when compared with sediment, indicating their inoculation due to turbulent conditions in south-west monsoon. The abundance of V. cholerae was influenced by salinity, temperature, and SPM, and was positively correlated to plankton; relating their distribution with disease dynamics and ecosystem functioning is a step ahead. Such an assessment is important from the perspective of human health and marine bioinvasion.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Spatio-temporal Variations in Bacterial Abundance with an Emphasis on Fecal Indicator Bacteria and Vibrio spp. in and around Visakhapatnam Port, East Coast of India

Khandeparker

Desai

Sawant

et al. 2020

AJSTD

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“…This may be responsible for the variations in archaeal community at different latitudes. Intriguingly, although closely located along the west coastline of India, the archaeal communities in the Mandovi Estuary and Zuari Estuary are quite different ( Singh et al, 2010 ; Khandeparker et al, 2017 ). The authors pointed out that the distinct microbial communities in these two estuaries might be affected by different localized interactions, however, more thorough investigations are needed to explain such differences.…”

Section: Community Structure Of Estuarine Archaeamentioning

confidence: 99%

Community, Distribution, and Ecological Roles of Estuarine Archaea

Zou

Liu

2020

Front. Microbiol.

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Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota , and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota , leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota . We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.

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“…Chicalim is an anthropogenically influenced area in the Zuari estuary. Recently, Khandeparker et al (2017b) used Next-Generation Sequencing (NGS) approach using Ion Torrent PGM TM to elucidate the microbial community structure of Mandovi-Zuari estuarine sediment. The results indicated that Chicalim in Zuari estuary was dominated by Proteobacteria, mainly Gammaproteobacteria, which comprises of most of the pathogenic groups such as Enterobacteriaceae, Pseudomonadaceae, and Vibrionaceae, which are euryhaline and mostly introduced anthropogenically.…”

Section: Resultsmentioning

confidence: 99%

Application of Fluorescence in situ hybridization-Flow cytometry (FISH-FCM) technique to detect and quantify Vibrio cholerae population from different geographic regions

Khandeparker

Desai

Anil

et al. 2018

AJSTD

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Rapid and species-specific detection, and quantification of pathogenic bacteria are fundamental for monitoring and assessment of the risk they pose to any ecosystem. The study employed Vibrio cholerae, a human pathogen responsible for the life-threatening diarrhoeal disease, cholera and one among the most unwanted from marine bioinvasion point of view. The present study coupled fluorescence in situ hybridization (FISH) technique, a powerful tool in molecular phylogenetic discrimination, with flow cytometry (FCM), a technique used for rapid and accurate quantification of both viable but non-cultivable and non-viable microorganisms. The FISH-FCM technique was used for the first time to quantify V. cholerae (includes cultivable and non-cultivable) from different geographic regions of Southeast Asia (Brunei, Indonesia, Lao PDR, Myanmar, Philippines, Singapore, Thailand, Vietnam) and India (Goa, west coast of India). The data acquired from the analyses provides a snap shot view of the total bacterial abundance with special reference to V. cholerae. As the method developed, it was evaluated with bacterial samples collected from different sites in Southeast Asia and India, and the application of this technique to different geographical regions appears feasible. Considering that the continuous growth of the shipping industry and ballast water as one of the primary vectors responsible for the global transport of pathogenic microorganisms, the risk they present needs immediate attention. This technique will be useful in the quick and accurate detection of specific pathogens. It may also provide significant insights to quarantine measures for Ballast Water Management.

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Microbial community structure of surface sediments from a tropical estuarine environment using next generation sequencing

Cited by 39 publications

References 75 publications

Spatio-temporal Variations in Bacterial Abundance with an Emphasis on Fecal Indicator Bacteria and Vibrio spp. in and around Visakhapatnam Port, East Coast of India

Spatio-temporal Variations in Bacterial Abundance with an Emphasis on Fecal Indicator Bacteria and Vibrio spp. in and around Visakhapatnam Port, East Coast of India

Community, Distribution, and Ecological Roles of Estuarine Archaea

Application of Fluorescence in situ hybridization-Flow cytometry (FISH-FCM) technique to detect and quantify Vibrio cholerae population from different geographic regions

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