Quantitative analyses of denitrifying bacterial diversity from a seasonally hypoxic monsoon governed tropical coastal region

Gomes, Jasmine; Khandeparker, Rakhee; Bandekar, Mandar; Meena, Ramavatar; Ramaiah, N.

doi:10.1016/j.dsr2.2017.12.012

Cited by 14 publications

(12 citation statements)

References 42 publications

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“…When the oxygen concentrations are low, many facultative aerobic, heterotrophic bacterial genera begin resorting to nitrate (NO 3 -) and sulphate (SO 4 2-) as electron acceptors for organic matter oxidation) [3,9]. This process seems to be strongly influenced by reduced oxygen in particular during SuM and FIM in the study area [6,12,13]. Post-upwelling, adequate availability of nitrate and organic carbon under reduced DO concentrations lead to denitrification [3,4].…”

Section: Discussionmentioning

confidence: 98%

“…The up-welled water is nitrate rich and oxygen poor and these nutrient-rich waters support very high primary production. Consequently, leading to higher consumption of oxygen during organic matter decomposition [4], which leads to subsequent intensification of denitrification [12,13] as well as sulfate reduction.…”

Section: Discussionmentioning

confidence: 99%

“…The DO was depleted owing to degradation of organic matter that follows strong primary/ biological productivity. Many authors [4,5,12] have reported that along India's west coast, upwelling during the SWM (June to October) nitrate rich waters are entrained into photic layers ultimately leading to denitrification. Observations since 1997 [4] have also shown that high concentrations ([ 1 lM) of nitrite invariably persist when denitrification is at its peak and, later on ammonia builds up in the water column turning near/totally anoxic.…”

Section: Discussionmentioning

confidence: 99%

“…All these steps are described in our previous publication [12]. Canonical Correspondence analysis to analyze the effect of environmental parameters on the bacterial community composition and Hierarchical Cluster Analysis (HCA) to identify the similarities in the selected stations was perfomed using PAST-3 software (https://folk.uio.no/ ohammer/past/).…”

Section: Construction Of Clone Libraries Sequencing and Statistical mentioning

confidence: 99%

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Bacterial Community Composition Markedly Altered by Coastal Hypoxia

et al. 2019

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Monsoonal upwelling along south and central west coast of India leads to intense biological productivity. As a consequence of excess organic matter production following upwelling during June-October and low dissolved oxygen in the upwelled waters, denitrification occurs in the near shore waters. Implicitly, these processes ought to bring alterations in microbial communities. Therefore, diversity and community structure of bacteria from subsurface layers of a tropical region experiencing intense seasonal lows of oxygen were analyzed through sequencing of 16S rRNA gene clones. The overall diversity was more during hypoxic period of Fall intermonsoon (FIM, October) compared either to Spring intermonsoon (SIM, March) or summer monsoon (SuM, June) months. As many as 14 lineages of bacterial domains: Gammaproteobacteria (37%), Alphaproteobacteria (21%), Cyanobacteria (20%), Deltaproteobacteria (3%), Firmicutes (3%), Betaproteobacteria (2%), Acidobacteria (2%), Actinobacteria (7%), Marinimicrobia (2%), Bacteroidetes (1%), Verrucomicrobia (1%), Planctomycetes (0.4%), Chloroflexi (0.2%) and Omnitrophica bacterium (0.2%), were recognized from our coastal location. Notably, sequences of Planctomycetes, Chloroflexi and Omnitrophica bacterium were found exclusively during FIM. A generally higher representation of sequences of Betaproteobacteria during SuM and of Actinobacteria and Firmicutes during SIM was discernible. This study is thus useful to recognize that microbial community might undergo strong temporal shifts in the monsoon affected tropical coastal ecosystems. Keywords Tropical coastal ecosystem Á Goa Á Upwelling Á Hypoxia Á Bacterial community Á 16S rDNA clones Á Phylogenetic composition Electronic supplementary material The online version of this article (

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Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Construction Of Clone Libraries Sequencing and Statistical mentioning

confidence: 99%

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Bacterial Community Composition Markedly Altered by Coastal Hypoxia

et al. 2019

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“…Denitrification and denitrifying microbial communities have recently received widespread research attention due to their important contributions to the global nitrogen cycle 1,8,43 . Functional genes involved in nitrite reduction, especially the cytochrome cd1-containing nitrite reductase encoding gene, nirS, are commonly used as molecular markers to detect denitrifying populations and potential activities 8,[43][44][45][46] . Concomitantly, the recent development of a novel gene amplification procedure, LAMP, has shown great promise in overcoming the numerous drawbacks of conventional PCR gene amplification methods.…”

Section: Discussionmentioning

confidence: 99%

Rapid detection of cytochrome cd1-containing nitrite reductase encoding gene nirS of denitrifying bacteria with loop-mediated isothermal amplification assay

Zhang

Yang

Zhang

et al. 2020

Sci Rep

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The cytochrome cd1-containing nitrite reductase, nirS, plays an important role in biological denitrification. Consequently, investigating the presence and abundance of nirS is a commonly used approach to understand the distribution and potential activity of denitrifying bacteria, in addition to denitrifier communities. Herein, a rapid method for detecting nirS gene with loop-mediated isothermal amplification (LAMP) was developed, using Pseudomonas aeruginosa PAO1 (P. aeruginosa PAO1) as model microorganism to optimize the assay. The LAMP assay relied on a set of four primers that were designed to recognize six target sequence sites, resulting in high target specificity. The limit of detection for the LAMP assay under optimized conditions was 1.87 pg/reaction of genomic DNA, which was an order of magnitude lower than that required by conventional PCR assays. Moreover, it was validated that P. aeruginosa PAO1 cells as well as genomic DNA could be directly used as template. Only 1 h was needed from the addition of bacterial cells to the reaction to the verification of amplification success. The nirS gene of P. aeruginosa PAO1 in spiked seawater samples could be detected with both DNA-template based LAMP assay and cell-template based LAMP assay, demonstrating the practicality of in-field use.

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Nitrous oxide emission and denitrifier bacteria communities in calcareous soil as affected by drip irrigation with saline water

Guo

Wei

2019

Applied Soil Ecology

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Quantitative analyses of denitrifying bacterial diversity from a seasonally hypoxic monsoon governed tropical coastal region

Cited by 14 publications

References 42 publications

Bacterial Community Composition Markedly Altered by Coastal Hypoxia

Bacterial Community Composition Markedly Altered by Coastal Hypoxia

Rapid detection of cytochrome cd1-containing nitrite reductase encoding gene nirS of denitrifying bacteria with loop-mediated isothermal amplification assay

Nitrous oxide emission and denitrifier bacteria communities in calcareous soil as affected by drip irrigation with saline water

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