Diverse key nitrogen cycling genes nifH, nirS and nosZ associated with Pichavaram mangrove rhizospheres as revealed by culture-dependent and culture-independent analyses

Baskaran, Viswanathan; Prabavathy, V. R.

doi:10.1007/s00203-021-02661-4

Cited by 10 publications

(4 citation statements)

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“…Since the reduction of N 2 O to N 2 via the nos Z gene encoding the N 2 O reductase is the only known microbial process that can consume N 2 O, , the increased Chl-a concentration (i.e., algal biomass accumulation) likely inhibited both the denitrifying and N 2 O-reducing bacteria. Gammaproteobacteria as the predominant representing denitrifiers harboring both nir S and nos Z genes were found to be the most abundant denitrifying population in lakes, mangroves, estuaries, and marine sediments. , Thus, the dominant presence of Gammaproteobacteria in Lake Taihu indicated that denitrifiers indeed played key roles during the N 2 O production and consumption in the lake. A combination of isotopic and microbial analysis has been used to determine the denitrification and N 2 O reduction activities in water and sediments .…”

Section: Discussionmentioning

confidence: 94%

“…Gammaproteobacteria as the predominant representing denitrifiers harboring both nirS and nosZ genes were found to be the most abundant denitrifying population in lakes, mangroves, estuaries, and marine sediments. 55,56 Thus, the dominant presence of Gammaproteobacteria in Lake Taihu indicated that denitrifiers indeed played key roles during the N 2 O production and consumption in the lake. A combination of isotopic and microbial analysis has been used to determine the denitrification and N 2 O reduction activities in water and sediments.…”

Section: Microbial-driven N 2 O Production and Consumption Mechanismsmentioning

confidence: 99%

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Nitrification Regulates the Spatiotemporal Variability of N₂O Emissions in a Eutrophic Lake

Liang

Wang

Gao

et al. 2022

Environ. Sci. Technol.

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Nitrous oxide (N 2 O) emissions from lakes exhibit significant spatiotemporal heterogeneity, and quantitative identification of the different N 2 O production processes is greatly limited, causing the role of nitrification to be undervalued or ignored in models of a lake's N 2 O emissions. Here, the contributions of nitrification and denitrification to N 2 O production were quantitatively assessed in the eutrophic Lake Taihu using molecular biology and isotope mapping techniques. The N 2 O fluxes ranged from −41.48 to 28.84 μmol m −2 d −1 in the lake, with lower N 2 O concentrations being observed in spring and summer and significantly higher N 2 O emissions being observed in autumn and winter. The 15 N site preference and relevant isotopic evidence demonstrated that denitrification contributed approximately 90% of the lake's gross N 2 O production during summer and autumn, 27−83% of which was simultaneously eliminated via N 2 O reduction. Surprisingly, nitrification seemed to act as a key process promoting N 2 O production and contributing to the lake as a source of N 2 O emissions. A combination of N 2 O isotopocule-based approaches and molecular techniques can be used to determine the precise characteristics of microbial N 2 O production and consumption in eutrophic lakes. The results of this study provide a basis for accurately assessing N 2 O emissions from lakes at the regional and global scales.

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Section: Discussionmentioning

confidence: 94%

Section: Microbial-driven N 2 O Production and Consumption Mechanismsmentioning

confidence: 99%

Nitrification Regulates the Spatiotemporal Variability of N₂O Emissions in a Eutrophic Lake

Liang

Wang

Gao

et al. 2022

Environ. Sci. Technol.

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“…Previous studies reported that Pseudolabrys has the ability to use nitrogen by converting NH4 + -N fixation to microbial nitrogen, thus reducing nitrification and denitrification processes in soil ( Li et al, 2022 ; Yu et al, 2022 ) Alphaproteobacteria is a dominant player in root-associated soil ( Wu et al, 2009 ) and acts as a nitrogen fixer in coastal–saline soil ecosystems ( Yousuf et al, 2014a ). Gammaproteobacteria represent both nitrogen fixers and denitrifiers ( Baskaran and Prabavathy, 2022 ). The presence of these core species suggested a significant contribution to the nitrogen cycle.…”

Section: Discussionmentioning

confidence: 99%

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress

Wang

et al. 2023

Front. Microbiol.

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IntroductionSoil salinization is a serious abiotic stress for grapevines. The rhizosphere microbiota of plants can help counter the negative effects caused by salt stress, but the distinction between rhizosphere microbes of salt-tolerant and salt-sensitive varieties remains unclear.MethodsThis study employed metagenomic sequencing to explore the rhizosphere microbial community of grapevine rootstocks 101-14 (salt tolerant) and 5BB (salt sensitive) with or without salt stress.Results and DiscussionCompared to the control (treated with ddH2O), salt stress induced greater changes in the rhizosphere microbiota of 101-14 than in that of 5BB. The relative abundances of more plant growth-promoting bacteria, including Planctomycetes, Bacteroidetes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes, Chloroflexi, and Firmicutes, were increased in 101-14 under salt stress, whereas only the relative abundances of four phyla (Actinobacteria, Gemmatimonadetes, Chloroflexi, and Cyanobacteria) were increased in 5BB under salt stress while those of three phyla (Acidobacteria, Verrucomicrobia, and Firmicutes) were depleted. The differentially enriched functions (KEGG level 2) in 101-14 were mainly associated with pathways related to cell motility; folding, sorting, and degradation functions; glycan biosynthesis and metabolism; xenobiotics biodegradation and metabolism; and metabolism of cofactors and vitamins, whereas only the translation function was differentially enriched in 5BB. Under salt stress, the rhizosphere microbiota functions of 101-14 and 5BB differed greatly, especially pathways related to metabolism. Further analysis revealed that pathways associated with sulfur and glutathione metabolism as well as bacterial chemotaxis were uniquely enriched in 101-14 under salt stress and therefore might play vital roles in the mitigation of salt stress on grapevines. In addition, the abundance of various sulfur cycle-related genes, including genes involved in assimilatory sulfate reduction (cysNC, cysQ, sat, and sir), sulfur reduction (fsr), SOX systems (soxB), sulfur oxidation (sqr), organic sulfur transformation (tpa, mdh, gdh, and betC), increased significantly in 101-14 after treatment with NaCl; these genes might mitigate the harmful effects of salt on grapevine. In short, the study findings indicate that both the composition and functions of the rhizosphere microbial community contribute to the enhanced tolerance of some grapevines to salt stress.

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“…In our work, within a collection of a few hundred isolates, we mainly identified strains closely related to previously described species (>97% 16S rRNA gene sequence identity) and one new species, Nit1536 T strain, affiliated to the genus Nitratireductor . The isolation and description of a novel strain belonging to a bacterial group poorly characterized but consistently detected in the environment, such as Nitratireductor in mangroves ( Booth et al, 2019b ; Li et al, 2020 ; Baskaran and Prabavathy, 2022 ; Fusi et al, 2022 ), represent an opportunity to better understand (i) the microbial adaptation strategies adopted to survive in the extreme and stressful conditions of such environment and (ii) their ecological/functional role in the sediment microbial community and mangrove ecosystem. According to LPSN (see text footnote 4), at the time of writing, only one Nitratireductor species was obtained from a mangrove, i.e., N. mangrovi ( Ye et al, 2020 ), even if its nomenclature status is not yet validly published.…”

Section: Discussionmentioning

confidence: 99%

The identification of the new species Nitratireductor thuwali sp. nov. reveals the untapped diversity of hydrocarbon-degrading culturable bacteria from the arid mangrove sediments of the Red Sea

et al. 2023

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IntroductionThe geological isolation, lack of freshwater inputs and specific internal water circulations make the Red Sea one of the most extreme—and unique—oceans on the planet. Its high temperature, salinity and oligotrophy, along with the consistent input of hydrocarbons due to its geology (e.g., deep-sea vents) and high oil tankers traffic, create the conditions that can drive and influence the assembly of unique marine (micro)biomes that evolved to cope with these multiple stressors. We hypothesize that mangrove sediments, as a model-specific marine environment of the Red Sea, act as microbial hotspots/reservoirs of such diversity not yet explored and described.MethodsTo test our hypothesis, we combined oligotrophic media to mimic the Red Sea conditions and hydrocarbons as C-source (i.e., crude oil) with long incubation time to allow the cultivation of slow-growing environmentally (rare or uncommon) relevant bacteria.Results and discussionThis approach reveals the vast diversity of taxonomically novel microbial hydrocarbon degraders within a collection of a few hundred isolates. Among these isolates, we characterized a novel species, Nitratireductor thuwali sp. nov., namely, Nit1536T. It is an aerobic, heterotrophic, Gram-stain-negative bacterium with optimum growth at 37°C, 8 pH and 4% NaCl, whose genome and physiological analysis confirmed the adaptation to extreme and oligotrophic conditions of the Red Sea mangrove sediments. For instance, Nit1536T metabolizes different carbon substrates, including straight-chain alkanes and organic acids, and synthesizes compatible solutes to survive in salty mangrove sediments. Our results showed that the Red Sea represent a source of yet unknown novel hydrocarbon degraders adapted to extreme marine conditions, and their discovery and characterization deserve further effort to unlock their biotechnological potential.

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Diverse key nitrogen cycling genes nifH, nirS and nosZ associated with Pichavaram mangrove rhizospheres as revealed by culture-dependent and culture-independent analyses

Cited by 10 publications

References 59 publications

Nitrification Regulates the Spatiotemporal Variability of N₂O Emissions in a Eutrophic Lake

Nitrification Regulates the Spatiotemporal Variability of N₂O Emissions in a Eutrophic Lake

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress

The identification of the new species Nitratireductor thuwali sp. nov. reveals the untapped diversity of hydrocarbon-degrading culturable bacteria from the arid mangrove sediments of the Red Sea

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Diverse key nitrogen cycling genes nifH, nirS and nosZ associated with Pichavaram mangrove rhizospheres as revealed by culture-dependent and culture-independent analyses

Cited by 10 publications

References 59 publications

Nitrification Regulates the Spatiotemporal Variability of N2O Emissions in a Eutrophic Lake

Nitrification Regulates the Spatiotemporal Variability of N2O Emissions in a Eutrophic Lake

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress

The identification of the new species Nitratireductor thuwali sp. nov. reveals the untapped diversity of hydrocarbon-degrading culturable bacteria from the arid mangrove sediments of the Red Sea

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Nitrification Regulates the Spatiotemporal Variability of N₂O Emissions in a Eutrophic Lake

Nitrification Regulates the Spatiotemporal Variability of N₂O Emissions in a Eutrophic Lake