Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments

Liu, Qing; Yang, Jian; Wang, Beichen; Li, Wen; Hua, Zheng-Shuang; Jiang, Hongchen

doi:10.3389/fmicb.2022.1019010

Cited by 13 publications

(4 citation statements)

References 67 publications

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“…Sulfur cycle genes could be regulated by salinity. The abundances of some genes related to dissimilatory sulfur reduction and oxidation, the link between inorganic and organic sulfur transformation, and sulfur disproportionation and reduction decreased with increasing salinity, while genes involved in assimilatory sulfate reduction and sulfur oxidation tended to increase ( Liu, Q. et al, 2022 ). In the present study, some genes related to the sulfur cycle increased in 101-14 after treatment with NaCl.…”

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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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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Section: Resultsmentioning

confidence: 99%

“…The decomposition of the composite carbon source generated abundant accessible organic substrates, which furnished the growth of heterotrophic microbes and impacted the composition of microbial community [50]. Ultimately, the changes in the composition of microbial communities led to variations in the composition of functional genes closely related to taxonomic composition [51]. In terms of the denitrification functional genes, the prevailing functional genes of denitrification in C0 and C5 were napA and napB, which can encode nitrate reductase and promote the conversion of nitrate to nitrite.…”

Section: Changes In Nitrogen Cycling Processes and Involved Functiona...mentioning

confidence: 99%

The Microbiome and Antibiotic Resistome in Soil under Biodegradable Composite Carbon Source Amendment

Yang

Lou

Yan

et al. 2023

JoX

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The decomposition of biodegradable composite carbon sources generates a large amount of biodegradable microplastics, which may not only furnish microbial denitrification, but might also pose potential environmental risks. In the present study, the effects of different dosages of a biodegradable composite carbon source on the microbial communities, the nitrogen metabolic pathways and the antibiotic resistome were explored through Illumina MiSeq sequencing analysis and metagenomic analysis. The results of partial least-square discriminant analysis (PLS-DA) and analysis of similarity (ANOSIM) demonstrated that the response of the bacterial community to a biodegradable composite carbon source was more obvious than the fungal community. The application of biodegradable microplastics diminished the complexity of the microbial communities to some extent and obviously stimulated denitrification. Antibiotics resistance gene (ARG) dispersal was not evidently accelerated after the addition of biodegradable composite carbon source. Lysobacter, Methylobacillus, Phyllobacterium, Sinorhizobium, Sphingomonas from Proteobacteria and Actinomadura, Agromyces, Gaiella and Micromonospora from Actinobacteria were the major ARG hosts. Overall, the addition of a biodegradable composite carbon source shaped microbial communities and their antibiotic resistance profiles in this study.

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“…They found that S changes could reduce ammonium and nitrite oxidation potential to 42%, and other metabolic processes related to the nitrogen cycle were positively influenced. Liu et al (2022) showed that S changes in response to different nutrientcycling genes and found that decreasing S can modify nitrogen metabolic genes in aquatic environments.…”

Section: Prokaryotic Metabolic Potential In Response To the Differenc...mentioning

confidence: 99%

Water mass structure determine the prokaryotic community and metabolic pattern in the Korea Strait during fall 2018 and 2019

Thangaraj

Kim

et al. 2023

Front. Mar. Sci.

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The Korea Strait (KS) is a crucial marine passage for transporting heat, salt, and materials from the South Sea to the East Sea. The Tsushima Warm Water (TWW) and Korea Strait Bottom Cold Water (KSBCW) are major water masses that flow across the strait, but their effects on prokaryotic communities have been unclear. We used high-throughput sequencing to study the impact of TWW and KSBCW on prokaryotic composition and metabolic changes in the upper (0–50m; UL), middle (50–75m; ML), and bottom (75–150m; BL) layers during the fall of 2018 and 2019. The results showed that the UL had a freshwater influence from Changjiang Diluted Water in 2019, altering prokaryotic compositions and metabolic potentials. The KSBCW in the BL transported new bacterial communities with unique metabolic characteristics. Key genes involved in carbon metabolism had water mass impacts, preferring lower saline and temperature environments, and carbon fixation potential shifted from phototrophs in 2018 to chemotrophs in 2019. Temperature changes induced acclimation processes producing heat- and cold-shock genes/proteins. Our findings indicate that the freshwater influence and KSBCW modified the prokaryotic composition and metabolic function differentially. These results are important in understanding the relationship between water masses and ongoing environmental changes in this understudied region.

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Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments

Cited by 13 publications

References 67 publications

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

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

The Microbiome and Antibiotic Resistome in Soil under Biodegradable Composite Carbon Source Amendment

Water mass structure determine the prokaryotic community and metabolic pattern in the Korea Strait during fall 2018 and 2019

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