Metagenomic insights into seasonal variations in the soil microbial community and function in a Larix gmelinii forest of Mohe, China

Bao, Tong; Deng, Shilin; Yu, Kaiyue; Li, Weiyi; Dong, Airong

doi:10.1007/s11676-019-01090-w

Cited by 11 publications

(6 citation statements)

References 46 publications

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“…Rich vegetation at IT sites can produce a large amount of litter, which promotes the abundance of CAZy genes and ultimately improves the nutrient status of the soil in the tiankeng. Soil temperature is also an important factor affecting enzyme activity, and the wet and cold environment inside the tiankeng may also affect the activity of carbohydrate-active enzymes [ 38 ]. Microbial community metabolic pathway analysis indicated that the availabilities of resources and microbial interactions are important factors in the response of microbial communities to environmental change [ 39 , 40 ].…”

Section: Discussionmentioning

confidence: 99%

Metagenomic analysis reveals the different characteristics of microbial communities inside and outside the karst tiankeng

et al. 2022

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Background Karst tiankengs serve as a reservoir of biodiversity in the degraded karst landscape areas. However, the microbial diversity of karst tiankengs is poorly understood. Here, we investigated the composition and function of the microbial community in a karst tiankeng. Results We found that habitat differences inside and outside the karst tiankeng changed the composition and structure of the soil microbial communities, and the dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria. The Shannon–Wiener diversity of microbial communities inside and outside the tiankeng was significantly different, and it was higher inside the tiankeng (IT). Venn and LEfSe analysis found that the soil microbial communities inside the tiankeng had 640 more endemic species and 39 more biomarker microbial clades than those identified outside of the tiankeng (OT)..Functional prediction indicated that soil microorganisms in outside the tiankeng had a high potential for carbohydrate metabolism, translation and amino acid metabolism. There were biomarker pathways associated with several of human diseases at both IT and OT sites. Except for auxiliary activities (AA), other CAZy classes had higher abundance at IT sites, which can readily convert litter and fix carbon and nitrogen, thereby supporting the development of underground forests. The differences in microbial communities were mainly related to the soil water content and soil total nitrogen. Conclusions Our results provide a metagenomic overview of the karst tiankeng system and provide new insights into habitat conservation and biodiversity restoration in the area.

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Section: Discussionmentioning

confidence: 99%

Metagenomic analysis reveals the different characteristics of microbial communities inside and outside the karst tiankeng

et al. 2022

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“…Also, functional screening can allow us to deduce the role of these microbial communities. Besides, it can unravel the novel genes that were not reported in previous sequencing analysis datasets (Abia et al, 2019;Al-Hebshi et al, 2018;Bao et al, 2020;Shobo et al, 2020). In the current study, functional databases of egg-NOG, CAZy, and KEGG were employed to analyze the metagenomic sequencing data, and it was found that the giant panda's vaginal microbiome was actively involved in metabolic functions.…”

Section: Discussionmentioning

confidence: 94%

Analysis of the vaginal microbiome of giant pandas using metagenomics sequencing

Zhang

Zhai

et al. 2020

MicrobiologyOpen

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“…Of functional gene modules related to the C cycle, the relative abundance of the ‘amino acid metabolism’ module increases in acidic soils, indicating a possibility of higher amino acid mineralization and CO 2 production (Vinolasa et al ., 2001). Amino acid metabolism is strongly linked to microbial growth and development (Feng et al ., 2018; Bao et al ., 2020), N cycling processes such as glutamate metabolism, and N availability for plants (Lea & Azevedo, 2007; Tan et al ., 2022). Apart from being used directly by both plants and microorganisms (Ikoyi et al ., 2018), amino acids (e.g.…”

Section: Discussionmentioning

confidence: 99%

“…Of functional gene modules related to the C cycle, the relative abundance of the 'amino acid metabolism' module increases in acidic soils, indicating a possibility of higher amino acid mineralization and CO 2 production (Vinolasa et al, 2001). Amino acid metabolism is strongly linked to microbial growth and development (Feng et al, 2018;Bao et al, 2020), N cycling processes…”

Section: Implications For Carbon and Nutrient Cyclingmentioning

confidence: 99%

Effects of nitrogen deposition on carbon and nutrient cycling along a natural soil acidity gradient as revealed by metagenomics

et al. 2023

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Nitrogen (N) deposition and soil acidification are environmental challenges affecting ecosystem functioning, health, and biodiversity, but their effects on functional genes are poorly understood.Here, we utilized metabarcoding and metagenomics to investigate the responses of soil functional genes to N deposition along a natural soil pH gradient. Soil N content was uncorrelated with pH, enabling us to investigate their effects separately.Soil acidity strongly and negatively affected the relative abundances of most cluster of orthologous gene categories of the metabolism supercategory. Similarly, soil acidity negatively affected the diversity of functional genes related to carbon and N but not phosphorus cycling. Multivariate analyses showed that soil pH was the most important factor affecting microbial and functional gene composition, while the effects of N deposition were less important. Relative abundance of KEGG functional modules related to different parts of the studied cycles showed variable responses to soil acidity and N deposition. Furthermore, our results suggested that the diversity-function relationship reported for other organisms also applies to soil microbiomes.Since N deposition and soil pH affected microbial taxonomic and functional composition to a different extent, we conclude that N deposition effects might be primarily mediated through soil acidification in forest ecosystems.

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Metagenomic insights into seasonal variations in the soil microbial community and function in a Larix gmelinii forest of Mohe, China

Cited by 11 publications

References 46 publications

Metagenomic analysis reveals the different characteristics of microbial communities inside and outside the karst tiankeng

Metagenomic analysis reveals the different characteristics of microbial communities inside and outside the karst tiankeng

Analysis of the vaginal microbiome of giant pandas using metagenomics sequencing

Effects of nitrogen deposition on carbon and nutrient cycling along a natural soil acidity gradient as revealed by metagenomics

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