Geochemical-compositional-functional changes in arctic soil microbiomes post land submergence revealed by metagenomics

Nengfei Wang, Yudong Guo, Gaoyang Li, Yan Xia, Mingyang Ma, Jiaye Zang, Yue Ma, Xiaofei Yin, Wenbing Han, Jinjiang Lv, Huansheng Cao

Research output: Contribution to journalArticle

Abstract

Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3–V4 region. Dominant phyla in sediments and soils included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae; sediments contained a unique phylum, Euryarchaeota, with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.

Original languageEnglish (US)
Pages (from-to)180-190
Number of pages11
JournalMicrobes and Environments
Volume34
Issue number2
DOIs
StatePublished - Jan 1 2019

Fingerprint

functional change
submergence
Arctic region
sediments
Otus
sediment
soil
gene
nitrites
nitrite
geochemistry
genes
ribosomal RNA
Euryarchaeota
Acidobacteria
lakes
Actinobacteria
Proteobacteria
snowmelt
landscape change

Keywords

  • 16S rRNA gene
  • Meltwater
  • Metagenome
  • Soil microbiomes
  • The Arctic

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Soil Science
  • Plant Science

Cite this

Geochemical-compositional-functional changes in arctic soil microbiomes post land submergence revealed by metagenomics. / Wang, Nengfei; Guo, Yudong; Li, Gaoyang; Xia, Yan; Ma, Mingyang; Zang, Jiaye; Ma, Yue; Yin, Xiaofei; Han, Wenbing; Lv, Jinjiang; Cao, Huansheng.

In: Microbes and Environments, Vol. 34, No. 2, 01.01.2019, p. 180-190.

Research output: Contribution to journalArticle

Wang, Nengfei ; Guo, Yudong ; Li, Gaoyang ; Xia, Yan ; Ma, Mingyang ; Zang, Jiaye ; Ma, Yue ; Yin, Xiaofei ; Han, Wenbing ; Lv, Jinjiang ; Cao, Huansheng. / Geochemical-compositional-functional changes in arctic soil microbiomes post land submergence revealed by metagenomics. In: Microbes and Environments. 2019 ; Vol. 34, No. 2. pp. 180-190.
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AU - Wang, Nengfei

AU - Guo, Yudong

AU - Li, Gaoyang

AU - Xia, Yan

AU - Ma, Mingyang

AU - Zang, Jiaye

AU - Ma, Yue

AU - Yin, Xiaofei

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AU - Lv, Jinjiang

AU - Cao, Huansheng

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N2 - Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3–V4 region. Dominant phyla in sediments and soils included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae; sediments contained a unique phylum, Euryarchaeota, with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.

AB - Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3–V4 region. Dominant phyla in sediments and soils included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae; sediments contained a unique phylum, Euryarchaeota, with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.

KW - 16S rRNA gene

KW - Meltwater

KW - Metagenome

KW - Soil microbiomes

KW - The Arctic

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