Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers
Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2...
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doaj-818f50b343bd4ca684f37c0275b9c8c42020-11-25T00:11:01ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2017-05-01810.3389/fmicb.2017.00945260931Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth LayersRen Bai0Jun-Tao Wang1Ye Deng2Ye Deng3Ji-Zheng He4Ji-Zheng He5Kai Feng6Kai Feng7Li-Mei Zhang8Li-Mei Zhang9State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, ChinaState Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, ChinaKey Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, ChinaCollege of Resources and Environment, University of Chinese Academy of SciencesBeijing, ChinaState Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, ChinaFaculty of Veterinary and Agricultural Sciences, The University of Melbourne, MelbourneVIC, AustraliaState Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, ChinaCollege of Resources and Environment, University of Chinese Academy of SciencesBeijing, ChinaState Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, ChinaCollege of Resources and Environment, University of Chinese Academy of SciencesBeijing, ChinaPaddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.http://journal.frontiersin.org/article/10.3389/fmicb.2017.00945/fullpaddy soilGeoChipMi-Seq sequencingmicrobial communitysoil profilesoil type |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ren Bai Jun-Tao Wang Ye Deng Ye Deng Ji-Zheng He Ji-Zheng He Kai Feng Kai Feng Li-Mei Zhang Li-Mei Zhang |
spellingShingle |
Ren Bai Jun-Tao Wang Ye Deng Ye Deng Ji-Zheng He Ji-Zheng He Kai Feng Kai Feng Li-Mei Zhang Li-Mei Zhang Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers Frontiers in Microbiology paddy soil GeoChip Mi-Seq sequencing microbial community soil profile soil type |
author_facet |
Ren Bai Jun-Tao Wang Ye Deng Ye Deng Ji-Zheng He Ji-Zheng He Kai Feng Kai Feng Li-Mei Zhang Li-Mei Zhang |
author_sort |
Ren Bai |
title |
Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers |
title_short |
Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers |
title_full |
Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers |
title_fullStr |
Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers |
title_full_unstemmed |
Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers |
title_sort |
microbial community and functional structure significantly varied among distinct types of paddy soils but responded differently along gradients of soil depth layers |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2017-05-01 |
description |
Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils. |
topic |
paddy soil GeoChip Mi-Seq sequencing microbial community soil profile soil type |
url |
http://journal.frontiersin.org/article/10.3389/fmicb.2017.00945/full |
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