Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing
In soil microbiology, there is a ‘paradox’ of soil organic carbon (SOC) mineralization, which is that even though chloroform fumigation destroys majority of the soil microbial biomass, SOC mineralization continues at the same rate as in the non-fumigated soil during the incubation period. Soil micro...
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doaj-3c9364e839a74176899b14babe357ac62020-11-24T22:51:08ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2015-10-01610.3389/fmicb.2015.01149156512Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencingLin eChen0Jianming eXu1Youzhi eFeng2Juntao eWang3Yongjie eYu4Philip C. Brookes5Institute of Soil and Water Resources and Environmental Science, College of Environmental & Resource Sciences, Zhejiang UniversityInstitute of Soil and Water Resources and Environmental Science, College of Environmental & Resource Sciences, Zhejiang UniversityState Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesState Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesNanjing University of Information Science & TechnologyInstitute of Soil and Water Resources and Environmental Science, College of Environmental & Resource Sciences, Zhejiang UniversityIn soil microbiology, there is a ‘paradox’ of soil organic carbon (SOC) mineralization, which is that even though chloroform fumigation destroys majority of the soil microbial biomass, SOC mineralization continues at the same rate as in the non-fumigated soil during the incubation period. Soil microeukaryotes as important SOC decomposers, however, their community-level responses to chloroform fumigation are not well understood. Using the 18S rRNA gene amplicon sequencing, we analyzed the composition, diversity and C-metabolic functions of a grassland soil and an arable soil microeukaryotic community in response to fumigation followed by a 30-day incubation. The grassland and arable soil microeukaryotic communities were dominated by the fungal Ascomycota (80.5–93.1% of the fungal sequences), followed by the protistan Cercozoa and Apicomplexa. In the arable soil fungal community, the predominance of the class Sordariomycetes was replaced by the class Eurotiomycetes after fumigation at days 7 and 30 of the incubation. Fumigation changed the microeukaryotic α-diversity in the grassland soil at days 0 and 7, and β-diversity in the arable soil at days 7 and 30. Network analysis indicated that after fumigation fungi were important groups closely related to other taxa. Most phylotypes (especially Sordariomycetes, Dothideomycetes, Coccidia and uncultured Chytridiomycota) were inhibited, and only a few were positively stimulated by fumigation. Despite the inhibited Sordariomycetes, the fumigated communities mainly consisted of Eurotiomycetes and Sordariomycetes (21.9% and 36.5% relative frequency, respectively), which are able to produce hydrolytic enzymes associated with SOC mineralization. Our study suggests that fumigation not only decreases biomass size, but modulates the composition and diversity of the soil microeukaryotic communities, which are capable of driving SOC mineralization by release of hydrolytic enzymes during short-term fumigation-incubation.http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.01149/fullEnzymesFumigationFungiNetwork analysisprotist |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Lin eChen Jianming eXu Youzhi eFeng Juntao eWang Yongjie eYu Philip C. Brookes |
spellingShingle |
Lin eChen Jianming eXu Youzhi eFeng Juntao eWang Yongjie eYu Philip C. Brookes Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing Frontiers in Microbiology Enzymes Fumigation Fungi Network analysis protist |
author_facet |
Lin eChen Jianming eXu Youzhi eFeng Juntao eWang Yongjie eYu Philip C. Brookes |
author_sort |
Lin eChen |
title |
Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing |
title_short |
Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing |
title_full |
Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing |
title_fullStr |
Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing |
title_full_unstemmed |
Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing |
title_sort |
responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by miseq amplicon sequencing |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2015-10-01 |
description |
In soil microbiology, there is a ‘paradox’ of soil organic carbon (SOC) mineralization, which is that even though chloroform fumigation destroys majority of the soil microbial biomass, SOC mineralization continues at the same rate as in the non-fumigated soil during the incubation period. Soil microeukaryotes as important SOC decomposers, however, their community-level responses to chloroform fumigation are not well understood. Using the 18S rRNA gene amplicon sequencing, we analyzed the composition, diversity and C-metabolic functions of a grassland soil and an arable soil microeukaryotic community in response to fumigation followed by a 30-day incubation. The grassland and arable soil microeukaryotic communities were dominated by the fungal Ascomycota (80.5–93.1% of the fungal sequences), followed by the protistan Cercozoa and Apicomplexa. In the arable soil fungal community, the predominance of the class Sordariomycetes was replaced by the class Eurotiomycetes after fumigation at days 7 and 30 of the incubation. Fumigation changed the microeukaryotic α-diversity in the grassland soil at days 0 and 7, and β-diversity in the arable soil at days 7 and 30. Network analysis indicated that after fumigation fungi were important groups closely related to other taxa. Most phylotypes (especially Sordariomycetes, Dothideomycetes, Coccidia and uncultured Chytridiomycota) were inhibited, and only a few were positively stimulated by fumigation. Despite the inhibited Sordariomycetes, the fumigated communities mainly consisted of Eurotiomycetes and Sordariomycetes (21.9% and 36.5% relative frequency, respectively), which are able to produce hydrolytic enzymes associated with SOC mineralization. Our study suggests that fumigation not only decreases biomass size, but modulates the composition and diversity of the soil microeukaryotic communities, which are capable of driving SOC mineralization by release of hydrolytic enzymes during short-term fumigation-incubation. |
topic |
Enzymes Fumigation Fungi Network analysis protist |
url |
http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.01149/full |
work_keys_str_mv |
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