Microbial Ecology

, Volume 72, Issue 1, pp 240–251 | Cite as

Assessment of Bacterial Communities and Predictive Functional Profiling in Soils Subjected to Short-Term Fumigation-Incubation

  • Lin Chen
  • Yu Luo
  • Jianming Xu
  • Zhuyun Yu
  • Kaile Zhang
  • Philip C. Brookes
Soil Microbiology


Previous investigations observed that when soil was fumigated with ethanol-free CHCl3 for 24 h and then incubated under appropriate conditions, after the initial flush of CO2 was over, soil organic carbon (SOC) mineralization continued at the same rate as in the non-fumigated soil. This indicates that, following fumigation, the much diminished microbial population still retained the same ability to mineralize SOC as the much larger non-fumigated population. We hypothesize that although fumigation drastically alters the soil bacterial community abundance, composition, and diversity, it has little influence on the bacterial C-metabolic functions. Here, we conducted a 30-day incubation experiment involving a grassland soil and an arable soil with and without CHCl3 fumigation. At days 0, 7, and 30 of the incubation, the bacterial abundances were determined by quantitative PCR, and the bacterial community composition and diversity were assessed via the 16S rRNA gene amplicon sequencing. PICRUSt was used to predict the metagenome functional content from the sequence data. Fumigation considerably changed the composition and decreased the abundance and diversity of bacterial community at the end of incubation. At day 30, Firmicutes (mainly Bacilli) accounted for 70.9 and 94.6 % of the total sequences in the fumigated grassland and arable soil communities, respectively. The two fumigated soil communities exhibited large compositional and structural differences during incubation. The families Paenibacillaceae, Bacillaceae, and Symbiobacteriaceae dominated the bacterial community in the grassland soil, and Alicyclobacillaceae in the arable soil. Fumigation had little influence on the predicted abundances of KEGG orthologs (KOs) assigned to the metabolism of the main acid esters, saccharides, amino acids, and lipids in the grassland soil community. The saccharide-metabolizing KO abundances were decreased, but the acid ester- and fatty acid-metabolizing KO abundances were elevated by fumigation in the arable soil community. Our study suggests functional redundancy regarding the bacterial genetic potential associated with SOC mineralization.


Fumigation qPCR MiSeq sequencing Bacterial community Metagenome functions 



All authors are very grateful to the two reviewers for their insightful comments that improved this manuscript greatly. We thank Dr. Youzhi Feng and Dr. Yongjie Yu for the help in MiSeq sequencing and data processing, and Jiangye Li for the grassland soil sampling and analysis. This work is jointly supported by the National Natural Science Foundation of China (41371246), the National Basic Research Program (973 Program) of China (2014CB441003), and China Postdoctoral Science Foundation (2015M581944).

Supplementary material

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Lin Chen
    • 1
    • 2
  • Yu Luo
    • 1
  • Jianming Xu
    • 1
  • Zhuyun Yu
    • 1
  • Kaile Zhang
    • 1
  • Philip C. Brookes
    • 1
  1. 1.Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentZhejiang UniversityHangzhouPeople’s Republic of China
  2. 2.State Key Laboratory of Soil and Sustainable AgricultureInstitute of Soil Science, Chinese Academy of SciencesNanjingPeople’s Republic of China

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