Skip to main content
SpringerLink
Log in

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

  • Soil Microbiology
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Fierer N, Strickland MS, Liptzin D, Bradford MA, Cleveland CC (2009) Global patterns in belowground communities. Ecol Lett 12:1238–1249. doi:10.1111/j.1461-0248.2009.01360.x

    Article  PubMed  Google Scholar 

  2. Jenkinson DS, Powlson DS (1976) Effects of biocidal treatments on metabolism in soil. I. Fumigation with chloroform. Soil Biol Biochem 8:167–177

    Article  CAS  Google Scholar 

  3. Wu J, Brookes PC, Jenkinson DS (1996) Evidence for the use of a control in the fumigation-incubation method for measuring microbial biomass carbon in soil. Soil Biol Biochem 28:511–518. doi:10.1016/0038-0717(95)00193-x

    Article  CAS  Google Scholar 

  4. Kemmitt SJ, Lanyon CV, Waite IS, Wen Q, Addiscott TM, Bird NRA, O'Donnell AG, Brookes PC (2008) Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass—a new perspective. Soil Biol Biochem 40:61–73. doi:10.1016/j.soilbio.2007.06.021

    Article  CAS  Google Scholar 

  5. Zelles L, Palojarvi A, Kandeler E, VonLutzow M, Winter K, Bai QY (1997) Changes in soil microbial properties and phospholipid fatty acid fractions after chloroform fumigation. Soil Biol Biochem 29:1325–1336. doi:10.1016/s0038-0717(97)00062-x

    Article  CAS  Google Scholar 

  6. Dickens HE, Anderson JM (1999) Manipulation of soil microbial community structure in bog and forest soils using chloroform fumigation. Soil Biol Biochem 31:2049–2058. doi:10.1016/s0038-0717(99)00128-5

    Article  CAS  Google Scholar 

  7. Chen L, Xu J, Feng Y, Wang J, Yu Y, Brookes PC (2015) Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing. Front Microbiol 6:1149. doi:10.3389/fmicb.2015.01149

    PubMed  PubMed Central  Google Scholar 

  8. Swift MJ, Heal OW, Anderson JM (1979) Decomposition in terrestrial ecosystems. Blackwell, Oxford

    Google Scholar 

  9. Poll C, Marhan S, Ingwersen J, Kandeler E (2008) Dynamics of litter carbon turnover and microbial abundance in a rye detritusphere. Soil Biol Biochem 40:1306–1321. doi:10.1016/j.soilbio.2007.04.002

    Article  CAS  Google Scholar 

  10. Dominguez-Mendoza CA, Bello-Lopez JM, Navarro-Noya YE, de Leon-Lorenzana AS, Delgado-Balbuena L, Gomez-Acata S, Ruiz-Valdiviezo VM, Ramirez-Villanueva DA, Luna-Guido M, Dendooven L (2014) Bacterial community structure in fumigated soil. Soil Biol Biochem 73:122–129. doi:10.1016/j.soilbio.2014.02.012

    Article  CAS  Google Scholar 

  11. Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RLV, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814–821. doi:10.1038/nbt.2676

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Vance E, Brookes P, Jenkinson D (1987) An extraction method for measuring soil microbial biomass C. Soil Biol Biochem 19:703–707

    Article  CAS  Google Scholar 

  13. Wu J, Joergensen RG, Pommerening B, Chaussod R, Brookes PC (1990) Measurement of soil microbial biomass C by fumigation extraction—an automated procedure. Soil Biol Biochem 22:1167–1169. doi:10.1016/0038-0717(90)90046-3

    Article  CAS  Google Scholar 

  14. Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH (2008) Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci U S A 105:10583–10588. doi:10.1073/pnas.0709942105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Tumbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. doi:10.1038/nmeth.f.303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200. doi:10.1093/bioinformatics/btr381

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461. doi:10.1093/bioinformatics/btq461

    Article  CAS  PubMed  Google Scholar 

  18. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R (2010) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266–267. doi:10.1093/bioinformatics/btp636

    Article  CAS  PubMed  Google Scholar 

  19. Ganesh S, Parris DJ, De Long EF, Stewart FJ (2014) Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. ISME J 8:187–211. doi:10.1038/ismej.2013.144

    Article  CAS  PubMed  Google Scholar 

  20. Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650. doi:10.1093/molbev/msp077

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61:1–10. doi:10.1016/0006-3207(92)91201-3

    Article  Google Scholar 

  22. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235. doi:10.1128/AEM.71.12.8228-8235.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Bray JR, Curtis JT (1957) An ordination of the upland forest communities of southern Wisconsin. Ecol Monogr 27:326–349

    Article  Google Scholar 

  24. Development Core Team R (2010) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna

    Google Scholar 

  25. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–94. doi:10.1038/nature11237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Luo YQ, Hui DF, Zhang DQ (2006) Elevated CO2 stimulates net accumulations of carbon and nitrogen in land ecosystems: a meta-analysis. Ecology 87:53–63. doi:10.1890/04-1724

    Article  PubMed  Google Scholar 

  27. Blagodatskaya E, Kuzyakov Y (2013) Active microorganisms in soil: critical review of estimation criteria and approaches. Soil Biol Biochem 67:192–211. doi:10.1016/j.soilbio.2013.08.024

    Article  CAS  Google Scholar 

  28. Brookes PC, Powlson DS, Jenkinson DS (1982) Measurement of microbial biomass phosphorus in soil. Soil Biol Biochem 14:319–329. doi:10.1016/0038-0717(82)90001-3

    Article  CAS  Google Scholar 

  29. Morrissey EM, McHugh TA, Preteska L, Hayer M, Dijkstra P, Hungate BA, Schwartz E (2015) Dynamics of extracellular DNA decomposition and bacterial community composition in soil. Soil Biol Biochem 86:42–49. doi:10.1016/j.soilbio.2015.03.020

    Article  CAS  Google Scholar 

  30. Brookes PC, Kemmitt SJ, Addiscott TM, Bird N (2009) Reply to Kuzyakov et al’.s comments on our paper:‘Kemmitt, S.J., Lanyon, C.V., Waite, I.S., Wen, Q., O’Donnell, A.G., Brookes, P.C., 2008. Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass—a new perspective. Soil Biol Biochem 40, 61–73’. Soil Biol Biochem 41:440–443. doi:10.1016/j.soilbio.2008.09.002

    Article  CAS  Google Scholar 

  31. Paredes-Sabja D, Setlow P, Sarker MR (2011) Germination of spores of Bacillales and Clostridiales species: mechanisms and proteins involved. Trends Microbiol 19:85–94. doi:10.1016/j.tim.2010.10.004

    Article  CAS  PubMed  Google Scholar 

  32. Setlow P (2003) Spore germination. Curr Opin Microbiol 6:550–556. doi:10.1016/j.mib.2003.10.001

    Article  CAS  PubMed  Google Scholar 

  33. Paredes-Sabja D, Torres JA, Setlow P, Sarker MR (2008) Clostridium perfringens spore germination: characterization of germinants and their receptors. J Bacteriol 190:1190–1201. doi:10.1128/jb.01748-07

    Article  CAS  PubMed  Google Scholar 

  34. Carr KA, Janes BK, Hanna PC (2010) Role of the gerP operon in germination and outgrowth of Bacillus anthracis spores. Plos One 5:e9128. doi:10.1371/journal.pone.0009128

    Article  PubMed  PubMed Central  Google Scholar 

  35. Xiao Y, Francke C, Abee T, Wells-Bennik MHJ (2011) Clostridial spore germination versus bacilli: genome mining and current insights. Food Microbiol 28:266–274. doi:10.1016/j.fm.2010.03.016

    Article  PubMed  Google Scholar 

  36. Spinelli ACNF, Sant'Ana AS, Pacheco-Sanchez CP, Massaguer PR (2010) Influence of the hot-fill water-spray-cooling process after continuous pasteurization on the number of decimal reductions and on Alicyclobacillus addoterrestris CRA 7152 growth in orange juice stored at 35 °C. Int J Food Microbiol 137:295–298. doi:10.1016/j.ijfoodmicro.2009.11.003

    Article  CAS  PubMed  Google Scholar 

  37. Silva LP, Gonzales-Barron U, Cadavez V, Sant'Ana AS (2015) Modeling the effects of temperature and pH on the resistance of Alicyclobacillus acidoterrestris in conventional heat-treated fruit beverages through a meta-analysis approach. Food Microbiol 46:541–552. doi:10.1016/j.fm.2014.09.019

    Article  CAS  PubMed  Google Scholar 

  38. Pathma J, Sakthivel N (2013) Molecular and functional characterization of bacteria isolated from straw and goat manure based vermicompost. Appl Soil Ecol 70:33–47. doi:10.1016/j.apsoil.2013.03.011

    Article  Google Scholar 

  39. Wang Y, Liu Q, Yan L, Gao Y, Wang Y, Wang W (2013) A novel lignin degradation bacterial consortium for efficient pulping. Bioresour Technol 139:113–119. doi:10.1016/j.biortech.2013.04.033

    Article  CAS  PubMed  Google Scholar 

  40. Bandounas L, Wierckx NJP, de Winde JH, Ruijssenaars HJ (2011) Isolation and characterization of novel bacterial strains exhibiting ligninolytic potential. BMC Biotechnol 11:94. doi:10.1186/1472-6750-11-94

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Feng Y, Chen R, Hu J, Zhao F, Wang J, Chu H, Zhang J, Dolfing J, Lin X (2015) Bacillus asahii comes to the fore in organic manure fertilized alkaline soils. Soil Biol Biochem 81:186–194. doi:10.1016/j.soilbio.2014.11.021

    Article  CAS  Google Scholar 

  42. Garrity GM (2005) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York

    Google Scholar 

  43. Rocca JD, Hall EK, Lennon JT, Evans SE, Waldrop MP, Cotner JB, Nemergut DR, Graham EB, Wallenstein MD (2015) Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed. ISME J 9:1693–1699. doi:10.1038/ismej.2014.252

    Article  PubMed  Google Scholar 

  44. Schimel JP, Schaeffer SM (2012) Microbial control over carbon cycling in soil. Front Microbiol 3:348. doi:10.3389/fmicb.2012.00348

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Dungait JAJ, Hopkins DW, Gregory AS, Whitmore AP (2012) Soil organic matter turnover is governed by accessibility not recalcitrance. Glob Chang Biol 18:1781–1796. doi:10.1111/j.1365-2486.2012.02665.x

    Article  Google Scholar 

  46. Kuzyakov Y, Blagodatskaya E, Blagodatsky S (2009) Comments on the paper by Kemmitt et al. (2008) ‘Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass—a new perspective’ [Soil Biol Biochem 40, 61–73]: the biology of the regulatory gate. Soil Biol Biochem 41:435–439. doi:10.1016/j.soilbio.2008.07.023

    Article  CAS  Google Scholar 

  47. Nannipieri P (2006) Role of stabilized enzymes in microbial ecology and enzyme extraction from soil with potential applications in soil proteomics. In: Nannipieri P, Smalla K (eds) Nucleic acids and proteins in soil. Springer, Berlin, pp 75–94

    Chapter  Google Scholar 

  48. Burns RG, DeForest JL, Marxsen J, Sinsabaugh RL, Stromberger ME, Wallenstein MD, Weintraub MN, Zoppini A (2013) Soil enzymes in a changing environment: current knowledge and future directions. Soil Biol Biochem 58:216–234. doi:10.1016/j.soilbio.2012.11.009

    Article  CAS  Google Scholar 

Download references

Acknowledgments

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).

Author information

Authors and Affiliations

  1. Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, People’s Republic of China

    Lin Chen, Yu Luo, Jianming Xu, Zhuyun Yu, Kaile Zhang & Philip C. Brookes

  2. State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, People’s Republic of China

    Lin Chen

Authors
  1. Lin Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yu Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jianming Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zhuyun Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kaile Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Philip C. Brookes
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Philip C. Brookes.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Fig S1

(DOCX 261 kb)

Fig S2

(DOCX 426 kb)

Fig S3

(DOCX 236 kb)

Fig S4

(DOCX 483 kb)

Fig S5

(DOCX 177 kb)

Table S1

(DOCX 15 kb)

Table S2

(DOCX 16 kb)

Table S3

(DOCX 23 kb)

Table S4

(DOCX 15 kb)

Table S5

(DOCX 21 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chen, L., Luo, Y., Xu, J. et al. Assessment of Bacterial Communities and Predictive Functional Profiling in Soils Subjected to Short-Term Fumigation-Incubation. Microb Ecol 72, 240–251 (2016). https://doi.org/10.1007/s00248-016-0766-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-016-0766-0

Keywords

Search

Navigation