Skip to main content
SpringerLink
Log in

16S rRNA-based bacterial community structure is a sensitive indicator of soil respiration activity

  • Soils, Sec 5 • Soil and Landscape Ecology • Short Original Communication
  • Published:
Journal of Soils and Sediments Aims and scope Submit manuscript

Abstract

Purpose

Understanding the relationships between soil respiration activity (SRA) and soil microbial community abundance and composition is pivotal for soil respiration prediction, modelling and management. This study aimed to assess value of the bacterial 16S ribosomal DNA (rDNA)- or ribosomal RNA (rRNA)-related indices (BRIs) in relation to SRA.

Materials and methods

Soil samples collected from a Tibetan alpine meadow were amended with different amounts of glutamate to establish a SRA gradient. Several BRIs including 16S rDNA copies, rRNA copies, the ratio of 16S rRNA copies to 16S rDNA copies and 16S rDNA- or rRNA-based community structure were analysed using real-time PCR or terminal-restriction fragment length polymorphism (T-RFLP).

Results and discussion

Except 16S rRNA copies and the ratio of 16S rRNA copies to 16S rDNA copies, all of the BRIs significantly correlated with the SRA. However, the 16S rRNA-based bacterial community structure explained 72.7 % of the SRA variations, which clearly outperformed all other BRIs.

Conclusions

The results imply that the 16S rRNA-based bacterial community structure provides a sensitive and robust BRI to support future studies on the relationships between SRA and microbial communities.

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

References

  • Barnard RL, Osborne CA, Firestone MK (2014) Changing precipitation pattern alters soil microbial community response to wet-up under a Mediterranean-type climate. ISME J

  • Blazewicz SJ, Barnard RL, Daly RA, Firestone MK (2013) Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses. ISME J 7:2061–2068

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • Campbell BJ, Kirchman DL (2013) Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient. ISME J 7:210–220

    Article  CAS  Google Scholar 

  • Chen H et al (2013) The impacts of climate change and human activities on biogeochemical cycles on the Qinghai-Tibetan Plateau. Glob Chang Biol 19:2940–2955

    Article  Google Scholar 

  • Devevre OC, Horwath WR (2000) Decomposition of rice straw and microbial carbon use efficiency under different soil temperatures and moistures. Soil Biol Biochem 32:1773–1785

    Article  CAS  Google Scholar 

  • Eilers KG, Lauber CL, Knight R, Fierer N (2010) Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil. Soil Biol Biochem 42:896–903

    Article  CAS  Google Scholar 

  • Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354–1364

    Article  Google Scholar 

  • Giovannoni SJ (1991) The polymerase chain reaction. In: Stackebrandt E, Goodfellow MD (eds) Nucleic acid techniques in bacterial systematics, 1st edn. Wiley, New York, pp 177–203

    Google Scholar 

  • Goberna M, Navarro-Cano JA, Valiente-Banuet A, Garcia C, Verdu M (2014) Abiotic stress tolerance and competition-related traits underlie phylogenetic clustering in soil bacterial communities. Ecol Lett 17:1191–1201

    Article  Google Scholar 

  • Goldfarb KC, Karaoz U, Hanson CA, Santee CA, Bradford MA, Treseder KK, Wallenstein MD, Brodie EL (2011) Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol 2:94

    Article  Google Scholar 

  • Hartmann A, Schmid M, van Tuinen D, Berg G (2009) Plant-driven selection of microbes. Plant Soil 321:235–257

    Article  CAS  Google Scholar 

  • Kerkhof L, Kemp P (1999) Small ribosomal RNA content in marine Proteobacteria during non-steady-state growth. FEMS Microbiol Ecol 30:253–260

    Article  CAS  Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow MD (eds) Nucleic acid techniques in bacterial systematics, 1st edn. Wiley, New York, pp 115–175

    Google Scholar 

  • Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci 82:6955–6959

    Article  CAS  Google Scholar 

  • Lipson DA, Schmidt SK, Monson RK (1999) Links between microbial population dynamics and nitrogen availability in an alpine ecosystem. Ecology 80:1623–1631

    Article  Google Scholar 

  • Liu HS, Li LH, Han XG, Huang JH, Sun JX, Wang HY (2006) Respiratory substrate availability plays a crucial role in the response of soil respiration to environmental factors. Appl Soil Ecol 32:284–292

    Article  Google Scholar 

  • Moriyama A, Yonemura S, Kawashima S, Du M, Tang Y (2013) Environmental indicators for estimating the potential soil respiration rate in alpine zone. Ecol Indic 32:245–252

    Article  CAS  Google Scholar 

  • Muyzer G, Dewaal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700

    CAS  Google Scholar 

  • Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H (2014) Vegan: community ecology package. http://CRAN.R-project.org/package=vegan

  • Placella SA, Brodie EL, Firestone MK (2012) Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups. Proc Natl Acad Sci U S A 109:10931–10936

    Article  CAS  Google Scholar 

  • R Core Team (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, http://www.R-project.org/

    Google Scholar 

  • van Hees PAW, Jones DL, Finlay R, Godbold DL, Lundstomd US (2005) The carbon we do not see—the impact of low molecular weight compounds on carbon dynamics and respiration in forest soils: a review. Soil Biol Biochem 37:1–13

    Article  Google Scholar 

  • Wang GX, Qian J, Cheng GD, Lai YM (2002) Soil organic carbon pool of grassland soils on the Qinghai-Tibetan Plateau and its global implication. Sci Total Environ 291:207–217

    Article  CAS  Google Scholar 

  • Wang WJ, Dalal RC, Moody PW, Smith CJ (2003) Relationships of soil respiration to microbial biomass, substrate availability and clay content. Soil Biol Biochem 35:273–284

    Article  CAS  Google Scholar 

  • WRB (1998) World reference base for soil resources. FAO/ISRIC/ISSS, Italy

    Google Scholar 

Download references

Acknowledgments

This work was supported by the Strategic Priority Research Program (B) of the Chinese Academy of Sciences (XDB15010201), the National Natural Science Foundation of China (grant No. 41230750) and the National Basic Research Program (2013CB956000). We sincerely thank Ruicheng Li and the Haibei research station staff for sampling assistance.

Author information

Authors and Affiliations

  1. College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China

    Rongxiao Che, Fang Wang, Yanfen Wang & Xiaoyong Cui

  2. Griffith University, Nathan, 4111, Queensland, Australia

    Rongxiao Che, Weijin Wang & Zhihong Xu

  3. Nanjing Normal University, Nanjing, 210097, China

    Yongcui Deng

  4. Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China

    Yongcui Deng

  5. Department of Science, Information Technology and Innovation (DSITI), Brisbane, 4068, Australia

    Weijin Wang

Authors
  1. Rongxiao Che
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yongcui Deng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Fang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Weijin Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zhihong Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yanfen Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Xiaoyong Cui
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xiaoyong Cui.

Additional information

Responsible editor: Jizheng He

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(DOCX 29 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Che, R., Deng, Y., Wang, F. et al. 16S rRNA-based bacterial community structure is a sensitive indicator of soil respiration activity. J Soils Sediments 15, 1987–1990 (2015). https://doi.org/10.1007/s11368-015-1152-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11368-015-1152-0

Keywords

Search

Navigation