Assessing soil microbial respiration capacity using rDNA- or rRNA-based indices: a review

Abstract

Purpose

Understanding soil heterotrophic respiration in relation to microbial properties is not only fundamental to soil respiration modelling, prediction, and regulation through management, but also essential to interpreting microbial community dynamics from an ecologically meaningful perspective. This paper reviewed the recent advances in knowledge and proposed future directions for exploring the respiration-microbe relationships by means of rDNA- or rRNA-based indices (i.e. rDNA copies, rRNA copies, and rDNA- or rRNA-based community structures).

Materials and methods

We first elucidated the theoretical basis for using rDNA- or rRNA-based indices to probe into soil microbial respiration. Then, the published studies that simultaneously measured soil microbial respiration and the rDNA- or rRNA-based indices were synthesized, extracted, and analysed to further explore the respiration-microbe relationships. At last, the uncertainties and perspectives for establishing the respiration-microbe links were proposed and discussed.

Results and discussion

The rDNA- or rRNA-based indices are theoretically promising for pinpointing the relationships between soil heterotrophic respiration and microbial properties. Our systematic review suggested that the correlations between bacterial rDNA copies and microbial respiration are inconsistent across studies, while the fungal and archaeal rDNA (or ITS) copies showed moderately positive and negative correlations with soil microbial respiration, respectively. Bacterial 16S rDNA-based community structures were significantly correlated with soil microbial respiration in some studies, but not in some short-term situations. Although rRNA copies are widely used as the proxies of microbial activity, no significant correlations between rRNA copies and soil microbial respiration have been found in previous studies. Bacterial 16S rRNA-based community structures were correlated well with the short-term responses of soil microbial respiration to rewetting or labile carbon amendments and clearly outperformed other rDNA- or rRNA-based indices. As respiration-microbe relationships can be affected by many factors, such as soil physicochemical properties and even the analysis methods of microbial indices, the 69 previous studies included in this review actually provided limited information on them, and the aforementioned results still need to be further confirmed in future studies.

Conclusions and perspectives

Overall, the relationships between soil microbial respiration and rDNA- or rRNA-based indices are still far from being well established. Future research should be directed to systematically understanding the respiration-microbe links, with more attention to the fungus-, archaea- and RNA-related molecular indices. The relationships between microbial specific lineages and total respiration rates should be explored in future studies, and the effects of edaphic properties on the respiration-microbe relationships should also be evaluated.

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Acknowledgments

This work was supported by the Strategic Priority Research Program (B) of the Chinese Academy of Sciences (XDB15010201), National Natural Science Foundations of China (41230750 and 31570518), and National Basic Research Program (2013CB956000). Rongxiao Che also received the Joint PhD Scholarship under the agreement between Griffith University and University of Chinese Academy of Sciences. We would like to express our sincere thanks to Damien Finn, Yongcui Deng, Li Tang, Qiushi Ning, and Linfeng Li for their insightful and constructive comments on improving the manuscript.

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Che, R., Wang, W., Zhang, J. et al. Assessing soil microbial respiration capacity using rDNA- or rRNA-based indices: a review. J Soils Sediments 16, 2698–2708 (2016). https://doi.org/10.1007/s11368-016-1563-6

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Keywords

  • Soil microorganism
  • Carbon cycle
  • Microbial respiration
  • rRNA
  • Microbial activity