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

• Published in: Journal of soils and sediments Vol. 16; no. 12; pp. 2698 - 2708
• Main Authors: Che, Rongxiao, Wang, Weijin, Zhang, Jing, Nguyen, Thi Thu Nhan, Tao, Juan, Wang, Fang, Wang, Yanfen, Xu, Zhihong, Cui, Xiaoyong
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.12.2016; Springer Nature B.V
• Subjects: Biogeochemistry; carbon; Carbon cycle; community structure; Earth and Environmental Science; Environment; Environmental Physics; fungi; internal transcribed spacers; Microbial activity; microbial communities; Physicochemical properties; prediction; Respiration; respiratory rate; ribosomal DNA; ribosomal RNA; Sec 3 • Remediation and Management of Contaminated or Degraded Lands • Review Article; soil chemical properties; Soil microorganisms; soil physical properties; Soil properties; soil respiration; Soil Science & Conservation; Soils; systematic review; uncertainty; Carbon cycle; Microbial activity; Soil microorganism; rRNA; Microbial respiration
• ISSN: 1439-0108; 1614-7480
• DOI: 10.1007/s11368-016-1563-6

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.