electronic supplementary material

soils, sec 3 • remediation and management of contaminated or degraded lands • review article

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

Rongxiao Che1,2,3• Weijin Wang2,4• Jing Zhang1•Thi Thu Nhan Nguyen2,5 • Juan Tao1,6• Fang Wang1•Yanfen Wang1• Zhihong Xu2•Xiaoyong Cui1

Received: 1 June 2016 / Accepted: 12 September 2016

© Springer-Verlag Berlin Heidelberg 2016

Responsible editor: Hong Jie Di

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

2Environmental Futures Research Institute and School of Natural Sciences, Griffith University, Brisbane 4111, Australia

3Sino-Danish Centre for Education and Research/Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China

4Department of Science, Information Technology and Innovation, Brisbane 4068, Australia

5Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD 4558, Australia

6Australian Rivers Institute, Griffith University, Brisbane 4111, Australia

()Xiaoyong Cui

()Zhihong Xu

Table S1 The rDNA- or rRNA-based indices used in published studies

rDNA- or rRNA-based Indices / Targeting Microbes / Potential
Implications / Research Cases
16S rDNA copies / Bacteria / Abundance / (Kim et al. 2014)
16S rDNA copies / Archaea / Abundance / (Andert and Mumme 2015)
16S rDNA copies / Prokaryotes / Abundance / (Dlott et al. 2015)
18S rDNA copies / Fungi / Abundance / (Siles and Margesin 2016)
28S rDNA copies / Fungi / Abundance / (Barnard et al. 2015)
ITS copies / Bacteria / Abundance / Potential index
ITS copies / Fungi / Abundance / (Vogel et al. 2014)
SSU rDNA copies / All / Abundance / (Demeter et al. 2015)
16S rDNA-based CS / Bacteria / Total CS / (Flores-Renteria et al. 2016)
16S rDNA-based CS / Archaea / Total CS / (Kato et al. 2011)
16S rDNA-based CS / Prokaryotes / Total CS / (Couradeau et al. 2016)
18S rDNA-based CS / Fungi / Total CS / (Qin et al. 2014)
18S rDNA-based CS / Eukaryotes / Total CS / (Shen et al. 2014)
28S rDNA-based CS / Fungi / Total CS / (Barnard et al. 2015)
ITS-based CS / Bacteria / Total CS / (Waldrop and Firestone 2004)
ITS-based CS / Fungi / Total CS / (Zifcakova et al. 2016)
SSU rDNA-based CS / all / Total CS / (Liang et al. 2016)
16S rRNA copies / Bacteria / Potential activity / (Schindlbacher et al. 2011)
16S rRNA copies / Archaea / Potential activity / (Barnard et al. 2015)
16S rRNA copies / Prokaryotes / Potential activity / (Dlott et al. 2015)
18S rRNA copies / Fungi / Potential activity / (Becker et al. 2014)
28S rRNA copies / Fungi / Potential activity / (Barnard et al. 2015)
ITSRNA copies / Fungi / Potential activity / (Beaulieu et al. 2011)
ITS RNA copies / Bacteria / Potential activity / Potential index
SSU rRNA copies / All / Potential activity / Potential index
16S rRNA-based CS / Bacteria / Potentially active CS / (Che et al. 2015)
16S rRNA-based CS / Archaea / Potentially active CS / (Angel et al. 2013)
16S rRNA-based CS / Prokaryotes / Potentially active CS / (Dlott et al. 2015)
18S rRNA-based CS / Fungi / Potentially active CS / (Kuramae et al. 2013)
18S rRNA-based CS / Eukaryotes / Potentially active CS / (Lehembre et al. 2013)
28S rRNA-based CS / Fungi / Potentially active CS / (Barnard et al. 2015)
ITS RNA-based CS / Bacteria / Potentially active CS / Potential index
ITS RNA-based CS / Fungi / Potentially active CS / (Baldrian et al. 2012)
SSU rRNA-based CS / all / Potentially active CS / (Burow et al. 2014)

CS, community structure; the sub-domain level rDNA- or rRNA-related indices were not included in this table

Table S2 Correlations between bacterial 16S rDNA-based lineages and soil microbial respiration

Positive Correlation / Negative Correlation / Treatments / Sequencing Methods / References
Bac / Aci / Cross sites / Sanger / (Fierer et al. 2007)
β-Proteobacteria-Pro / Cross sites / Sanger / (Fierer et al. 2007)
Phycicoccus-Act / Kutzneria-Act / Moisture, Season / 454 / (Yuste et al. 2014)
Arthrobacter-Act / Actinomadura-Act / Moisture, Season / 454 / (Yuste et al. 2014)
Microbacterium-Act / Corallococcus-Pro / Moisture, Season / 454 / (Yuste et al. 2014)
Spirosoma-Bac / Roseateles-Pro / Moisture, Season / 454 / (Yuste et al. 2014)
Flavitalea-Bac / Bryobacter-Aci / Moisture, Season / 454 / (Yuste et al. 2014)
Phenylobacterium-Pro / Gp17-Aci / Moisture, Season / 454 / (Yuste et al. 2014)
Rhodanobacter-Pro / Gp11-Aci / Moisture, Season / 454 / (Yuste et al. 2014)
Dokdonella-Pro / Gp10 -Aci / Moisture, Season / 454 / (Yuste et al. 2014)
Lysobacter-Pro / Subdivision3_gis -Ver / Moisture, Season / 454 / (Yuste et al. 2014)
Act / Aci / Land management, Year / 454 / (Orr et al. 2015)
Fir / Land management, Year / 454 / (Orr et al. 2015)
WS3 / Land management, Year / 454 / (Orr et al. 2015)

Pro, Proteobacteria; Act, Actinobacteria;Bac, Bacteroidetes,Aci, Acidobacteria; Ver, Verrucomicrobia; Fir,Firmicutes

Fig.S1 The geographical distributions of the studies that simultaneously measured soil microbial respiration and rDNA- or rRNA-based indices

Fig.S2 Microbial domains targeted and techniques used in the studies that simultaneously measured soil microbial respiration and rDNA- or rRNA-based indices during the periods of 2003-2009 and 2010-2016

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