PMID- 29576979
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20201001
IS  - 2167-8359 (Print)
IS  - 2167-8359 (Electronic)
IS  - 2167-8359 (Linking)
VI  - 6
DP  - 2018
TI  - Assessing soil bacterial community and dynamics by integrated high-throughput 
      absolute abundance quantification.
PG  - e4514
LID - 10.7717/peerj.4514 [doi]
LID - e4514
AB  - Microbial ecological studies have been remarkably promoted by the high-throughput 
      sequencing approach with explosive information of taxonomy and relative 
      abundance. However, relative abundance does not reflect the quantity of the 
      microbial community and the inter-sample differences among taxa. In this study, 
      we refined and applied an integrated high-throughput absolute abundance 
      quantification (iHAAQ) method to better characterize soil quantitative bacterial 
      community through combining the relative abundance (by high-throughput 
      sequencing) and total bacterial quantities (by quantitative PCR). The proposed 
      iHAAQ method was validated by an internal reference strain EDL933 and a 
      laboratory strain WG5. Application of the iHAAQ method to a soil phenanthrene 
      biodegradation study showed that for some bacterial taxa, the changes of relative 
      and absolute abundances were coincident, while for others the changes were 
      opposite. With the addition of a microbial activity inhibitor (NaN(3)), the 
      absolute abundances of soil bacterial taxa, including several dominant genera of 
      Bacillus, Flavobacterium, and Paenibacillus, decreased significantly, but their 
      relative abundances increased after 28 days of incubation. We conclude that the 
      iHAAQ method can offer more comprehensive information to reflect the dynamics of 
      soil bacterial community with both relative and absolute abundances than the 
      relative abundance from high-throughput sequencing alone.
FAU - Lou, Jun
AU  - Lou J
AD  - Institute of Soil and Water Resources and Environmental Science, College of 
      Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of 
      Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.
FAU - Yang, Li
AU  - Yang L
AD  - Institute of Soil and Water Resources and Environmental Science, College of 
      Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of 
      Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.
FAU - Wang, Haizhen
AU  - Wang H
AD  - Institute of Soil and Water Resources and Environmental Science, College of 
      Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of 
      Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.
FAU - Wu, Laosheng
AU  - Wu L
AD  - Institute of Soil and Water Resources and Environmental Science, College of 
      Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of 
      Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.
AD  - Department of Environmental Sciences, University of California, Riverside, United 
      States of America.
FAU - Xu, Jianming
AU  - Xu J
AD  - Institute of Soil and Water Resources and Environmental Science, College of 
      Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of 
      Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.
LA  - eng
PT  - Journal Article
DEP - 20180314
PL  - United States
TA  - PeerJ
JT  - PeerJ
JID - 101603425
PMC - PMC5857175
OTO - NOTNLM
OT  - Absolute abundance
OT  - High-throughput sequencing
OT  - Quantitative bacterial ecology
OT  - Soil
OT  - iHAAQ
OT  - qPCR
COIS- The authors declare there are no competing interests.
EDAT- 2018/03/27 06:00
MHDA- 2018/03/27 06:01
CRDT- 2018/03/27 06:00
PHST- 2017/12/14 00:00 [received]
PHST- 2018/02/26 00:00 [accepted]
PHST- 2018/03/27 06:00 [entrez]
PHST- 2018/03/27 06:00 [pubmed]
PHST- 2018/03/27 06:01 [medline]
AID - 4514 [pii]
AID - 10.7717/peerj.4514 [doi]
PST - epublish
SO  - PeerJ. 2018 Mar 14;6:e4514. doi: 10.7717/peerj.4514. eCollection 2018.