Comparison of microbial taxonomic and functional shift pattern along contamination gradient.
The interaction mechanism between microbial communities and environment is a key issue in microbial ecology. Microbial communities usually change significantly under environmental stress, which has been studied both phylogenetically and functionally, however which method is more effective in assessing the relationship between microbial communities shift and environmental changes still remains controversial.



By comparing the microbial taxonomic and functional shift pattern along heavy metal contamination gradient, we found that both sedimentary composition and function shifted significantly along contamination gradient. For example, the relative abundance of Geobacter and Fusibacter decreased along contamination gradient (from high to low), while Janthinobacterium and Arthrobacter increased their abundances. Most genes involved in heavy metal resistance (e.g., metc, aoxb and mer) showed higher intensity in sites with higher concentration of heavy metals. Comparing the two shift patterns, there were correlations between them, because functional and phylogenetic β-diversities were significantly correlated, and many heavy metal resistance genes were derived from Geobacter, explaining their high abundance in heavily contaminated sites. However, there was a stronger link between functional composition and environmental drivers, while stochasticity played an important role in formation and succession of phylogenetic composition demonstrated by null model test.



Overall our research suggested that the responses of functional traits depended more on environmental changes, while stochasticity played an important role in formation and succession of phylogenetic composition for microbial communities. So profiling microbial functional composition seems more appropriate to study the relationship between microbial communities and environment, as well as explore the adaptation and remediation mechanism of microbial communities to heavy metal contamination.
School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.|Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.|College of Food Science and Technology, Hunan Agricultural University, Changsha, 410083, China.
Youhua
Y
Ren
School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.|Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.
Jiaojiao
J
Niu
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
Wenkun
W
Huang
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
Deliang
D
Peng
School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.|Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.
Yunhua
Y
Xiao
School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.|Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.
Xian
X
Zhang
School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.|Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.
Yili
Y
Liang
School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.|Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.
Xueduan
X
Liu
School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China. yinhuaqun@gmail.com.|Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China. yinhuaqun@gmail.com.
Huaqun
H
Yin
D001419:Bacteria / Q000145:classification* / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification; D044822:Biodiversity; D002681:China; D002965:Classification / Q000379:methods*; D004269:DNA, Bacterial / Q000235:genetics; D004463:Ecology; D017753:Ecosystem; D004783:Environmental Microbiology; D004787:Environmental Pollution; D052918:Environmental Restoration and Remediation; D019015:Geologic Sediments / Q000737:chemistry / Q000382:microbiology; D019216:Metals, Heavy / Q000008:administration & dosage / Q000737:chemistry* / Q000633:toxicity; D056265:Microbial Interactions / Q000502:physiology*; D064307:Microbiota / Q000187:drug effects / Q000235:genetics / Q000502:physiology*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012988:Soil Microbiology; D012989:Soil Pollutants
D004269:DNA, Bacterial; D019216:Metals, Heavy; D012336:RNA, Ribosomal, 16S; D012989:Soil Pollutants
Heavy metal contamination; Microbial remediation; Null model test; Taxonomic and functional composition