title: The shifts of sediment microbial community phylogenetic and functional structures during chromium (VI) reduction.
abstract: The Lanzhou reach of the Yellow River, located at the upstream of Lanzhou, has been contaminated by heavy metals and polycyclic aromatic hydrocarbons over a long-time. We hypothesized that indigenous microbial communities would remediate those contaminants and some unique populations could play an important role in this process. In this study, we investigated the sediment microbial community structure and function from the Lanzhou reach. Sediment samples were collected from two nearby sites (site A and site B) in the Lanzhou reach along the Yellow River. Sediment geochemical property data showed that site A sediment samples contained significantly (p < 0.05) higher heavy metals than site B, such as chromium (Cr), manganese (Mn), and copper (Cu). Both site A and B samples were incubated with or without hexavalent chromium (Cr (VI)) for 30 days in the laboratory, and Cr (VI) reduction was only observed in site A sediment samples. After incubation, MiSeq sequencing of 16S rRNA gene amplicons revealed that the phylogenetic composition and structure of microbial communities changed in both samples, and especially Proteobacteria, as the most abundant phylum increased from 45.1 % to 68.2 % in site A, and 50.1 % to 71.3 % in site B, respectively. Some unique OTUs and populations affiliated with Geobacter, Clostridium, Desulfosporosinus and Desulfosporosinus might be involved in Cr (VI) reduction in site A. Furthermore, GeoChip 4.0 (a comprehensive functional gene array) data showed that genes involved in carbon and nitrogen cycling and metal resistance significantly (p < 0.05) increased in site A sediment samples. All the results indicated that indigenous sediment microbial communities might be able to remediate contaminants like Cr (VI), and this information provides possible strategies for future bioremediation of the Lanzhou reach.
authors.affiliation: Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China.
authors.forename: Zhengsheng
authors.initials: Z
authors.lastname: Yu
authors.affiliation: Department of Microbiology and Plant Biology and Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA.
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.affiliation: Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China.
authors.forename: Xuanyu
authors.initials: X
authors.lastname: Tao
authors.affiliation: Department of Microbiology and Plant Biology and Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA.
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
authors.affiliation: State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
authors.forename: Yunfeng
authors.initials: Y
authors.lastname: Yang
authors.affiliation: State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
authors.forename: Mengxin
authors.initials: M
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Zheng
authors.affiliation: Department of Microbiology and Plant Biology and Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA.
authors.forename: Tong
authors.initials: T
authors.lastname: Yuan
authors.affiliation: Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China.
authors.forename: Pu
authors.initials: P
authors.lastname: Liu
authors.affiliation: Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China.
authors.forename: Virgo
authors.initials: V
authors.lastname: Nolan
authors.affiliation: Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China. xkli@lzu.edu.cn.
authors.forename: Xiangkai
authors.initials: X
authors.lastname: Li
mesh_terms: D001419:Bacteria / Q000145:classification / Q000187:drug effects*; D001673:Biodegradation, Environmental; D002857:Chromium / Q000633:toxicity*; D004784:Environmental Monitoring; D019015:Geologic Sediments / Q000382:microbiology*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S; D045483:Rivers; D014871:Water Microbiology; D014874:Water Pollutants, Chemical / Q000633:toxicity*
chemical_list: D012336:RNA, Ribosomal, 16S; D014874:Water Pollutants, Chemical; D002857:Chromium; C074702:chromium hexavalent ion
keywords: Cr (VI) reduction; GeoChip; MiSeq sequencing; Microbial community diversity; Yellow River