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Yuan Z, Yi H, Wang T, Zhang Y, Zhu X, Yao J. Application of phosphate solubilizing bacteria in immobilization of Pb and Cd in soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:21877-21884. [PMID: 28779341 DOI: 10.1007/s11356-017-9832-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
In the present study, heavy metal (HM)-tolerant phosphate solubilizing bacteria (PSB) were isolated and their performance during the remediation of Pb and Cd in contaminated soil was studied. A total of 16 bacterial strains and one consortium were isolated, and the consortium had the highest phosphate solubilizing ability and HM tolerance. Great variations between the Fourier transform infrared (FTIR) spectra of consortium cells before and after adsorption of Pb2+ and Cd2+ revealed that amide I/amide II bonds and carboxyl on the cell surface were involved in binding of metal ions. High-throughput sequencing technique revealed that the consortium was composed of Enterobacter spp., Bacillus spp., and Lactococcus spp. The consortium was added into contaminated soil, and its potential ability in dissolution of phosphate from Ca3(PO4)2 and subsequent immobilization of HMs was tested. Results showed that when Ca3(PO4)2 was applied at 10.60 mg/g soil, PSB addition significantly increased soil available phosphate content from 12.28 to 17.30 mg/kg, thereby enhancing the immobilization rate of Pb and Cd from 69.95 to 80.76% and from 28.38 to 30.81%, respectively. Microcalorimetric analysis revealed that PSB addition significantly improved soil microbial activity, which was possibly related with the decreased HMs availability and the nutrient effect of the solubilized phosphate. The present study can provide a cost-effective and environmental-friendly strategy to remediate multiple HM-contaminated soils.
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Affiliation(s)
- Zhimin Yuan
- School of Energy & Environmental Engineering, and National International Cooperation Base on Environment and Energy, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Honghong Yi
- School of Energy & Environmental Engineering, and National International Cooperation Base on Environment and Energy, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China.
| | - Tianqi Wang
- School of Energy & Environmental Engineering, and National International Cooperation Base on Environment and Energy, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Yiyue Zhang
- School of Energy & Environmental Engineering, and National International Cooperation Base on Environment and Energy, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Xiaozhe Zhu
- School of Energy & Environmental Engineering, and National International Cooperation Base on Environment and Energy, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Jun Yao
- School of Energy & Environmental Engineering, and National International Cooperation Base on Environment and Energy, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China.
- School of Water Resource and Environmental Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China.
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102
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Jiang J, Song Z, Yang X, Mao Z, Nie X, Guo H, Peng X. Microbial community analysis of apple rhizosphere around Bohai Gulf. Sci Rep 2017; 7:8918. [PMID: 28827532 PMCID: PMC5566992 DOI: 10.1038/s41598-017-08398-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/12/2017] [Indexed: 11/21/2022] Open
Abstract
Bohai Gulf is the main area for apple tree cultivation in China. Consecutive replanting significantly affects the yield and quality of apple trees in this area. Microecological imbalance in apple trees' rhizospheres caused by variation in the soil microbial community is considered the primary cause of apple replant disease (ARD). This study analysed the microbial communities of the rhizospheres of perennial apple trees (PAT) and apple tree saplings under replanting (ATS) around Bohai Gulf using high-throughput sequencing. The results revealed increased populations of typical pathogenic fungi Verticillium and bacteria Xanthomonadaceae, and decreased populations of beneficial bacterial populations Pseudomonas and Bacillus with replanting, suggesting that competition between pathogens and beneficial microbes varies according to the ratio of pathogens to beneficial microbes in rhizosphere soil under the replanting system. Meanwhile, replanting was accompanied by an increase in the antagonistic bacteria Arthrobacter and fungus Chaetomium, suggesting that increased numbers of pathogens can lead to more instances of antagonism. Redundancy analysis (RDA) revealed site position and the main soil properties (pH, organic matter, available N, available K, available P, and moisture) affected the microbial community composition. It found clear differences in soil microbial communities and demonstrated a better understanding of the causes for ARD.
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Affiliation(s)
- Jihang Jiang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Zhen Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaotong Yang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Zhiquan Mao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271000, China
| | - Xiaohong Nie
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Hui Guo
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Xiawei Peng
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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103
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Yu B, Tian J, Feng L. Remediation of PAH polluted soils using a soil microbial fuel cell: Influence of electrode interval and role of microbial community. JOURNAL OF HAZARDOUS MATERIALS 2017; 336:110-118. [PMID: 28494298 DOI: 10.1016/j.jhazmat.2017.04.066] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/25/2017] [Accepted: 04/27/2017] [Indexed: 05/20/2023]
Abstract
The soil microbial fuel cells (SMFCs) were constructed to remediate soils contaminated by polycyclic aromatic hydrocarbons (PAHs). With a maximum power density of 12.1mWm-2 and an internal resistance of 470Ω, a closed SMFC showed electricity generation comparable to that by an open SMFC after 175days of operation and meanwhile increased the removal rates of anthracene, phenanthrene, and pyrene to 54.2±2.7%, 42.6±1.9% and 27.0±2.1% from 20.8±1.1%, 17.3±1.2% and 11.7±0.9%, respectively, by the open SMFC. Both the electricity generation and the removal of PAHs increased with the decreased electrode interval. When the electrode interval ranged between 4cm and 10cm, the more closely the electrodes were positioned, the more efficient the electricity generation and removal of PAHs became. Dominated by the genus of Geobacter, the SMFC was enriched in electrogenic bacteria at the anode surface, and the growth of certain microbes other than electrogenic bacteria in the soil was improved by electrical stimulation. This finding reveals the critical mechanism underlying electricity generation and improved the removal of PAHs.
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Affiliation(s)
- Bao Yu
- Department of Environmental Sciences and Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jing Tian
- Department of Environmental Sciences and Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Liu Feng
- Department of Environmental Sciences and Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China.
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104
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Pham HN, Michalet S, Bodillis J, Nguyen TD, Nguyen TKO, Le TPQ, Haddad M, Nazaret S, Dijoux-Franca MG. Impact of metal stress on the production of secondary metabolites in Pteris vittata L. and associated rhizosphere bacterial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:16735-16750. [PMID: 28567675 DOI: 10.1007/s11356-017-9167-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
Plants adapt to metal stress by modifying their metabolism including the production of secondary metabolites in plant tissues. Such changes may impact the diversity and functions of plant associated microbial communities. Our study aimed to evaluate the influence of metals on the secondary metabolism of plants and the indirect impact on rhizosphere bacterial communities. We then compared the secondary metabolites of the hyperaccumulator Pteris vittata L. collected from a contaminated mining site to a non-contaminated site in Vietnam and identified the discriminant metabolites. Our data showed a significant increase in chlorogenic acid derivatives and A-type procyanidin in plant roots at the contaminated site. We hypothesized that the intensive production of these compounds could be part of the antioxidant defense mechanism in response to metals. In parallel, the structure and diversity of bulk soil and rhizosphere communities was studied using high-throughput sequencing. The results showed strong differences in bacterial composition, characterized by the dominance of Proteobacteria and Nitrospira in the contaminated bulk soil, and the enrichment of some potential human pathogens, i.e., Acinetobacter, Mycobacterium, and Cupriavidus in P. vittata's rhizosphere at the mining site. Overall, metal pollution modified the production of P. vittata secondary metabolites and altered the diversity and structure of bacterial communities. Further investigations are needed to understand whether the plant recruits specific bacteria to adapt to metal stress.
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Affiliation(s)
- Hoang Nam Pham
- UMR 5557, Ecologie Microbienne, CNRS, INRA, VetagroSup, UCBL, Université de Lyon, 43 Boulevard du 11 Novembre, F-69622, Villeurbanne, France
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Serge Michalet
- UMR 5557, Ecologie Microbienne, CNRS, INRA, VetagroSup, UCBL, Université de Lyon, 43 Boulevard du 11 Novembre, F-69622, Villeurbanne, France
| | - Josselin Bodillis
- UMR 5557, Ecologie Microbienne, CNRS, INRA, VetagroSup, UCBL, Université de Lyon, 43 Boulevard du 11 Novembre, F-69622, Villeurbanne, France
| | - Tien Dat Nguyen
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Thi Kieu Oanh Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Thi Phuong Quynh Le
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Mohamed Haddad
- UMR 152 Pharma-DEV, Université de Toulouse, IRD, UPS, Toulouse, France
| | - Sylvie Nazaret
- UMR 5557, Ecologie Microbienne, CNRS, INRA, VetagroSup, UCBL, Université de Lyon, 43 Boulevard du 11 Novembre, F-69622, Villeurbanne, France.
| | - Marie-Geneviève Dijoux-Franca
- UMR 5557, Ecologie Microbienne, CNRS, INRA, VetagroSup, UCBL, Université de Lyon, 43 Boulevard du 11 Novembre, F-69622, Villeurbanne, France
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105
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Zhou Z, Nie K, Huang Q, Li K, Sun Y, Zhou R, Wang Z, Hu S. Changes of cecal microflora in chickens following Eimeria tenella challenge and regulating effect of coated sodium butyrate. Exp Parasitol 2017; 177:73-81. [PMID: 28455119 DOI: 10.1016/j.exppara.2017.04.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 04/10/2017] [Accepted: 04/23/2017] [Indexed: 12/18/2022]
Abstract
Eimeria tenella, one of the most important parasitic protozoa in the genus Eimeria, is responsible for chicken caecal coccidiosis resulting in huge economic losses to poultry industry. The present study investigated the changes in caecal microflora of E. tenella-infected chickens and the regulating effect of coated sodium butyrate, a potential alternative to antibiotics. Using high-throughput sequencing of 16S rRNA V3-V4 region of bacteria we found significant changes in caecal microflora of E. tenella-infected chickens indicated by an increase of Firmicutes (mainly Ruminococcaceae, Lachnospiraceae and vadin BB60) and Proteobacteria (mainly Enterobacteriaceae) and a decrease of Bacteroidetes (predominantly Bacteroidaceae). Inclusion of coated sodium butyrate in the diet of chickens per se had no significant effect on caecal microflora of normal healthy chickens but significantly prevented the increase in Firmicute abundance and decrease of Bacteroidetes abundance in E. tenella-infected birds. No significant changes to caecal microflora were observed at the phylum level between control and E. tenella-infected birds given coated sodium butyrate. In conclusion, our results show that coated sodium butyrate can balance the disorders of cecal microflora caused by E. tenella; thus, it can be a useful supplement for the control of avian coccidiosis.
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Affiliation(s)
- Zuoyong Zhou
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China; Veterinary Science Engineering Research Center of Chongqing, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China.
| | - Kui Nie
- College of Animal Science and Technology, Southwest University, Beibei District Chongqing, 400715, China
| | - Qingzhou Huang
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China; Veterinary Science Engineering Research Center of Chongqing, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China
| | - Kai Li
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China
| | - Yingying Sun
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China
| | - Rongqiong Zhou
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China; Veterinary Science Engineering Research Center of Chongqing, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China
| | - Zhiying Wang
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China; Veterinary Science Engineering Research Center of Chongqing, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China
| | - Shijun Hu
- Department of Veterinary Medicine, Rongchang Campus of Southwest University, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China; Veterinary Science Engineering Research Center of Chongqing, 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China
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106
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Zhang Y, Dong S, Gao Q, Liu S, Ganjurjav H, Wang X, Su X, Wu X. Soil bacterial and fungal diversity differently correlated with soil biochemistry in alpine grassland ecosystems in response to environmental changes. Sci Rep 2017; 7:43077. [PMID: 28262753 PMCID: PMC5338028 DOI: 10.1038/srep43077] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/19/2017] [Indexed: 01/11/2023] Open
Abstract
To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH4-N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands. Soil microbial biomass carbon and phosphorus along with the sucrase and phosphatase activities were generally stable under different treatments. Soil NO3-N, available phosphorus, urease activity and microbial biomass nitrogen were increased by overgrazing in the cultivated grassland. Soil bacterial diversity was positively correlated with, while soil fungal diversity negatively with soil microbial biomass and enzyme activities. Soil bacterial diversity was negatively correlated with, while soil fungal diversity positively with soil available nutrients. Our findings indicated soil bacteria and fungi played different roles in affecting soil nutrients and microbiological activities that might provide an important implication to understand why soil biochemistry was generally stable under environmental changes in alpine grassland ecosystems.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
- National Plateau Wetland Research Center, Southwest Forestry University, Kunming, 650224, China
| | - Shikui Dong
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Qingzhu Gao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shiliang Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Hasbagan Ganjurjav
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuexia Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xukun Su
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xiaoyu Wu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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107
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Xu X, Zhang Z, Hu S, Ruan Z, Jiang J, Chen C, Shen Z. Response of soil bacterial communities to lead and zinc pollution revealed by Illumina MiSeq sequencing investigation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:666-675. [PMID: 27744590 DOI: 10.1007/s11356-016-7826-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/03/2016] [Indexed: 05/17/2023]
Abstract
Soil provides a critical environment for microbial community development. However, microorganisms may be sensitive to substances such as heavy metals (HMs), which are common soil contaminants. This study investigated bacterial communities using 16S ribosomal RNA (rRNA) gene fragment sequencing in geographic regions with and without HM pollution to elucidate the effects of soil properties and HMs on bacterial communities. No obvious changes in the richness or diversity of bacterial communities were observed between samples from mining and control areas. Significant differences in bacterial richness and diversity were detected between samples from different geographic regions, indicating that the basic soil characteristics were the most important factors affecting bacterial communities other than HMs. However, the abundances of several phyla and genera differed significantly between mining and control samples, suggesting that Zn and Pb pollution may impact the soil bacterial community composition. Moreover, regression analyses showed that the relative abundances of these phyla and genera were correlated significantly with the soil-available Zn and Pb contents. Redundancy analysis indicated that the soil K, ammoniacal nitrogen (NH4+-N), total Cu, and available Zn and Cu contents were the most important factors. Our results not only suggested that the soil bacteria were sensitive to HM stresses but also indicated that other soil properties may affect soil microorganisms to a greater extent.
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Affiliation(s)
- Xihui Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Zhou Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Shunli Hu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Zhepu Ruan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jiandong Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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108
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Foulon J, Zappelini C, Durand A, Valot B, Girardclos O, Blaudez D, Chalot M. Environmental metabarcoding reveals contrasting microbial communities at two poplar phytomanagement sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 571:1230-40. [PMID: 27474992 DOI: 10.1016/j.scitotenv.2016.07.151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 05/06/2023]
Abstract
The aim of the present study is to deepen the current understanding of the microbial communities at two poplar phytomanagement sites to reveal the environmental factors that drive the abundance, diversity and composition of microbial communities. A soil analysis revealed that the two soils displayed contrasting physico-chemical characteristics, with significant lower pH and higher Cd, Zn and Mn CaCl2-extractable fractions at Leforest site, compared with Pierrelaye site. The fungal and bacterial community profiles in the poplar roots and soils were assessed through Illumina MiSeq sequencing. Diversity indices and β-diversity measures illustrated that the root microbial communities were well separated from the soil microbial communities at both sites. A detailed study of the fungal composition showed that Ascomycota dominated the overall fungal communities on poplar soil, the root samples at Pierrelaye, and the unplanted soil at the experimental sites. Conversely, Basidiomycota accounted for a much higher percentage of the fungal community in poplar root samples from the Leforest site. The root bacterial communities were dominated by Alphaproteobacteria and Actinobacteria, and the soil samples were dominated by Alphaproteobacteria and Acidobacteria. The occurrence and dominance of the ectomycorrhizal community at Leforest but not at Pierrelaye is the major feature of our data set. Overall, ectomycorrhizal root symbionts appeared to be highly constrained by soil characteristics at the phytomanagement sites. Our data support the view that mycorrhizal inoculation is needed in highly stressed and nutrient-poor environments.
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Affiliation(s)
- Julie Foulon
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Cyril Zappelini
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Alexis Durand
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Benoit Valot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Olivier Girardclos
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Damien Blaudez
- CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, BP70239, 54506 Vandoeuvre-lès-Nancy, France; Université de Lorraine, LIEC UMR7360, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Michel Chalot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France; Université de Lorraine, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-les-Nancy, France.
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109
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Spatial Variability of PAHs and Microbial Community Structure in Surrounding Surficial Soil of Coal-Fired Power Plants in Xuzhou, China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13090878. [PMID: 27598188 PMCID: PMC5036711 DOI: 10.3390/ijerph13090878] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 11/25/2022]
Abstract
This work investigated the spatial profile and source analysis of polycyclic aromatic hydrocarbons (PAHs) in soil that surrounds coal-fired power plants in Xuzhou, China. High-throughput sequencing was employed to investigate the composition and structure of soil bacterial communities. The total concentration of 15 PAHs in the surface soils ranged from 164.87 to 3494.81 μg/kg dry weight. The spatial profile of PAHs was site-specific with a concentration of 1400.09–3494.81 μg/kg in Yaozhuang. Based on the qualitative and principal component analysis results, coal burning and vehicle emission were found to be the main sources of PAHs in the surface soils. The phylogenetic analysis revealed differences in bacterial community compositions among different sampling sites. Proteobacteria was the most abundant phylum, while Acidobacteria was the second most abundant. The orders of Campylobacterales, Desulfobacterales and Hydrogenophilales had the most significant differences in relative abundance among the sampling sites. The redundancy analysis revealed that the differences in bacterial communities could be explained by the organic matter content. They could also be explicated by the acenaphthene concentration with longer arrows. Furthermore, OTUs of Proteobacteria phylum plotted around particular samples were confirmed to have a different composition of Proteobacteria phylum among the sample sites. Evaluating the relationship between soil PAHs concentration and bacterial community composition may provide useful information for the remediation of PAH contaminated sites.
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110
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Hakim JA, Koo H, Kumar R, Lefkowitz EJ, Morrow CD, Powell ML, Watts SA, Bej AK. The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles. FEMS Microbiol Ecol 2016; 92:fiw146. [PMID: 27368709 PMCID: PMC5975844 DOI: 10.1093/femsec/fiw146] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/28/2016] [Accepted: 06/27/2016] [Indexed: 12/29/2022] Open
Abstract
In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. The gut digesta and egested fecal pellets exhibited a microbial profile comprised of Gammaproteobacteria, mainly Vibrio, and Bacteroidetes. Both the seagrass and surrounding sea water revealed Alpha- and Betaproteobacteria. Bray-Curtis distances of microbial communities indicated a clustering profile with low intrasample variation. Predictive metagenomics performed on the microbial communities revealed that the gut tissue had high relative abundances of metabolisms assigned to the KEGG-Level-2 designation of energy metabolisms compared to the gut digesta, which had higher carbohydrate, amino acid and lipid metabolisms. Overall, the results of this study elaborate the spatial distribution of microbial communities in the gut ecosystem of L. variegatus, and specifically a selective attribute for Campylobacteraceae in the gut tissue. Also, the predictive functional significance of bacterial communities in uniquely compartmentalized gut ecosystems of L. variegatus has been described.
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Affiliation(s)
- Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA
| | - Hyunmin Koo
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA
| | - Ranjit Kumar
- Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Elliot J Lefkowitz
- Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA
| | - Mickie L Powell
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA
| | - Stephen A Watts
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA
| | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA
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111
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Zhang Y, Dong S, Gao Q, Liu S, Zhou H, Ganjurjav H, Wang X. Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands of the Qinghai-Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 562:353-363. [PMID: 27100015 DOI: 10.1016/j.scitotenv.2016.03.221] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/25/2016] [Accepted: 03/28/2016] [Indexed: 06/05/2023]
Abstract
Alpine ecosystems are known to be sensitive to climate change and human disturbances. However, the knowledge about the changes of their underground microbial communities is inadequate. We explored the diversity and structure of soil bacterial and fungal communities using Ilumina MiSeq sequencing in native alpine grasslands (i.e. the alpine meadow, alpine steppe) and cultivated grassland of the Qinghai-Tibetan Plateau (QTP) under three-year treatments of overgrazing, warming and enhanced rainfall. Enhanced rainfall rather than warming significantly reduced soil microbial diversity in native alpine grasslands. Variable warming significantly reduced it in the cultivated grassland. Over 20% and 40% variations of microbial diversity could be explained by soil nutrients and moisture in the alpine meadow and cultivated grassland, separately. Soil microbial communities could be clustered into different groups according to different treatments in the alpine meadow and cultivated grassland. For the alpine steppe, with the lowest soil nutrients and moistures, <10% variations of microbial diversity was explained by soil properties; and the soil microbial communities among different treatments were similar. The soil microbial community in the cultivated grassland was varied from it in native grasslands. Over 50% variations of soil microbial communities among different treatments were explained by soil nutrients and moisture in each grassland type. Our results suggest that climate change and human activities strongly affected soil microbial communities by changing soil nutrients and moistures in alpine grassland ecosystems.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Shikui Dong
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China; Department of Natural Resources, Cornell University, Ithaca, NY 14853-3001, USA.
| | - Qingzhu Gao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Shiliang Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Huakun Zhou
- Northwest Institute of Plateau Biology, Chinese Academy of Science, Xining 810008, China
| | - Hasbagan Ganjurjav
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuexia Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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112
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Xing W, Li D, Li J, Hu Q, Deng S. Nitrate removal and microbial analysis by combined micro-electrolysis and autotrophic denitrification. BIORESOURCE TECHNOLOGY 2016; 211:240-7. [PMID: 27019127 DOI: 10.1016/j.biortech.2016.03.044] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/05/2016] [Accepted: 03/08/2016] [Indexed: 05/20/2023]
Abstract
A process combining micro-electrolysis and autotrophic denitrification (CEAD) with iron-carbon micro-electrolysis carriers was developed for nitrate removal. The process was performed using organic-free influent with a NO3(-)-N concentration of 40.0±3.0mg/L and provided an average nitrate removal efficiency of 95% in stable stages. The total nitrogen removal efficiency reached 75%, with 21% of NO3(-)-N converted into NH4(+)-N. The corresponding hydraulic retention time was 8-10h, and the optimal pH ranged from 8.5 to 9.5. Microbial analysis with high-throughput sequencing revealed that dominant microorganisms in the reactor belonged to the classes of β-, γ-, and α-Proteobacteria. The abundance of the genera Thermomonas significantly increased during the operation, comprising 21.4% and 24.1% in sludge attached to the carriers in the middle and at the bottom of the reactor, respectively. The developed CEAD achieved efficient nitrate removal from water without organics, which is suitable for practical application.
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Affiliation(s)
- Wei Xing
- School of Civil Engineering, Beijing Jiaotong University, Beijing 100044, China; Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Beijing 100044, China.
| | - Desheng Li
- School of Civil Engineering, Beijing Jiaotong University, Beijing 100044, China; Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Beijing 100044, China.
| | - Jinlong Li
- School of Civil Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Qianyi Hu
- School of Civil Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Shihai Deng
- School of Civil Engineering, Beijing Jiaotong University, Beijing 100044, China
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113
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Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing "Stress-on-Stress" Responses. Int J Mol Sci 2016; 17:ijms17060933. [PMID: 27314330 PMCID: PMC4926466 DOI: 10.3390/ijms17060933] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 05/17/2016] [Accepted: 06/06/2016] [Indexed: 01/19/2023] Open
Abstract
Many microbial ecology studies have demonstrated profound changes in community composition caused by environmental pollution, as well as adaptation processes allowing survival of microbes in polluted ecosystems. Soil microbial communities in polluted areas with a long-term history of contamination have been shown to maintain their function by developing metal-tolerance mechanisms. In the present work, we review recent experiments, with specific emphasis on studies that have been conducted in polluted areas with a long-term history of contamination that also applied DNA-based approaches. We evaluate how the “costs” of adaptation to metals affect the responses of metal-tolerant communities to other stress factors (“stress-on-stress”). We discuss recent studies on the stability of microbial communities, in terms of resistance and resilience to additional stressors, focusing on metal pollution as the initial stress, and discuss possible factors influencing the functional and structural stability of microbial communities towards secondary stressors. There is increasing evidence that the history of environmental conditions and disturbance regimes play central roles in responses of microbial communities towards secondary stressors.
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114
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Chen F, Yang Y, Ma Y, Hou H, Zhang S, Ma J. Effects of CO2 leakage on soil bacterial communities from simulated CO2-EOR areas. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2016; 18:547-554. [PMID: 27056285 DOI: 10.1039/c5em00571j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
CO2-EOR (enhanced oil recovery) has been proposed as a viable option for flooding oil and reducing anthropogenic CO2 contribution to the atmospheric pool. However, the potential risk of CO2 leakage from the process poses a threat to the ecological system. High-throughput sequencing was used to investigate the effects of CO2 emission on the composition and structure of soil bacterial communities. The diversity of bacterial communities notably decreased with increasing CO2 flux. The composition of bacterial communities varied along the CO2 flux, with increasing CO2 flux accompanied by increases in the relative abundance of Bacteroidetes and Firmicutes phyla, but decreases in the relative abundance of Acidobacteria and Chloroflexi phyla. Within the Firmicutes phylum, the genus Lactobacillus increased sharply when the CO2 flux was at its highest point. Alpha and beta diversity analysis revealed that differences in bacterial communities were best explained by CO2 flux. The redundancy analysis (RDA) revealed that differences in bacterial communities were best explained by soil pH values which related to CO2 flux. These results could be useful for evaluating the risk of potential CO2 leakages on the ecosystems associated with CO2-EOR processes.
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Affiliation(s)
- Fu Chen
- Low Carbon Energy Institute, China University of Mining and Technology, Xuzhou, Jiangsu 221008, China.
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115
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Lin H, Jin D, Freitag TE, Sun W, Yu Q, Fu J, Ma J. A compositional shift in the soil microbiome induced by tetracycline, sulfamonomethoxine and ciprofloxacin entering a plant-soil system. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 212:440-448. [PMID: 26952272 DOI: 10.1016/j.envpol.2016.02.043] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/19/2016] [Accepted: 02/21/2016] [Indexed: 06/05/2023]
Abstract
Antibiotics entering the soil likely disturb the complex regulatory network of the soil microbiome, which is closely associated with soil quality and ecological function. This study investigated the effects of tetracycline (TC), sulfamonomethoxine (SMM), ciprofloxacin (CIP) and their combination (AM) on the bacterial community in a soil-microbe-plant system and identified the main bacterial responders. Antibiotic effects on the soil microbiome depended on antibiotic type and exposure time. TC resulted in an acute but more rapidly declining effect on soil microbiome while CIP and SMM led to a delayed antibiotic effect. The soil exposed to AM presented a highly similar bacterial structure to that exposed to TC rather than to SMM and CIP. TC, SMM and CIP had their own predominantly impacted taxonomic groups that include both resistance and sensitive bacteria. The antibiotic sensitive responders predominantly distributed within the phylum Proteobacteria. The potential bacteria resistant to each antibiotic exhibited phyla preference to some extent, particularly those resistant to TC. CIP and SMM resistance in soil was increased with exposure time while TC resistance gave the opposite result. Overall, the work extended the understanding of antibiotic effects on soil microbiome after introduced into the soil during greenhouse vegetable cultivation.
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Affiliation(s)
- Hui Lin
- The Institute of Environmental Resource and Soil Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China
| | - Danfeng Jin
- The Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330096, PR China
| | - Thomas E Freitag
- The James Hutton Institute, Craigiebuckler, Aberdeen, Scotland, United Kingdom
| | - Wanchun Sun
- The Institute of Environmental Resource and Soil Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China
| | - Qiaogang Yu
- The Institute of Environmental Resource and Soil Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China
| | - Jianrong Fu
- The Institute of Environmental Resource and Soil Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China
| | - Junwei Ma
- The Institute of Environmental Resource and Soil Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China.
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