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Sun Z, Sun C, Zhang T, Liu J, Wang X, Feng J, Li S, Tang S, Jin K. Soil microbial community variation among different land use types in the agro-pastoral ecotone of northern China is likely to be caused by anthropogenic activities. Front Microbiol 2024; 15:1390286. [PMID: 38841072 PMCID: PMC11150776 DOI: 10.3389/fmicb.2024.1390286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024] Open
Abstract
There are various types of land use in the agricultural and pastoral areas of northern China, including natural grassland and artificial grassland, scrub land, forest land and farmland, may change the soil microbial community However, the soil microbial communities in these different land use types remain poorly understood. In this study, we compared soil microbial communities in these five land use types within the agro-pastoral ecotone of northern China. Our results showed that land use has had a considerable impact on soil bacterial and fungal community structures. Bacterial diversity was highest in shrubland and lowest in natural grassland; fungal diversity was highest in woodland. Microbial network structural complexity also differed significantly among land use types. The lower complexity of artificial grassland and farmland may be a result of the high intensity of anthropogenic activities in these two land-use types, while the higher structural complexity of the shrubland and woodland networks characterised by low-intensity management may be a result of low anthropogenic disturbance. Correlation analysis of soil properties (e.g., soil physicochemical properties, soil nutrients, and microbiomass carbon and nitrogen levels) and soil microbial communities demonstrated that although microbial taxa were correlated to some extent with soil environmental factors, these factors did not sufficiently explain the microbial community differences among land use types. Understanding variability among soil microbial communities within agro-pastoral areas of northern China is critical for determining the most effective land management strategies and conserving microbial diversity at the regional level.
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Affiliation(s)
- Zhaokai Sun
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Chongzhi Sun
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Tongrui Zhang
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Jia Liu
- School of Grass Academy, Qingdao Agriculture University, Qingdao, China
| | - Xinning Wang
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Jing Feng
- School of Grass Academy, Qingdao Agriculture University, Qingdao, China
| | - Shucheng Li
- Anhui Science and Technology University, College of Agriculture, Huainan, China
| | - Shiming Tang
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Ke Jin
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
- Department of International Cooperation, Chinese Academy of Agricultural Sciences, Beijing, China
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Li S, Xiang X, Shi Z, Liu WH, Liang G, Zhang Y, Li W. The impact of mixed planting of Poaceae species in the Qinghai-Tibet plateau region on forage yield, soil nutrients, and soil microbial communities. FRONTIERS IN PLANT SCIENCE 2024; 15:1370593. [PMID: 38742217 PMCID: PMC11089163 DOI: 10.3389/fpls.2024.1370593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/25/2024] [Indexed: 05/16/2024]
Abstract
Establishing cultivated grassland in the Qinghai-Tibet Plateau region is an effective method to address the conflict between vegetation and livestock. However, the high altitude, low temperature, and arid climate in the region result in slow regeneration and susceptibility to degradation of mixed cultivation grassland containing perennial legumes and gramineous plants. Therefore, we aim to through field experiments, explore the feasibility of establishing mixed cultivation grassland of Poaceae species in the region by utilizing two grass species, Poa pratensis L. and Puccinellia tenuiflora. By employing a mixture of P. pratensis and P. tenuiflora to establish cultivated grassland, we observed significant changes in forage yield over time. Specifically, during the 3rd to 6th years of cultivation, the yield in the mixed grassland was higher than in monocultures. It exceeded the yield of monoculture P. tenuiflora by 19.38% to 29.14% and surpassed the monoculture of P. pratensis by 17.18% to 62.98%. Through the analysis of soil physicochemical properties and soil microbial communities in the cultivated grassland, the study suggests that the mixed grassland with Poaceae species can enhance soil enzyme activity and improve soil microbial communities. Consequently, this leads to increased soil nutrient levels, enhanced nitrogen fixation efficiency, and improved organic phosphorus conversion efficiency. Therefore, establishing mixed grasslands with Poaceae species in the Qinghai-Tibet Plateau region is deemed feasible.
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Affiliation(s)
- Sida Li
- Key Laboratory of Superior Forage Germplasm in the Qinghai‐Tibetan plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
| | - Xuemei Xiang
- Key Laboratory of Superior Forage Germplasm in the Qinghai‐Tibetan plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Zhenghai Shi
- Key Laboratory of Superior Forage Germplasm in the Qinghai‐Tibetan plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
| | - Wen-hui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai‐Tibetan plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
| | - Guoling Liang
- Key Laboratory of Superior Forage Germplasm in the Qinghai‐Tibetan plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
| | - Yongchao Zhang
- Key Laboratory of Superior Forage Germplasm in the Qinghai‐Tibetan plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
| | - Wen Li
- Key Laboratory of Superior Forage Germplasm in the Qinghai‐Tibetan plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai, China
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Zou H, He J, Chu Y, Xu B, Li W, Huang S, Guan X, Liu F, Li H. Revealing discrepancies and drivers in the impact of lomefloxacin on groundwater denitrification throughout microbial community growth and succession. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133139. [PMID: 38056273 DOI: 10.1016/j.jhazmat.2023.133139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/31/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
The coexistence of antibiotics and nitrates has raised great concern about antibiotic's impact on denitrification. However, conflicting results in these studies are very puzzling, possibly due to differences in microbial succession stages. This study investigated the effects of the high-priority urgent antibiotic, lomefloxacin (LOM), on groundwater denitrification throughout microbial growth and succession. The results demonstrated that LOM's impact on denitrification varied significantly across three successional stages, with the most pronounced effects exhibited in the initial stage (53.8% promotion at 100 ng/L-LOM, 84.6% inhibition at 100 μg/L-LOM), followed by the decline stage (13.3-18.2% inhibition), while no effect in the stable stage. Hence, a distinct pattern encompassing susceptibility, insusceptibility, and sub-susceptibility in LOM's impact on denitrification was discovered. Microbial metabolism and environment variation drove the pattern, with bacterial numbers and antibiotic resistance as primary influencers (22.5% and 15.3%, p < 0.01), followed by carbon metabolism and microbial community (5.0% and 3.68%, p < 0.01). The structural equation model confirmed results reliability. Bacterial numbers and resistance influenced susceptibility by regulating compensation and bacteriostasis, while carbon metabolism and microbial community impacted energy, electron transfer, and gene composition. These findings provide valuable insights into the complex interplay between antibiotics and denitrification patterns in groundwater.
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Affiliation(s)
- Hua Zou
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Jiangtao He
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China.
| | - Yanjia Chu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Baoshi Xu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Wei Li
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Shiwen Huang
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Xiangyu Guan
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; School of Ocean Sciences, China University of Geosciences (Beijing), Beijing 100083, China
| | - Fei Liu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Haiyan Li
- School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
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Peng Y, Yao Y, Pang J, Di T, Du G, Chen B. Genetic Diversity and Virulence Variation of Metarhizium rileyi from Infected Spodoptera frugiperda in Corn Fields. Microorganisms 2024; 12:264. [PMID: 38399668 PMCID: PMC10892884 DOI: 10.3390/microorganisms12020264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/10/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Metarhizium rileyi is an entomopathogenic fungus that naturally infects the larvae of Spodoptera frugiperda, and has biocontrol potential. To explore more natural entomopathogenic fungi resources, a total of 31 strains were isolated from 13 prefectures in Yunnan Province. All the strains were identified using morphology and molecular biology. The genetic diversity of the 31 isolates of M. rileyi was analyzed using inter-simple sequence repeat (ISSR) techniques. Seven primers with good polymorphism were selected, and fifty-four distinct amplification sites were obtained by polymerase chain reaction amplification. Among them, 50 were polymorphic sites, and the percentage of polymorphic sites was 94.44%. The thirty-one strains were divided into eight subpopulations according to the regions. The Nei's gene diversity was 0.2945, and the Shannon information index was 0.4574, indicating that M. rileyi had rich genetic diversity. The average total genetic diversity of the subpopulations in the different regions was 0.2962, the gene diversity within the populations was 0.1931, the genetic differentiation coefficient was 0.3482 (>0.25), and the gene flow was 0.9360 (<1). The individual cluster analysis showed that there was no obvious correlation between the genetic diversity of the strains and their geographical origin, which also indicated that the virulence of the strains was not related to their phylogeny. Thus, the genetic distance of the different populations of M. rileyi in Yunnan Province was not related to the geographical distance. The virulence of those 32 strains against the 3rd-instar larvae of S. frugiperda were varied with the differences in geographical locations. On the 10th day of inoculation, seventeen strains had an insect mortality rate of 70.0%, and seven strains had an insect mortality rate of 100%. The half-lethal times of the M. rileyi SZCY201010, XSBN200920, and MDXZ200803 strains against the S. frugiperda larvae were less than 4 d. Thus, they have the potential to be developed into fungal insecticidal agents.
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Affiliation(s)
| | | | | | | | | | - Bin Chen
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (Y.P.); (Y.Y.); (J.P.); (T.D.); (G.D.)
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Wang M, Pu W, Wang S, Zeng X, Sui X, Wang X. pH-Related Changes in Soil Bacterial Communities in the Sanjiang Plain, Northeast China. Microorganisms 2023; 11:2950. [PMID: 38138094 PMCID: PMC10745975 DOI: 10.3390/microorganisms11122950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Soil bacteria are crucial components of terrestrial ecosystems, playing an important role in soil biogeochemical cycles. Although bacterial community diversity and composition are regulated by many abiotic and biotic factors, how soil physiochemical properties impact the soil bacteria community diversity and composition in wetland ecosystems remains largely unknown. In this study, we used high-throughput sequencing technology to investigate the diversity and composition of a soil bacterial community, as well as used the structural equation modeling (SEM) method to investigate the relationships of the soil's physicochemical properties (i.e., soil pH, soil organic carbon (SOC), total nitrogen (TN), ammonium nitrogen (NH4+N), electrical conductivity (EC) and nitrate nitrogen (NO3-N)), and soil bacterial community structures in three typical wetland sites in the Sanjiang Plain wetland. Our results showed that the soil physicochemical properties significantly changed the α and β-diversity of the soil bacteria communities, e.g., soil TN, NH4+N, NO3-N, and SOC were the main soil factors affecting the soil bacterial α-diversity. The soil TN and pH were the key soil factors affecting the soil bacterial community. Our results suggest that changes in soil pH indirectly affect soil bacterial communities by altering the soil nitrogenous nutrient content.
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Affiliation(s)
- Mingyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Wenmiao Pu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Shenzheng Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Xiannan Zeng
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin 150088, China;
| | - Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Xin Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
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Lei H, Jin C, Xiao Z, Chen J, Leghari SJ, Pan H. Relationship between pepper (Capsicum annuum L.) root morphology, inter-root soil bacterial community structure and diversity under water-air intercropping conditions. PLANTA 2023; 257:98. [PMID: 37067628 DOI: 10.1007/s00425-023-04134-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 04/10/2023] [Indexed: 06/19/2023]
Abstract
The combination of water and gas at an aeration rate of 15 mg/L and irrigation amount of 0.8 Ep significantly promoted the root morphology, inter-root soil bacterial community structure and diversity of pepper, enhanced the structure of molecular symbiotic network, and stimulated the potential ecosystem function. Poor aeration adversely affects the root morphology of pepper (Capsicum annuum L.) and bacterial community. It is critical to understand the effects of water-air interactions on root morphology and bacterial community structure and diversity. A randomized block experiment was conducted under the two aeration rates of dissolved oxygen mass concentrations, including A: 15 mg/L, O: 40 mg/L, and C: non-aeration as control treatment, and two irrigation rates of W1 and W2 (0.8 Ep and 1.0 Ep). The results showed that aerated irrigation had a significant effect on the root morphology of pepper. Compared with treatment CW1, treatment AW1 increased root dry weight, root length, root volume, and root surface area by 13.63%, 11.09%, 59.47%, and 61.67%, respectively (P < 0.05). Aerated irrigation significantly increased the relative abundance of Actinobacteria, Gemmatimonadetes, Alphaproteobacteria, Gemmatimonas, Sphingomonas, and KD4-96 aerobic beneficial bacteria. It decreased the relative abundance of Proteobacteria, Monomycetes, Bacteroidetes, Corynebacterium, Gammaproteobacteria, Anaerolineae, Subgroup_6, MND1, Haliangium, and Thiobacillus. The Pielou_e, Shannon and Simpson indexes of treatment AW1 were significantly higher than treatments OW1 and CW1. The results of the β-diversity of bacterial communities showed that the structure of soil bacterial communities differed significantly among treatments. Actinobacteria was a key phylum affecting root morphology, and AW1 treatment was highly correlated with Actinobacteria. Molecular ecological network analysis showed a relatively high number of bacterial network nodes and more complex relationships among species under the aeration of level 15 mg/L and 0.8 Ep, as well as the emergence of new phylum-level beneficial species: Dependentiae, BRC1, Cyanobacteria, Deinococcus-Thermus, Firmicutes, and Planctomycetes. Therefore, the aeration of 15 mg/L and 0.8 times crop-evaporation coefficient can increase root morphology, inter-root soil bacterial community diversity and bacterial network structure, and enhance potential ecosystem functions in the rhizosphere.
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Affiliation(s)
- Hongjun Lei
- School of Water Conservancy, North China University of Water Resources and Electric Power, Zhengzhou, 450046, China
| | - Cuicui Jin
- School of Water Conservancy, North China University of Water Resources and Electric Power, Zhengzhou, 450046, China
| | - Zheyuan Xiao
- School of Water Conservancy, North China University of Water Resources and Electric Power, Zhengzhou, 450046, China
| | - Jian Chen
- School of Water Conservancy, North China University of Water Resources and Electric Power, Zhengzhou, 450046, China
| | - Shah Jahan Leghari
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hongwei Pan
- School of Water Conservancy, North China University of Water Resources and Electric Power, Zhengzhou, 450046, China.
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Lv L, Qiu K, Ge S, Jiao Z, Gao C, Fu H, Su R, Liu Z, Wang Y, Wang Y. Neutralization and Improvement of Bauxite Residue by Saline-Alkali Tolerant Bacteria. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:11590. [PMID: 36141868 PMCID: PMC9517105 DOI: 10.3390/ijerph191811590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
The high salt-alkalinity of bauxite residue (BR) hinders plant growth and revegetation of bauxite residue disposal areas (BRDA), which cause serious potential environmental and ecological risks. Bioneutralization is a promising method for improving the properties of BR and plant colonization. In the present study, a strong saline-alkali tolerant bacteria (ZH-1) was isolated from aged BR and identified as Bacillus sp. The medium of ZH-1 was optimized by orthogonal tests, and ZH-1 could decrease the medium pH from 11.8 to 6.01 (agitated culture) and 6.48 (static culture) by secretion of citric acid, oxalic acid and tartaric acid. With the inoculation of ZH-1, the pH of BR decreased from 11.6 to 8.76, and the water-soluble salt in BR increased by 68.11%. ZH-1 also changed the aggregate size distribution of BR, the mechanical-stable aggregates and water-stable aggregates increased by 18.76% and 10.83%, respectively. At the same time, the stability of the aggregates obviously increased and the destruction rate decreased from 94.37% to 73.46%. In addition, the microbial biomass carbon increased from 425 to 2794 mg/kg with the inoculation of ZH-1. Bacterial community analysis revealed that Clostridia, Bacilli, Gammaproteobacteria, Betaproteobacteria and Alphaproteobacteria were the main classes in the naturalized BR, and the inoculation of ZH-1 increased the diversity of bacteria in the BR. Overall, ZH-1 has great potential for neutralization and improvement the properties of BR and may be greatly beneficial for the revegetation of BRDA.
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Affiliation(s)
- Lv Lv
- National Demonstration Center for Environmental and Planning, College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Henan University, Ministry of Education, Kaifeng 475004, China
- Henan Engineering Research Center for Control & Remediation of Soil Heavy Metal Pollution, Henan University, Kaifeng 475004, China
| | - Kunyan Qiu
- Henan Key Laboratory for Monitoring and Remediation in Heavy Metal Polluted Soil, Jiyuan 459000, China
| | - Shiji Ge
- Henan Engineering Research Center for Control & Remediation of Soil Heavy Metal Pollution, Henan University, Kaifeng 475004, China
| | - Zhiqiang Jiao
- Henan Engineering Research Center for Control & Remediation of Soil Heavy Metal Pollution, Henan University, Kaifeng 475004, China
| | - Chenyang Gao
- Henan Engineering Research Center for Control & Remediation of Soil Heavy Metal Pollution, Henan University, Kaifeng 475004, China
| | - Haiguang Fu
- Henan Engineering Research Center for Control & Remediation of Soil Heavy Metal Pollution, Henan University, Kaifeng 475004, China
| | - Rongkui Su
- School of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Zhongkai Liu
- Zhengzhou Non-Ferrous Metals Research Institute Co., Ltd. of CHALCO, Zhengzhou 450041, China
| | - Yulong Wang
- National Demonstration Center for Environmental and Planning, College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Henan University, Ministry of Education, Kaifeng 475004, China
| | - Yangyang Wang
- National Demonstration Center for Environmental and Planning, College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
- Henan Engineering Research Center for Control & Remediation of Soil Heavy Metal Pollution, Henan University, Kaifeng 475004, China
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Deng Q, Wu Y, Zhao X, Qiu C, Xia S, Feng Y, Liu H. Influence of different irrigation methods on the alfalfa rhizosphere soil fungal communities in an arid region. PLoS One 2022; 17:e0268175. [PMID: 35714153 PMCID: PMC9205495 DOI: 10.1371/journal.pone.0268175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/25/2022] [Indexed: 11/30/2022] Open
Abstract
Xinjiang is the largest arid and saline agricultural region in China. The common irrigation methods in this area are traditional flood irrigation and drip irrigation. In this study, we investigated the effects of these two irrigation methods on the fungal diversity, community structures, and functions in alfalfa rhizosphere soil as well as the associated environmental factors in northern Tianshan Mountain (Xinjiang, China). Soil enzyme activities (urease and neutral phosphatase) were significantly higher in the drip-irrigated alfalfa rhizosphere soil than in the flood-irrigated alfalfa rhizosphere soil, whereas the fungal alpha diversity in the drip-irrigated alfalfa rhizosphere soil was significantly lower than that in the flood-irrigated alfalfa rhizosphere soil. Six dominant fungal phyla were identified (>0.1%), with Ascomycota being the most abundant in all soils, followed by Basidiomycota (5.47%), Mortierellomycota (1.07%), Glomeromycota (0.55%), Rozellomycota (0.27%), and Chytridiomycota (0.14%). Ascomycota and Glomeromycota species were significantly less abundant in drip-irrigated alfalfa rhizosphere soil than in flood-irrigated alfalfa rhizosphere soil. A LEFSe analysis identified Cladosporiaceae (20.8%) species as the most abundant marker fungi in drip-irrigated alfalfa rhizosphere soil. Of the 13 fungal functional groups identified on the basis of the functional annotation using the FUNGuild database, Ectomycorrhizal (22.29%) was the primary functional group. Compared with flood irrigation, drip irrigation significantly decreased the relative abundance of Ectomycorrhizal and Arbuscular_Mycorrhizal, while increasing the relative abundance of Plant_Pathogen, although not significantly (P = 0.19). Available potassium was revealed to be the main environmental factor influencing soil enzyme activities, fungal alpha diversity, fungal community structures, and fungal functions in response to the different irrigation methods. In conclusion, drip irrigation may be more appropriate than flood irrigation in the Tianshan dryland agricultural area for enhancing soil enzyme activities, but it may also increase the abundance of plant pathogenic fungi in the soil.
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Affiliation(s)
- Qizhang Deng
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- College of Chemistry and Life Sciences Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, China
| | - Yong Wu
- College of Chemistry and Life Sciences Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, China
| | - Xiang Zhao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Chengshu Qiu
- College of Chemistry and Life Sciences Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, China
| | - Shan Xia
- College of Chemistry and Life Sciences Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, China
| | - Yuanyuan Feng
- College of Chemistry and Life Sciences Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, China
| | - Hongling Liu
- College of Chemistry and Life Sciences Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, China
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Nnabuife OO, Ogbonna JC, Anyanwu C, Ike AC, Eze CN, Enemuor SC. Mixed bacterial consortium can hamper the efficient degradation of crude oil hydrocarbons. Arch Microbiol 2022; 204:306. [PMID: 35532873 DOI: 10.1007/s00203-022-02915-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/07/2022] [Accepted: 04/10/2022] [Indexed: 11/24/2022]
Abstract
Crude oil degradation efficiency can be improved because of co-metabolism that exists when bacterial consortium is applied. However, because of possible vulnerability to environmental conditions and/or antagonistic interactions among members of the consortium, the degradation efficiency can be hampered. In this laboratory-based study, the biodegradation potentials of pure bacterial isolates namely Pseudomonas aeruginosa strain W15 (MW320658), Providencia vermicola strain W8 (MW320661) and Serratia marcescens strain W13 (MW320662) earlier isolated from crude oil-contaminated site and their consortium were evaluated using 3% crude oil-supplemented Bushnell Haas media. The efficiency was evaluated based on the viable cell count, biosurfactant analyses, percentage hydrocarbon degradation using gravimetric analysis and gas chromatography-mass spectrophotometry (GC-MS) analysis. There was decline in the population of W13 and predominance of W15 in the consortium as the incubation period progressed. Accelerated biodegradation of the crude oil hydrocarbons through co-metabolism was not achieved with the consortium; neither was there any improved resilience nor resistance to environmental changes of strain W13. The GC-MS analyses showed that the highest degradation was produced by W15 (48.23%) compared to W8 (46.04%), W13 (45.24%) and the Consortium (28.51%). The biodegradation of the crude oil hydrocarbons by W15, W8, W13 axenic cultures and their consortium treatments demonstrated that the bacterial constituent in a consortium can influence the synergistic effect that improves bioremediation. Future research that focuses on evaluating possible improvement in bioremediation through maintenance of diversity by continuous bioaugmentation using vulnerable but efficient degraders in a consortium is necessary to further understand the application of consortia for bioremediation improvement.
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Affiliation(s)
- Obianuju Obiajulu Nnabuife
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria.
| | - James Chukwuma Ogbonna
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Chukwudi Anyanwu
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Anthony Chibuogwu Ike
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Chibuzor Nwadibe Eze
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Simeon Chukwuemeka Enemuor
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
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10
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Wu D, Zhao C, Bai H, Feng F, Sui X, Sun G. Characteristics and metabolic patterns of soil methanogenic archaea communities in the high-latitude natural forested wetlands of China. Ecol Evol 2021; 11:10396-10408. [PMID: 34367583 PMCID: PMC8328403 DOI: 10.1002/ece3.7842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/07/2021] [Accepted: 06/10/2021] [Indexed: 01/12/2023] Open
Abstract
Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic mcrA gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably influenced the methanogenic community composition. The methanogenic community structure in the Betula platyphylla-Larix gmelinii wetland was relatively different from the structure of the other two wetland types. Indicator species analysis further demonstrated that the corresponding species of indicator operational taxonomic units from the Alnus sibirica wetland and the Betula ovalifolia wetland were similar. Network analysis showed that cooperative and competitive relationships exist both within and between the same or different trophic methanogens. The core methanogens with higher abundance in each wetland were conducive to the adaptation to environmental disturbances. This information is crucial for the assessment of metabolic patterns of soil methanogenic archaea and future fluxes in the wetlands of the Xiaoxing'an Mountain region given their vulnerability.
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Affiliation(s)
- Di Wu
- Key Laboratory of Saline‐Alkali Vegetation Ecology Restoration (Northeast Forestry University)Ministry of EducationHarbinChina
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Caihong Zhao
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Hui Bai
- Key Laboratory of Fast‐Growing Tree Cultivating of Heilongjiang ProvinceForestry Science Research Institute of Heilongjiang ProvinceHarbinChina
| | - Fujuan Feng
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Xin Sui
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold RegionSchool of Life SciencesHeilongjiang UniversityHarbinChina
| | - Guangyu Sun
- Key Laboratory of Saline‐Alkali Vegetation Ecology Restoration (Northeast Forestry University)Ministry of EducationHarbinChina
- College of Life ScienceNortheast Forestry UniversityHarbinChina
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11
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Bernardes FS, de Souza Pereira MA, Hassan IAI, de Castro AP, Roche KF, Paulo PL. Change in microbial profile and environmental conditions in a constructed wetland system treating greywater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:34539-34552. [PMID: 33650054 DOI: 10.1007/s11356-021-12822-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
The objective of this work was to verify the relationships between environmental conditions and microbial processes along a raw-light greywater flow in an improved constructed wetland (CW) system. Physicochemical analysis and high-throughput DNA sequencing were performed in the different zones to investigate the environmental conditions and microbial communities. The results showed that the system operated predominantly under anaerobic conditions, with redox potential (Eh) increasing from the inlet (-342.9 mV) to the outlet (-316.4 mV). Conversely, the chemical oxygen demand (COD) decreased along the greywater flow, suggesting negative correlation between these characteristics. The zones of the evapotranspiration and treatment tank (CEvaT) were characterized by lower community diversity and richness and by the presence of specific groups: Proteobacteria and Synergistetes related to the first steps of the conversion of organic carbon, in the bottom layer inside the anaerobic chamber (AnC); methanogens (Methanosaeta and Methanobacterium) and sulphate-reducing bacteria (Desulfovibrio, Desulforhabdus and Desulfomonile) in the middle layer; and microorganisms associated with the nitrogen cycle and oxygen release (Acinetobacter, Novosphingobium, Candidatus Nitrososphaera) in the top layer. On the other hand, the increase of the ORP and decrease of organic matter concentrations were associated with higher community diversity and richness in the middle layer of the CW, which showed higher abundance of microorganisms involved in methane (Methylobacterium and Candidatus Koribacter) and sulphur (Rhodoblastus and Thiobacillus) oxidation.
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Affiliation(s)
- Fernando Silva Bernardes
- Faculty of Engineering, Architecture and Urbanism and Geography (FAENG), Federal University of Mato Grosso do Sul (UFMS), Campo Grande, MS, 79070-900, Brazil.
| | | | - Ismail Abdallah Ismail Hassan
- Faculty of Engineering, Architecture and Urbanism and Geography (FAENG), Federal University of Mato Grosso do Sul (UFMS), Campo Grande, MS, 79070-900, Brazil
| | | | - Kennedy Francis Roche
- Faculty of Engineering, Architecture and Urbanism and Geography (FAENG), Federal University of Mato Grosso do Sul (UFMS), Campo Grande, MS, 79070-900, Brazil
| | - Paula Loureiro Paulo
- Faculty of Engineering, Architecture and Urbanism and Geography (FAENG), Federal University of Mato Grosso do Sul (UFMS), Campo Grande, MS, 79070-900, Brazil
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Wang M, Wu J, Zhou T, Liang Y, Zheng L, Sun Y. Effects of copper and florfenicol on nirS- and nirK-type denitrifier communities and related antibiotic resistance in vegetable soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 213:112011. [PMID: 33592374 DOI: 10.1016/j.ecoenv.2021.112011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 12/20/2020] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
Denitrification play an important role in nitrogen cycle and is affected by veterinary drugs entering agricultural soils. In the present study, the effects of copper and florfenicol on denitrification, related antibiotic resistance and environmental variables were characterized using real-time quantitative PCR (qPCR) and amplicon sequencing in a short-term (30 d) soil model experiment. Drug additions significantly decreased the nirS gene abundance (P < 0.05) but maximized the abundance of gene nirK in soil containing florfenicol and moderate copper levels (150 mg kg-1). Surprisingly, copper additions decreased the fexB gene abundance, however, the abundance of gene pcoD significantly increased in soils containing florfenicol, moderate copper levels (150 mg kg-1), and florfenicol and low copper levels (30 mg kg-1), respectively (P < 0.05). Overall, the nirK-type community composition was more complex than that of nirS-type but Proteobacteria predominated (> 90%) in both communities. Correlation analysis indicated that the gene abundance of fexB was highly correlated with NH4+-N (P < 0.05) and NO3--N (P < -0.01), and floR gene abundance was positively correlated with nirK (P < 0.01). Besides, the abundance of nirS-type genera Bradyrhizobium and Pseudomonas were obviously related to total organic matter (TOM), total nitrogen (TN) or total phosphorus (TP) (P < 0.05), while the abundance of nirK-type Rhizobium, Sphingomonas and Bosea showed a significantly correlated with TOM, TN or copper contents (P < 0.05). Taken together, copper and florfenicol contamination increased the possibility of durg resistance genes spread in agricultural soils through nitrogen transformation.
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Affiliation(s)
- Mei Wang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Jing Wu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Tong Zhou
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Yi Liang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Lixuan Zheng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Yongxue Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China.
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13
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Chiba A, Uchida Y, Kublik S, Vestergaard G, Buegger F, Schloter M, Schulz S. Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition. Microorganisms 2021; 9:microorganisms9020357. [PMID: 33670245 PMCID: PMC7916959 DOI: 10.3390/microorganisms9020357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
This study aimed to investigate the effects of different levels of soil- and plant-associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gaiellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that litter-associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.
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Affiliation(s)
- Akane Chiba
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Crop Physiology, TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Yoshitaka Uchida
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany;
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Correspondence: ; Tel.: +49-(0)89-3187-3054
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14
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Deckmyn G, Flores O, Mayer M, Domene X, Schnepf A, Kuka K, Van Looy K, Rasse DP, Briones MJ, Barot S, Berg M, Vanguelova E, Ostonen I, Vereecken H, Suz LM, Frey B, Frossard A, Tiunov A, Frouz J, Grebenc T, Öpik M, Javaux M, Uvarov A, Vindušková O, Henning Krogh P, Franklin O, Jiménez J, Curiel Yuste J. KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models. I. review and model concept. PeerJ 2020; 8:e9750. [PMID: 32974092 PMCID: PMC7486829 DOI: 10.7717/peerj.9750] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/27/2020] [Indexed: 11/20/2022] Open
Abstract
The relatively poor simulation of the below-ground processes is a severe drawback for many ecosystem models, especially when predicting responses to climate change and management. For a meaningful estimation of ecosystem production and the cycling of water, energy, nutrients and carbon, the integration of soil processes and the exchanges at the surface is crucial. It is increasingly recognized that soil biota play an important role in soil organic carbon and nutrient cycling, shaping soil structure and hydrological properties through their activity, and in water and nutrient uptake by plants through mycorrhizal processes. In this article, we review the main soil biological actors (microbiota, fauna and roots) and their effects on soil functioning. We review to what extent they have been included in soil models and propose which of them could be included in ecosystem models. We show that the model representation of the soil food web, the impact of soil ecosystem engineers on soil structure and the related effects on hydrology and soil organic matter (SOM) stabilization are key issues in improving ecosystem-scale soil representation in models. Finally, we describe a new core model concept (KEYLINK) that integrates insights from SOM models, structural models and food web models to simulate the living soil at an ecosystem scale.
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Affiliation(s)
- Gaby Deckmyn
- Department of Biology, Plants and Ecosystems (PLECO), Universiteit Antwerpen, Antwerpen, Belgium
| | - Omar Flores
- Department of Biology, Plants and Ecosystems (PLECO), Universiteit Antwerpen, Antwerpen, Belgium
- Biogeography and Global Change, National Museum of Natural Sciences-Spanish National Research Council (MNCN-CSIC), Madrid, Spain
| | - Mathias Mayer
- Institute of Forest Ecology, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Biogeochemistry Group, Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Xavier Domene
- CREAF, Cerdanyola del Vallès, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Andrea Schnepf
- Agrosphere Institute, IBG, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Katrin Kuka
- Institute for Crop and Soil Science, Julius Kühn-Institut (JKI), Braunschwei, Germany
| | - Kris Van Looy
- OVAM, Flemish Institute for Materials and Soils, Mechelen, Belgium
| | - Daniel P. Rasse
- Department of Biogeochemistry and Soil Quality, Norwegian Institute of Bioeconomy Research (NIBIO), Aas, Norway
| | - Maria J.I. Briones
- Departamento de Ecología y Biología Animal, Universidad de Vigo, Vigo, Spain
| | - Sébastien Barot
- Institute of Ecology and Environmental Sciences, IRD, UPEC, CNRS, INRA, Sorbonne Université, Paris, France
| | - Matty Berg
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | | | - Ivika Ostonen
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Harry Vereecken
- Agrosphere Institute, IBG, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Laura M. Suz
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, London, UK
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Alexei Tiunov
- A.N. Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - Jan Frouz
- Institute for Environmental Studies, Charles University, Prague, Czech Republic
| | - Tine Grebenc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mathieu Javaux
- Agrosphere Institute, IBG, Forschungszentrum Jülich GmbH, Jülich, Germany
- Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Alexei Uvarov
- A.N. Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - Olga Vindušková
- Department of Biology, Plants and Ecosystems (PLECO), Universiteit Antwerpen, Antwerpen, Belgium
| | | | - Oskar Franklin
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
- International Institute for Applied Systems Analysis IIASA, Laxenburg, Austria
| | - Juan Jiménez
- Department of Biodiversity Conservation and Ecosystem Restoration, ARAID/IPE-CSIC, Jaca, Spain
| | - Jorge Curiel Yuste
- BC3-Basque Centre for Climate Change, Scientific Campus of the University of the Basque Country, Bilbao, Bizkaia, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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15
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Heydari M, Zeynali N, Omidipour R, Bazgir M, Kohzadian M, Prevosto B. Linkage between plant species diversity and soil-based functions along a post-agricultural succession is influenced by the vegetative forms. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:429. [PMID: 32535793 DOI: 10.1007/s10661-020-08378-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
There is a growing body of knowledge that ecosystem functions, in particular, soil-based ecosystem functions, are related to biodiversity. However, how plant species diversity influences soil-based functions along post-agricultural secondary succession is still a largely ignored question in Mediterranean semi-arid conditions. Therefore, we used the plant functional group approach to investigate the relationships between plant species diversity indices and soil-based functions including microbial biomass carbon (MBC), basal respiration (BR), and carbon sequestration (CS) across three different stages of the vegetation succession corresponding to ~ 5 years after agricultural abandonment, ~ 15 years after abandonment, and oak forests which represent the terminal stage. We also tested if these relationships are supported by the niche complementarity and selection effect hypotheses. The results showed that soil-based functions significantly increased with time since abandonment as BR, MBC, and CS increased respectively by 1.7, 1.5, and 2.7 times across the three successional stages. We also found strong correlations between the diversity indices and the soil-based functions BR, MBC, and CS which were positive for richness (R2 values 0.75, 0.74, and 0.75) and Shannon diversity (R2 values 0.61, 0.58, and 0.61) but negative for evenness (R2 values 0.38, 0.38, and 0.36 for, respectively). Similarly, richness and Shannon diversity of the different plant functional groups positively correlated with soil-based functions. However, contrasting results were found for evenness which positively correlated with soil-based functions for perennial grass only. We suggested that increasing the diversity of plant species and facilitating dominant species would be needed to improve the soil-based ecosystem functions after abandonment of degraded soils. This study also revealed that the mechanisms behind the relationships between biodiversity and ecosystem functions were influenced by the vegetative forms.
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Affiliation(s)
- Mehdi Heydari
- Department of Forest Science, Faculty of Agriculture, Ilam University, Ilam, Iran.
| | - Nasim Zeynali
- Department of Forest Science, Faculty of Agriculture, Ilam University, Ilam, Iran
| | - Reza Omidipour
- Department of Rangeland and Watershed Management, Faculty of Agriculture, Ilam University, Ilam, Iran
| | - Masoud Bazgir
- Department of Soil Science, Faculty of Agriculture, Ilam University, Ilam, Iran
| | | | - Bernard Prevosto
- INRAE, Aix Marseille Univ., UR RECOVER, Mediterranean Ecosystems and Risks, Aix-en-Provence, France
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16
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Jiang R, Wang M, Chen W, Li X, Balseiro-Romero M, Baveye PC. Ecological risk of combined pollution on soil ecosystem functions: Insight from the functional sensitivity and stability. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113184. [PMID: 31541819 DOI: 10.1016/j.envpol.2019.113184] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/23/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Assessing the ecological risk of combined pollution, especially from a holistic perspective with the consideration of the overarching functions of soil ecosystem, is crucial and beneficial to the improvement of ecological risk assessment (ERA) framework. In this study, four soils with similar physicochemical properties but contrasting heavy metals contamination levels were selected to explore changes in the integrated functional sensitivity (MSI), resistance (MRS) and resilience (MRL) of soil microbial communities subjected to herbicide siduron, based on which the ecological risk of the accumulation of siduron in the four studied soils were evaluated. The results suggested that the microbial biomass carbon, activity of denitrification enzyme and nitrogenase were indicative of MSI and MRS, and the same three parameters plus soil basal respiration were indicative of MRL. Significant dose-effect relationships between siduron residues in soils and MSI, MRS and MRL under combined pollution were observed. Heavy metal polluted soils showed higher sensitivity and lower resistance to the additional disturbance of herbicide siduron due to the lower microbial biomass, while the resilience of heavy metal polluted soils was much higher due to the pre-adaption to the chemical stresses. The quantifiable indicator microbial functional stability was incorporated in the framework of ERA and the results showed that the accumulation of siduron in the studied soils could exhibit potential harm to the integrated functional stability of soil microbial community. Thus, this work provides insights into the application of integrated function of soil microbial community into the framework of ERA.
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Affiliation(s)
- Rong Jiang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meie Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Weiping Chen
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xuzhi Li
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - María Balseiro-Romero
- UMR ECOSYS, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, Thiverval-Grignon, 78850, France; Department of Soil Science and Agricultural Chemistry, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - Philippe C Baveye
- UMR ECOSYS, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, Thiverval-Grignon, 78850, France
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Niu X, Xie W, Zhang J, Hu Q. Biodiversity of Entomopathogenic Fungi in the Soils of South China. Microorganisms 2019; 7:microorganisms7090311. [PMID: 31484332 PMCID: PMC6780753 DOI: 10.3390/microorganisms7090311] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/10/2019] [Accepted: 08/29/2019] [Indexed: 11/23/2022] Open
Abstract
The southern part of China, located in tropical and south subtropical areas has unique natural environments, but the distributions of entomopathogenic fungi (EFs) in the soil are not clear. In this research, 198 soil samples were collected from the four Provinces (Autonomous Region) of South China. The results indicated that a total of 292 fungal isolates were obtained from 176 soil samples. Then, based on the morphological and rDNA-ITS sequences analysis, 213 EFs isolates of 19 species in 12 genera were identified. Furthermore, Purpureocillium lilacinum with 75 isolates was recognized as the absolutely dominant EF species, while Isaria javanica, Metarhizium anisopliae, and Beauveria bassiana (respectively with 29, 26, and 26 isolates) were the richer species. The data also indicated that Guangxi Province has the best EFs diversity with the Shannon–Wiener index (SWI) of 2.29, the soils covered with grass had the best EFs diversity with the 2.14 SWI, while the orchard and fallow land had the lowest SWI of 1.52, which suggested that the diversity of plants and insects on ground, as well as the massive application of broad-spectrum fungicides, affect the EFs diversity in the soil. Finally, the rare species, Nectria mauritiicola and Scopulariopsis brumptii were first reported about their entomopathogenic activities against Bemisia tabaci. Our experiment will give new insights to the understanding of EFs distribution characteristics and their biodiversity conservation.
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Affiliation(s)
- Xiaoyan Niu
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Weiwen Xie
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Jing Zhang
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Qiongbo Hu
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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18
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Assessing the resilience of biodiversity-driven functions in agroecosystems under environmental change. ADV ECOL RES 2019. [DOI: 10.1016/bs.aecr.2019.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Jurburg SD, Nunes I, Stegen JC, Le Roux X, Priemé A, Sørensen SJ, Salles JF. Autogenic succession and deterministic recovery following disturbance in soil bacterial communities. Sci Rep 2017; 7:45691. [PMID: 28383027 PMCID: PMC5382530 DOI: 10.1038/srep45691] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 03/03/2017] [Indexed: 01/23/2023] Open
Abstract
The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given that they are often evaluated over macro-ecological time scales and end-point measurements. In order to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days. The disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response in which surviving taxa increased in abundance; a secondary response phase during which community dynamics slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme diversity and functional redundancy, respond to disturbances like many macro-ecological systems and exhibit path-dependent, autogenic dynamics during secondary succession. These results highlight the role of autogenic factors and successional dynamics in microbial recovery.
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Affiliation(s)
- Stephanie D Jurburg
- Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, Groningen, 9747 AG, The Netherlands
| | - Inês Nunes
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, Denmark
| | - James C Stegen
- Earth and Biological Sciences, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Xavier Le Roux
- Microbial Ecology Center, INRA (UMR 1418), CNRS, Université Lyon1, Université de Lyon, 69622 Villeurbanne, France
| | - Anders Priemé
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, Denmark
| | - Joana Falcão Salles
- Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, Groningen, 9747 AG, The Netherlands
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20
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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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21
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Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy. Appl Environ Microbiol 2016; 82:3525-3536. [PMID: 27060115 DOI: 10.1128/aem.00520-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/30/2016] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. IMPORTANCE In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial communities during and after Superstorm Sandy to provide fine time point resolution of dynamic changes in bacterial composition. This study adds to the current literature by revealing the variation in bacterial community structure during the course of a storm. This study employed high-throughput DNA sequencing, which generated a deep analysis of inter- and intracommunity responses during a significant storm event. This study has highlighted the utility of applying high-throughput sequencing for water quality monitoring purposes, as this approach enabled a more comprehensive investigation of the bacterial community structure. Altogether, these data suggest a drastic restructuring of the stream bacterial community during a storm event and highlight the potential of high-throughput sequencing approaches for assessing the microbiological quality of our environment.
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Pyrosequencing reveals changes in soil bacterial communities after conversion of Yungas forests to agriculture. PLoS One 2015; 10:e0119426. [PMID: 25793893 PMCID: PMC4368548 DOI: 10.1371/journal.pone.0119426] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/13/2015] [Indexed: 11/19/2022] Open
Abstract
The Southern Andean Yungas in Northwest Argentina constitute one of the main biodiversity hotspots in the world. Considerable changes in land use have taken place in this ecoregion, predominantly related to forest conversion to croplands, inducing losses in above-ground biodiversity and with potential impact on soil microbial communities. In this study, we used high-throughput pyrosequencing of the 16S ribosomal RNA gene to assess whether land-use change and time under agriculture affect the composition and diversity of soil bacterial communities. We selected two areas dedicated to sugarcane and soybean production, comprising both short- and long-term agricultural sites, and used the adjacent native forest soils as a reference. Land-use change altered the composition of bacterial communities, with differences between productive areas despite the similarities between both forests. At the phylum level, only Verrucomicrobia and Firmicutes changed in abundance after deforestation for sugarcane and soybean cropping, respectively. In cultivated soils, Verrucomicrobia decreased sharply (~80%), while Firmicutes were more abundant. Despite the fact that local diversity was increased in sugarcane systems and was not altered by soybean cropping, phylogenetic beta diversity declined along both chronosequences, evidencing a homogenization of soil bacterial communities over time. In spite of the detected alteration in composition and diversity, we found a core microbiome resistant to the disturbances caused by the conversion of forests to cultivated lands and few or none exclusive OTUs for each land-use type. The overall changes in the relative abundance of copiotrophic and oligotrophic taxa may have an impact in soil ecosystem functionality. However, communities with many taxa in common may also share many functional attributes, allowing to maintain at least some soil ecosystem services after forest conversion to croplands.
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Kato S, Yoshida R, Yamaguchi T, Sato T, Yumoto I, Kamagata Y. The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium. Front Microbiol 2014; 5:575. [PMID: 25400628 PMCID: PMC4214200 DOI: 10.3389/fmicb.2014.00575] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/13/2014] [Indexed: 11/13/2022] Open
Abstract
Investigation of microbial interspecies interactions is essential for elucidating the function and stability of microbial ecosystems. However, community-based analyses including molecular-fingerprinting methods have limitations for precise understanding of interspecies interactions. Construction of model microbial consortia consisting of defined mixed cultures of isolated microorganisms is an excellent method for research on interspecies interactions. In this study, a model microbial consortium consisting of microorganisms that convert acetate into methane directly (Methanosaeta thermophila) and syntrophically (Thermacetogenium phaeum and Methanothermobacter thermautotrophicus) was constructed and the effects of elevated CO2 concentrations on intermicrobial competition were investigated. Analyses on the community dynamics by quantitative RT-PCR and fluorescent in situ hybridization targeting their 16S rRNAs revealed that high concentrations of CO2 have suppressive effects on the syntrophic microorganisms, but not on the aceticlastic methanogen. The pathways were further characterized by determining the Gibbs free energy changes (ΔG) of the metabolic reactions conducted by each microorganism under different CO2 concentrations. The ΔG value of the acetate oxidation reaction (T. phaeum) under high CO2 conditions became significantly higher than -20 kJ per mol of acetate, which is the borderline level for sustaining microbial growth. These results suggest that high concentrations of CO2 undermine energy acquisition of T. phaeum, resulting in dominance of the aceticlastic methanogen. This study demonstrates that investigation on model microbial consortia is useful for untangling microbial interspecies interactions, including competition among microorganisms occupying the same trophic niche in complex microbial ecosystems.
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Affiliation(s)
- Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido UniversitySapporo, Japan
- Research Center for Advanced Science and Technology, The University of TokyoTokyo, Japan
| | - Rina Yoshida
- Department of Civil and Environmental Engineering, Nagaoka University of TechnologyNagaoka, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of TechnologyNagaoka, Japan
| | - Tomoyuki Sato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido UniversitySapporo, Japan
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