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Zhuo T, Yu K, Chai B, Tang Q, Gao X, Wang J, He L, Lei X, Li Y, Meng Y, Wu L, Chen B. Microplastics increase the microbial functional potential of greenhouse gas emissions and water pollution in a freshwater lake: A metagenomic study. ENVIRONMENTAL RESEARCH 2024; 257:119250. [PMID: 38844031 DOI: 10.1016/j.envres.2024.119250] [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: 01/31/2024] [Revised: 04/18/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
Aquatic ecosystems are being increasingly polluted by microplastics (MPs), which calls for an understanding of how MPs affect microbially driven biogenic element cycling in water environments. A 28-day incubation experiment was conducted using freshwater lake water added with three polymer types of MPs (i.e., polyethylene, polypropylene, polystyrene) separately or in combination at a concentration of 1 items/L. The effects of various MPs on microbial communities and functional genes related to carbon, nitrogen, phosphorus, and sulfur cycling were analyzed using metagenomics. Results showed that Sphingomonas and Novosphingobium, which were indicator taxa (genus level) in the polyethylene treatment group, made the largest functional contribution to biogenic element cycling. Following the addition of MPs, the relative abundances of genes related to methane oxidation (e.g., hdrD, frhB, accAB) and denitrification (napABC, nirK, norB) increased. These changes were accompanied by increased relative abundances of genes involved in organic phosphorus mineralization (e.g., phoAD) and sulfate reduction (cysHIJ), as well as decreased relative abundances of genes involved in phosphate transport (phnCDE) and the SOX system. Findings of this study underscore that MPs, especially polyethylene, increase the potential of greenhouse gas emissions (CO2, N2O) and water pollution (PO43-, H2S) in freshwater lakes at the functional gene level.
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Affiliation(s)
- Tianyu Zhuo
- School of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, China; Collaborative Innovation Center for Intelligent Regulation and Comprehensive Management of Water Resources, School of Water Conservancy and Hydroelectric, Hebei University of Engineering, Handan, 056038, China
| | - Kehong Yu
- School of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Beibei Chai
- Collaborative Innovation Center for Intelligent Regulation and Comprehensive Management of Water Resources, School of Water Conservancy and Hydroelectric, Hebei University of Engineering, Handan, 056038, China; Hebei Key Laboratory of Intelligent Water Conservancy, School of Water Conservancy and Hydroelectric, Hebei University of Engineering, Handan, 056038, China.
| | - Qingfeng Tang
- Beijing Center for Physical & Chemical Analysis, Beijing, 100089, China
| | - Xia Gao
- Beijing Center for Physical & Chemical Analysis, Beijing, 100089, China
| | - Jiamin Wang
- Beijing Center for Physical & Chemical Analysis, Beijing, 100089, China
| | - Lixin He
- Collaborative Innovation Center for Intelligent Regulation and Comprehensive Management of Water Resources, School of Water Conservancy and Hydroelectric, Hebei University of Engineering, Handan, 056038, China
| | - Xiaohui Lei
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China
| | - Yang Li
- School of Energy and Environment, Zhongyuan University of Technology, Zhengzhou, 450007, China
| | - Yuan Meng
- School of Water Conservancy and Hydroelectric Power, Hebei University of Engineering, Handan, 056038, China; School of Materials Science and Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Lifeng Wu
- Hebei Key Laboratory of Intelligent Water Conservancy, School of Water Conservancy and Hydroelectric, Hebei University of Engineering, Handan, 056038, China
| | - Bin Chen
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing, 100875, China; Innovation Center for Water Pollution Control and Water Ecological Remediation, Hebei University of Engineering, Handan, 056038, China.
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2
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Liu X, Yu Y, Yu H, Sarkar B, Zhang Y, Yang Y, Qin S. Nonbiodegradable microplastic types determine the diversity and structure of soil microbial communities: A meta-analysis. ENVIRONMENTAL RESEARCH 2024:119663. [PMID: 39043354 DOI: 10.1016/j.envres.2024.119663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/07/2024] [Accepted: 07/20/2024] [Indexed: 07/25/2024]
Abstract
As an emerging contaminant, microplastics (MPs) have received considerable attention for their potential threat to the soil environment. However, the response of soil bacterial and fungal communities to MPs exposure remains unclear. In this study, we conducted a global meta-analysis of 95 publications and 2,317 observations to assess the effects of nonbiodegradable MP properties and exposure conditions on soil microbial biomass, alpha and beta diversity, and community structure. Our results indicate that MPs increased (p < 0.05) soil active microbial biomass by 42%, with the effect varying with MPs type, exposure concentration, exposure time and soil pH. MPs concentration was identified as the most important factor controlling the response of soil microbial biomass to MPs. MPs addition decreased (p < 0.05) the soil bacterial Shannon and Chao1 indices by 2% and 3%, respectively, but had limited effects (p > 0.05) on soil fungal Shannon and Chao1 indices. The type of MPs and exposure time determined the effects of MPs on bacterial Shannon and Chao1 indices, while the type of MPs and soil pH controlled the response ratios of fungal Shannon and Chao1 indices to MPs. Specifically, soil organic carbon (SOC) was the major factor regulating the response ratio of bacterial alpha diversity index to MPs. The presence of MPs did not affect soil bacterial community structure and beta diversity. Our results highlight that MPs reduced bacterial diversity and richness but increased the soil active microbial biomass, suggesting that MPs could disrupt biogeochemical cycles by promoting the growth of specific microorganisms.
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Affiliation(s)
- Xinhui Liu
- Hebei Provincial Key Laboratory of Soil Ecology, Hebei Provincial Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, Hebei, China; University of Chinese Academy of Sciences, Beijing 100049, Peoples R China
| | - Yongxiang Yu
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Haiyang Yu
- College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Binoy Sarkar
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Yanyan Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuyi Yang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Shuping Qin
- Hebei Provincial Key Laboratory of Soil Ecology, Hebei Provincial Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, Hebei, China.
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3
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Barnett SE, Shade A. Seven years of microbial community metagenomes from temperate soils affected by an ongoing coal seam fire. Microbiol Resour Announc 2024; 13:e0019824. [PMID: 38752760 PMCID: PMC11237453 DOI: 10.1128/mra.00198-24] [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: 02/28/2024] [Accepted: 04/20/2024] [Indexed: 06/12/2024] Open
Abstract
We examined the dynamics of soil microbiomes under heat press disturbance from an underground coal mine fire in Centralia, PA. Here, we present metagenomic sequencing and assembly data from soil microbiomes across seven consecutive years at repeatedly sampled fire-affected sites along with unaffected reference sites.
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Affiliation(s)
- Samuel E. Barnett
- Department of Microbiology, Genetics, and Immunology, Michigan State University, Lansing, Michigan, USA
| | - Ashley Shade
- Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Laboratoire d'Ecologie Microbienne LEM, CNRS UMR5557, INRAE UMR1418, Villeurbanne, France
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4
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Liu W, Guo S, Zhang H, Chen Y, Shao Y, Yuan Z. Effect of Altitude Gradients on the Spatial Distribution Mechanism of Soil Bacteria in Temperate Deciduous Broad-Leaved Forests. Microorganisms 2024; 12:1034. [PMID: 38930416 PMCID: PMC11206066 DOI: 10.3390/microorganisms12061034] [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: 04/17/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
Soil bacteria are an important part of the forest ecosystem, and they play a crucial role in driving energy flow and material circulation. Currently, many uncertainties remain about how the composition and distribution patterns of bacterial communities change along altitude gradients, especially in forest ecosystems with strong altitude gradients in climate, vegetation, and soil properties. Based on dynamic site monitoring of the Baiyun Mountain Forest National Park (33°38'-33°42' N, 111°47'-111°51' E), this study used Illumina technology to sequence 120 soil samples at the site and explored the spatial distribution mechanisms and ecological processes of soil bacteria under different altitude gradients. Our results showed that the composition of soil bacterial communities varied significantly between different altitude gradients, affecting soil bacterial community building by influencing the balance between deterministic and stochastic processes; in addition, bacterial communities exhibited broader ecological niche widths and a greater degree of stochasticity under low-altitude conditions, implying that, at lower altitudes, community assembly is predominantly influenced by stochastic processes. Light was the dominant environmental factor that influenced variation in the entire bacterial community as well as other taxa across different altitude gradients. Moreover, changes in the altitude gradient could cause significant differences in the diversity and community composition of bacterial taxa. Our study revealed significant differences in bacterial community composition in the soil under different altitude gradients. The bacterial communities at low elevation gradients were mainly controlled by stochasticity processes, and bacterial community assembly was strongly influenced by deterministic processes at middle altitudes. Furthermore, light was an important environmental factor that affects differences. This study revealed that the change of altitude gradient had an important effect on the development of the soil bacterial community and provided a theoretical basis for the sustainable development and management of soil bacteria.
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Affiliation(s)
| | | | | | | | - Yizhen Shao
- College of Life Science, Henan Agricultural University, Zhengzhou 450046, China; (W.L.); (S.G.); (H.Z.); (Y.C.)
| | - Zhiliang Yuan
- College of Life Science, Henan Agricultural University, Zhengzhou 450046, China; (W.L.); (S.G.); (H.Z.); (Y.C.)
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5
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Wang QY, Wang QR, Wang TY, Zhang SQ, Yu HW. Impacts of polypropylene microplastics on the distribution of cadmium, enzyme activities, and bacterial community in black soil at the aggregate level. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170541. [PMID: 38290684 DOI: 10.1016/j.scitotenv.2024.170541] [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: 11/16/2023] [Revised: 01/17/2024] [Accepted: 01/27/2024] [Indexed: 02/01/2024]
Abstract
Microplastics (MPs) can co-occur widely with heavy metals in soil. This study intended to investigate the influences of the co-exposure of polyethylene MPs (0.5 %, w/w) and cadmium (Cd) in black soil on the Cd distribution, enzyme activities, and bacterial communities in both bulk soil and different sized soil aggregates (> 1, 0.50-1, 0.25-0.50, and < 0.25 mm aggregates) after a 90-day incubation. Our results showed that the existence of MPs increased the distributions of Cd in >1 mm and < 0.25 mm soil aggregates and decreased its distributions in 0.50-1 mm and 0.25-0.50 mm soil aggregates. About 12.15 %-17.65 % and 9.03 %-11.13 % of Cd were distributed in the exchangeable and oxidizable forms in bulk soil and various sized soil aggregates after the addition of MPs which were higher than those in the only Cd-treated soil (11.17 %-14.72 % and 8.66 %-10.43 %, respectively), while opposite tendency was found for Cd in the reducible form. Urease and β-glucosidase activities in the Cd-treated soils were 1.14-1.18 and 1.07-1.31 times higher than those in the Cd-MPs treated soils. MPs disturbed soil bacterial community at phylum level and increased the bacteria richness in bulk soil. The levels of predicted functional genes which are linked to the biodegradation and metabolism of exogenous substances and soil C and N cycles were altered by the co-exposure of Cd and MPs. The findings of this study could help deepen our knowledge about the responses of soil properties, especially microbial community, to the co-occurrence of MPs and heavy metals in soil.
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Affiliation(s)
- Quan-Ying Wang
- Key Laboratory of Wet Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Qi-Rong Wang
- Key Laboratory of Wet Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Tian-Ye Wang
- Key Laboratory of Wet Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Shao-Qing Zhang
- Key Laboratory of Wet Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Hong-Wen Yu
- Key Laboratory of Wet Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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6
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Zhou X, Xiao C, Zhang B, Chen T, Yang X. Effects of microplastics on carbon release and microbial community in mangrove soil systems. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133152. [PMID: 38056259 DOI: 10.1016/j.jhazmat.2023.133152] [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: 08/24/2023] [Revised: 11/08/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
Mangrove ecosystems are major carbon sink biomes and also a sink of microplastics (MPs). The final enrichment of MPs in sediments may have a significant impact on the microbial community and carbon turnover in the soil. However, the effects of MP pollution on the mangrove soil microbial communities and carbon release remain unknown. Here, we conducted a manipulative incubation experiment by adding MPs to soil at different soil depths to examine the effect of enriched MPs on soil microorganisms and its function (i.e., decomposition of soil carbon). The results showed that the addition of MPs had no significant effect on the microbial diversity and CO2 cumulative emission in the topsoil but significantly increased CO2 release from the subsoil. The promoting effect of polylactide (PLA) on the release of CO2 from the subsoil was stronger than that of polyethylene (PE) and aging PE. In the subsoil, the activity of soil extracellular enzymes related to N acquisition increased with the MP addition, indicating an increase in microbial N deficiency. The subsoil was more sensitive to MPs because of the exacerbated nitrogen limitation. MP addition reduced the microbial diversity of the subsoil and altered soil microbial interactions. The increasing abundance of some microbial taxa, especially bacteria related to the sulfur cycle, indicated more active electron transfer and organic carbon mineralization in the subsoil. Our findings suggest that MP contamination has potential effects on microbial communities, nutrient cycling, and carbon release in mangrove soils that vary depending on soil depth.
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Affiliation(s)
- Xu Zhou
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)
| | - Cunde Xiao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China
| | - Bingwei Zhang
- Zhuhai Branch of State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University at Zhuhai, Zhuhai 519087, China
| | - Tao Chen
- MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Xiaofan Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou).
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7
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Barnett SE, Shade A. Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance. Ecol Lett 2024; 27:e14393. [PMID: 38430049 DOI: 10.1111/ele.14393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 03/03/2024]
Abstract
Long-term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems and their functions. Many critical ecosystem functions, such as biogeochemical cycling, are facilitated by microbial communities. Understanding the functional consequences of microbiome responses to press disturbances requires ongoing observations of the active populations that contribute to functions. This study leverages a 7-year time series of a 60-year-old coal seam fire (Centralia, Pennsylvania, USA) to examine the resilience of soil bacterial microbiomes to a press disturbance. Using 16S rRNA and 16S rRNA gene amplicon sequencing, we assessed the interannual dynamics of the active subset and the 'whole' bacterial community. Contrary to our hypothesis, the whole communities demonstrated greater resilience than active subsets, suggesting that inactive members contributed to overall structural resilience. Thus, in addition to selection mechanisms of active populations, perceived microbiome resilience is also supported by mechanisms of dispersal, persistence, and revival from the local dormant pool.
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Affiliation(s)
- Samuel E Barnett
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
| | - Ashley Shade
- Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, Ecole Nationale Véterinaire de Lyon, Universite Claude Bernard Lyon 1, Villeurbanne, France
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8
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Sun B, Zhu R, Shi Y, Zhang W, Zhou Z, Ma D, Wang R, Dai H, Che C. Effects of coal-fired power plants on soil microbial diversity and community structures. J Environ Sci (China) 2024; 137:206-223. [PMID: 37980009 DOI: 10.1016/j.jes.2023.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 11/20/2023]
Abstract
Long-term deposition of atmospheric pollutants emitted from coal combustion and their effects on the eco-environment have been extensively studied around coal-fired power plants. However, the effects of coal-fired power plants on soil microbial communities have received little attention through atmospheric pollutant deposition and coal-stacking. Here, we collected the samples of power plant soils (PS), coal-stacking soils (CSS) and agricultural soils (AS) around three coal-fired power plants and background control soils (BG) in Huainan, a typical mineral resource-based city in East China, and investigated the microbial diversity and community structures through a high-throughput sequencing technique. Coal-stacking significantly increased (p < 0.05) the contents of total carbon, total nitrogen, total sulfur and Mo in the soils, whereas the deposition of atmospheric pollutants enhanced the levels of V, Cu, Zn and Pb. Proteobacteria, Actinobacteria, Thaumarchaeota, Thermoplasmata, Ascomycota and Basidiomycota were the dominant taxa in all soils. The bacterial community showed significant differences (p < 0.05) among PS, CSS, AS and BG, whereas archaeal and fungal communities showed significant differences (p < 0.01) according to soil samples around three coal-fired power plants. The predominant environmental variables affecting soil bacterial, archaeal and fungal communities were Mo-TN-TS, Cu-V-Mo, and organic matter (OM)-Mo, respectively. Certain soil microbial genera were closely related to multiple key factors associated with stacking coal and heavy metal deposition from power plants. This study provided useful insight into better understanding of the relationships between soil microbial communities and long-term disturbances from coal-fired power plants.
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Affiliation(s)
- Bowen Sun
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Renbin Zhu
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China.
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 450046, China
| | - Wanying Zhang
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Zeming Zhou
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Dawei Ma
- State Grid Anhui Electric Power Research Institute, Hefei 230601, China
| | - Runfang Wang
- State Grid Anhui Electric Power Research Institute, Hefei 230601, China
| | - Haitao Dai
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Chenshuai Che
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
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9
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Ning D, Wang Y, Fan Y, Wang J, Van Nostrand JD, Wu L, Zhang P, Curtis DJ, Tian R, Lui L, Hazen TC, Alm EJ, Fields MW, Poole F, Adams MWW, Chakraborty R, Stahl DA, Adams PD, Arkin AP, He Z, Zhou J. Environmental stress mediates groundwater microbial community assembly. Nat Microbiol 2024; 9:490-501. [PMID: 38212658 DOI: 10.1038/s41564-023-01573-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.
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Affiliation(s)
- Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yajiao Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yupeng Fan
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Jianjun Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Ping Zhang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Daniel J Curtis
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Renmao Tian
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Lauren Lui
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Terry C Hazen
- Department of Earth and Planetary Sciences, Bredesen Center, Department of Civil and Environmental Sciences, Center for Environmental Biotechnology, and Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Eric J Alm
- Department of Biological Engineering, Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew W Fields
- Center for Biofilm Engineering and Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Farris Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Paul D Adams
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Adam P Arkin
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
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10
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Bandla A, Akhtar H, Lupascu M, Sukri RS, Swarup S. Elevated methane flux in a tropical peatland post-fire is linked to depth-dependent changes in peat microbiome assembly. NPJ Biofilms Microbiomes 2024; 10:8. [PMID: 38253600 PMCID: PMC10803758 DOI: 10.1038/s41522-024-00478-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Fires in tropical peatlands extend to depth, transforming them from carbon sinks into methane sources and severely limit forest recovery. Peat microbiomes influence carbon transformations and forest recovery, yet our understanding of microbiome shifts post-fire is currently limited. Our previous study highlighted altered relationships between the peat surface, water table, aboveground vegetation, and methane flux after fire in a tropical peatland. Here, we link these changes to post-fire shifts in peat microbiome composition and assembly processes across depth. We report kingdom-specific and depth-dependent shifts in alpha diversity post-fire, with large differences at deeper depths. Conversely, we found shifts in microbiome composition across all depths. Compositional shifts extended to functional groups involved in methane turnover, with methanogens enriched and methanotrophs depleted at mid and deeper depths. Finally, we show that community shifts at deeper depths result from homogeneous selection associated with post-fire changes in hydrology and aboveground vegetation. Collectively, our findings provide a biological basis for previously reported methane fluxes after fire and offer new insights into depth-dependent shifts in microbiome assembly processes, which ultimately underlie ecosystem function predictability and ecosystem recovery.
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Affiliation(s)
- Aditya Bandla
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Hasan Akhtar
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Department of Geography, National University of Singapore, Singapore, Singapore
- School of Liberal Arts and Sciences, RV University, Bengaluru, Karnataka, India
| | - Massimo Lupascu
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Department of Geography, National University of Singapore, Singapore, Singapore
| | - Rahayu Sukmaria Sukri
- Institute for Biodiversity and Environmental Research, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Sanjay Swarup
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore.
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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11
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Fang C, He Y, Yang Y, Fu B, Pan S, Jiao F, Wang J, Yang H. Laboratory tidal microcosm deciphers responses of sediment archaeal and bacterial communities to microplastic exposure. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131813. [PMID: 37339576 DOI: 10.1016/j.jhazmat.2023.131813] [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: 04/03/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023]
Abstract
Microplastics (MPs) are 1-5 mm plastic particles that are serious global contaminants distributed throughout marine ecosystems. However, their impact on intertidal sediment microbial communities is poorly understood. In this study, we conducted a 30-day laboratory tidal microcosm experiment to investigate the effects of MPs on microbial communities. Specifically, we used the biodegradable polymers polylactic acid (PLA) and polybutylene succinate (PBS), as well as the conventional polymers polyethylene terephthalate (PET), polycarbonate (PC), and polyethylene (PE). Treatments with different concentrations (1-5%, w/w) of PLA- and PE-MPs were also included. We analyzed taxonomic variations in archaeal and bacterial communities using 16S rRNA high-throughput sequencing. PLA-MPs at concentrations of 1% (w/w) rapidly altered microbiome composition. Total organic carbon and nitrite nitrogen were the key physicochemical factors and urease was the major enzyme shaping MP-exposed sediment microbial communities. Stochastic processes predominated in microbial assembly and the addition of biodegradable MPs enhanced the contribution of ecological selections. The major keystone taxa of archaea and bacteria were Nitrososphaeria and Alphaproteobacteria, respectively. MPs exposure had less effect on archaeal functions while nitrogen cycling decreased in PLA-MPs treatments. These findings expanded the current understanding of the mechanism and pattern that MPs affect sediment microbial communities.
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Affiliation(s)
- Chang Fang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Yinglin He
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Yuting Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Bing Fu
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Sentao Pan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Fang Jiao
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Jun Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Huirong Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China.
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12
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Huang S, Guo T, Feng Z, Li B, Cai Y, Ouyang D, Gustave W, Ying C, Zhang H. Polyethylene and polyvinyl chloride microplastics promote soil nitrification and alter the composition of key nitrogen functional bacterial groups. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131391. [PMID: 37043864 DOI: 10.1016/j.jhazmat.2023.131391] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023]
Abstract
Microplastics (MPs) contamination in soils seriously threatens agroecosystems globally. However, very few studies have been done on the effects of MPs on the soil nitrogen cycle and related functional microorganisms. To assess MP's impact on the soil nitrogen cycle and related functional bacteria, we carried out a one-month soil incubation experiment using typical acidic soil. The soil was amended with alfalfa meal and was spiked with 1% and 5% (mass percentage) of low-density polyethylene (LDPE) and polyvinyl chloride (PVC) MPs. Our results showed that both LDPE and PVC addition significantly increased soil nitrification rate and nitrate reductase activity, which could further promote soil denitrification. The relative abundance of diazotrophs, ammonium oxidizing, and denitrifying bacterial groups were significantly altered with MPs addition. Moreover, the MPs treatments greatly enhanced denitrifying bacteria richness. Redundancy analysis showed that nitrate reductase activity was the most significant factor affecting the soil functional bacterial community. Correlation analysis shows that Nitrosospira genus might be for the improvement of soil nitrification rate. Our results implied that MPs exposure could significantly affect the soil nitrogen cycling in farmland ecosystems by influencing essential nitrogen functional microorganisms and related enzymatic activities.
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Affiliation(s)
- Shunyin Huang
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Ting Guo
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Zhen Feng
- School of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Baochen Li
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Yimin Cai
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Da Ouyang
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Williamson Gustave
- School of Chemistry, Environmental & Life Sciences, University of The Bahamas, Nassau, New Providence, Bahamas
| | - Chengfei Ying
- School of Humanities and Law, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Haibo Zhang
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China.
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13
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Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Prokaryotic Life Associated with Coal-Fire Gas Vents Revealed by Metagenomics. BIOLOGY 2023; 12:biology12050723. [PMID: 37237535 DOI: 10.3390/biology12050723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]
Abstract
The natural combustion of underground coal seams leads to the formation of gas, which contains molecular hydrogen and carbon monoxide. In places where hot coal gases are released to the surface, specific thermal ecosystems are formed. Here, 16S rRNA gene profiling and shotgun metagenome sequencing were employed to characterize the taxonomic diversity and genetic potential of prokaryotic communities of the near-surface ground layer near hot gas vents in an open quarry heated by a subsurface coal fire. The communities were dominated by only a few groups of spore-forming Firmicutes, namely the aerobic heterotroph Candidatus Carbobacillus altaicus, the aerobic chemolitoautotrophs Kyrpidia tusciae and Hydrogenibacillus schlegelii, and the anaerobic chemolithoautotroph Brockia lithotrophica. Genome analysis predicted that these species can obtain energy from the oxidation of hydrogen and/or carbon monoxide in coal gases. We assembled the first complete closed genome of a member of uncultured class-level division DTU015 in the phylum Firmicutes. This bacterium, 'Candidatus Fermentithermobacillus carboniphilus' Bu02, was predicted to be rod-shaped and capable of flagellar motility and sporulation. Genome analysis showed the absence of aerobic and anaerobic respiration and suggested chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, N-acetylglucosamine, and tricarboxylic acid cycle intermediates. Bu02 bacterium probably plays the role of a scavenger, performing the fermentation of organics formed by autotrophic Firmicutes supported by coal gases. A comparative genome analysis of the DTU015 division revealed that most of its members have a similar lifestyle.
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Affiliation(s)
- Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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14
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Shade A. Microbiome rescue: directing resilience of environmental microbial communities. Curr Opin Microbiol 2023; 72:102263. [PMID: 36657335 DOI: 10.1016/j.mib.2022.102263] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/30/2022] [Accepted: 12/18/2022] [Indexed: 01/18/2023]
Abstract
Earth's climate crisis threatens to disrupt ecosystem services and destabilize food security. Microbiome management will be a crucial component of a comprehensive strategy to maintain stable microbinal functions for ecosystems and plants in the face of climate change. Microbiome rescue is the directed, community-level recovery of microbial populations and functions lost after an environmental disturbance. Microbiome rescue aims to propel a resilience trajectory for community functions. Rescue can be achieved via demographic, functional, adaptive, or evolutionary recovery of disturbance-sensitive populations. Various ecological mechanisms support rescue, including dispersal, reactivation from dormancy, functional redundancy, plasticity, and diversification, and these mechanisms can interact. Notably, controlling microbial reactivation from dormancy is a potentially fruitful but underexplored target for rescue.
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Affiliation(s)
- Ashley Shade
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, École Centrale de Lyon, Ampère, UMR5005, 69134 Ecully cedex, France; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; The Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA; Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI 48824, USA; The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA.
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15
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Hou Z, Zhou Q, Mo F, Kang W, Ouyang S. Enhanced carbon emission driven by the interaction between functional microbial community and hydrocarbons: An enlightenment for carbon cycle. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161402. [PMID: 36638996 DOI: 10.1016/j.scitotenv.2023.161402] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 06/17/2023]
Abstract
Soil microbial communities are usually regarded as one of the key players in the global element cycling. Moreover, an important consequence of oil contamination altering the structure of microbial communities is likely to result in an increased carbon emission. However, understanding of the complex interactions between environmental factors and biological communities is clearly lagging behind. Here it showed that the flux of carbon emissions increased in oil-contaminated soils, up to 13.64 g C·(kg soil)-1·h-1. This phenomenon was mainly driven by the enrichment of rare degrading microorganisms (e.g., Methylosinus, Marinobacter, Pseudomonas, Alcanivorax, Yeosuana, Halomonas and Microbulbifer) in the aerobic layer, rather than the anaerobic layer, which is more conducive to methane formation. In addition, petroleum hydrocarbons and environmental factors are equally important in shaping the structure of microbial communities (the ecological stability) and functional traits (e.g., fatty acid metabolism, lipid metabolism and amino acid metabolism) due to the different ecological sensitivities of microorganisms. Thus, it can be believed that the variability of rare hydrocarbon degrading microorganisms is of greater concern than changes in dominant microorganisms in oil-contaminated soil. Undoubtedly, this study could reveal the unique characterization of bacterial communities that mediate carbon emission and provide evidence for understanding the conversion from carbon stores to carbon gas release in oil-contaminated soils.
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Affiliation(s)
- Zelin Hou
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Carbon Neutrality Science Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Qixing Zhou
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Carbon Neutrality Science Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Fan Mo
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Carbon Neutrality Science Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Weilu Kang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Carbon Neutrality Science Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Shaohu Ouyang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Carbon Neutrality Science Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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16
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Wang Z, Li J, Ma L, Liu X, Wei H, Xiao Y, Tao S. Metagenomic Sequencing Identified Specific Bacteriophage Signature Discriminating between Healthy and Diarrheal Neonatal Piglets. Nutrients 2023; 15:nu15071616. [PMID: 37049457 PMCID: PMC10097093 DOI: 10.3390/nu15071616] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Neonatal diarrhea is one of the most severe diseases in human beings and pigs, leading to high mortality and growth faltering. Gut microbiome-related studies mostly focus on the relationship between bacteria and neonatal diarrhea onset, and no research study has investigated the role of the gut virome in neonatal diarrhea. Here, using metagenomic sequencing, we characterized the fecal viral community of diarrheal and healthy neonatal piglets. We found that the viral community of diarrheal piglets showed higher individual heterogeneity and elevated abundance of Myoviridae. By predicting the bacterial host of the identified viral genomes, phages infecting Proteobacteria, especially E. coli, were the dominant taxa in neonatal diarrheal piglets. Consistent with this, the antibiotic resistance gene of E. coli origin was also enriched in neonatal diarrheal piglets. Finally, we established a random forest model to accurately discriminate between neonatal diarrheal piglets and healthy controls and identified genus E. coli- and genus listeria-infecting bacteriophages, including psa and C5 viruses, as key biomarkers. In conclusion, we provide the first glance of viral community and function characteristics in diarrheal and healthy neonatal piglets. These findings expand our understanding of the relationship among phages, bacteria and diarrhea, and may facilitate the development of therapeutics for the prevention and treatment of neonatal diarrhea.
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17
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Luo L, Wang P, Wang D, Shi X, Zhang J, Zhao Z, Zeng J, Liao J, Zhang Z, Liu Y. Rhodopseudomonas palustris PSB06 agent enhance pepper yield and regulating the rhizosphere microecological environment. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2023.1125538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Abstract
The Rhodopseudomonas palustris (R. palustris) PSB06 can promote crop growth, as it maybe regulates microbial communities in plant root soil, soil physicochemical properties, thus creating a favorable habitat for the crop growth. However, there are few studies on the yields and rhizosphere microbial community of R. palustris PSB06 agent. In the study, the high-throughput sequencing was used to study the changes of rhizosphere soil bacterial community after PSB06 treatment. The results indicated R. palustris PSB06 agent increased the pepper yield by 33.45% when compared to control group, with better effect than other treatments. And it also significantly increased soil nitrogen concentration. R. palustris PSB06 agent had improved pepper rhizosphere bacterial α diversity and changed the community structure. Acidobacteria, Proteobacteria, Actinomycetes and Firmicutes were dominant phyla in all the pepper rhizosphere soil samples. The results showed that soil bacterial community were significantly positively correlated with pH (R = 0.8537, P = 0.001) and total nitrogen (R = 0.4347, P = 0.003). The nine significantly enriched OTU in R.palustris PSB06 treatment (PB) group belong to Nitrososphaera (OTU_109, OTU_14, OTU_18, OTU_8), Lysobacter (OTU_2115, OTU_13), Arenimonas (OTU_26), Luteimonas (OTU_49), and Ramlibacter (OTU_70) were significantly positively correlated with the total yield of pepper (R > 0.5, P < 0.05). Overall, our results provide a theoretical basis for studying the microbial regulation of R.palustris PSB06 on rhizosphere soil.
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18
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Lee SH, Kang HJ, Kim Y, Kim NK, Park HD. Different contribution of exoelectrogens in methanogenesis via direct interspecies electron transfer (DIET) by the different substrate in continuous anaerobic bioreactor. BIORESOURCE TECHNOLOGY 2022; 364:128115. [PMID: 36252764 DOI: 10.1016/j.biortech.2022.128115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Direct interspecies electron transfer (DIET) is a syntrophic mechanism for electron transfer between exo- and endoelectrogens. Previous studies have demonstrated that methanogenesis performance was significantly improved via the DIET mechanism through conductive materials (CMs) under batch conditions with a single substrate, while that under continuous condition is still under investigation. To investigate how the DIET via CM on methanogenesis performance was changed in response to the different substrates (acetate versus glucose)-fed in continuous anaerobic bioreactors, continuous bioreactors were operated by cross-feeding with acetate and glucose. Acetate-fed conditions showed 0.40 day shorten lagtime, 1.88- and 1.22-folds higher methane production rate, and ultimate methane production than glucose-fed conditions, respectively. Burkholderiaceae- and Anaerolineaceae-related exo-electrogenic populations were enriched with low abundance of Geobacter species in batch reactors. Furthermore, influent substrates affected the distribution of the enriched populations. Taken together, the results suggested that different syntrophic associations contributed methane production by DIET in continuous bioreactors.
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Affiliation(s)
- Sang-Hoon Lee
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul 02841, South Korea
| | - Hyun-Jin Kang
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul 02841, South Korea
| | - Yonghoon Kim
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul 02841, South Korea
| | - Na-Kyung Kim
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul 02841, South Korea
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul 02841, South Korea.
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19
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Chen M, Bi M, Nie W, Chen Y. New insight into ammonium removal in riverbanks under the exposure of microplastics. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129725. [PMID: 35963085 DOI: 10.1016/j.jhazmat.2022.129725] [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: 07/10/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Riverbanks play the key role in ammonium removal from runoff entering river. Currently, microplastics (MPs) are frequently detected in riverbanks receiving urban and agricultural runoff. Nevertheless, the effect of MPs accumulation on ammonium removal in riverbanks is still unknown. We utilized sediment flow-through reactors to investigate the impact and mechanism of MPs accumulation on ammonium removal in riverbanks. These results revealed that MPs accumulation decreased ammonium removal in sediment by 8.2 %-12.8 % resulting from the reduction in nitrifier abundance (Nitrososphaera and Nitrososphaeraceae) and genes encoding ammonium and hydroxylamine oxidation (amoA, amoB, amoC, and hao) by MPs accumulation. Furthermore, MPs accumulation decreased the substrate and gene abundance of hydroxylamine oxidation process to reduce N2O emission (16.3 %-34.3 %). Notably, mathematic model verified that sediment physical properties changed by MPs accumulation were direct factors affecting ammonium removal in riverbank. It was suggested that both the biotoxicity of MPs and sediment physical properties should be considered in the ammonium removal process. To summarize, this study for the first time comprehensively clarifies the impact of MPs on the ammonium removal capacity of riverbanks, and provides information for taking measures to protect the ecological function of the riverbank and river ecosystem from MPs and ammonium pollution.
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Affiliation(s)
- Mengli Chen
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of education, Chongqing University, Chongqing 400045, China
| | - Mohan Bi
- Institute of Biology, Free University of Berlin, Berlin, Germany
| | - Wenbo Nie
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of education, Chongqing University, Chongqing 400045, China
| | - Yi Chen
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of education, Chongqing University, Chongqing 400045, China.
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20
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Chakraborty A, Rattray JE, Drake SS, Matthews S, Li C, Jørgensen BB, Hubert CRJ. Metabolic responses of thermophilic endospores to sudden heat-induced perturbation in marine sediment samples. Front Microbiol 2022; 13:958417. [PMID: 36033870 PMCID: PMC9411986 DOI: 10.3389/fmicb.2022.958417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Microbially mediated processes in a given habitat tend to be catalyzed by abundant populations that are ecologically adapted to exploit specific environmental characteristics. Typically, metabolic activities of rare populations are limited but may be stimulated in response to acute environmental stressors. Community responses to sudden changes in temperature and pressure can include suppression and activation of different populations, but these dynamics remain poorly understood. The permanently cold ocean floor hosts countless low-abundance microbes including endospores of thermophilic bacteria. Incubating sediments at high temperature resuscitates viable spores, causing the proliferation of bacterial populations. This presents a tractable system for investigating changes in a microbiome's community structure in response to dramatic environmental perturbations. Incubating permanently cold Arctic fjord sediments at 50°C for 216 h with and without volatile fatty acid amendment provoked major changes in community structure. Germination of thermophilic spores from the sediment rare biosphere was tracked using mass spectrometry-based metabolomics, radiotracer-based sulfate reduction rate measurements, and high-throughput 16S rRNA gene sequencing. Comparing community similarity at different intervals of the incubations showed distinct temporal shifts in microbial populations, depending on organic substrate amendment. Metabolite patterns indicated that amino acids and other sediment-derived organics were decomposed by fermentative Clostridia within the first 12–48 h. This fueled early and late phases of exponential increases in sulfate reduction, highlighting the cross-feeding of volatile fatty acids as electron donors for different sulfate-reducing Desulfotomaculia populations. The succession of germinated endospores triggered by sudden exposure to high temperature and controlled by nutrient availability offers a model for understanding the ecological response of dormant microbial communities following major environmental perturbations.
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Affiliation(s)
- Anirban Chakraborty
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
- *Correspondence: Anirban Chakraborty
| | - Jayne E. Rattray
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Sienna S. Drake
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Stuart Matthews
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Bo Barker Jørgensen
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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21
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Huo Y, Dijkstra FA, Possell M, Singh B. Ecotoxicological effects of plastics on plants, soil fauna and microorganisms: A meta-analysis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 310:119892. [PMID: 35932895 DOI: 10.1016/j.envpol.2022.119892] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/29/2022] [Accepted: 07/31/2022] [Indexed: 01/10/2023]
Abstract
The interactions of plastics and soil organisms are complex and inconsistent observations on the effects of plastics have been made in published studies. In this study, we assessed the effects of plastic exposure on plants, fauna and microbial communities, with a meta-analysis. Using a total of 2936 observations from 140 publications, we analysed how responses in plants, soil fauna and microorganisms depended on the plastic concentration, size, type, species and exposure media. We found that overall plastics caused substantial detrimental effects to plants and fauna, but less so to microbial diversity and richness. Plastic concentration was one of the most important factors explaining variations in plant and faunal responses. Larger plastics (>1 μm) caused unfavourable changes to plant growth, germination and oxidative stress, while nanoplastics (NPs; ≤ 1 μm) only increased oxidative stress. On the contrary, there was a clear trend showing that small plastics adversely affected fauna reproduction, survival and locomotion than large plastics. Plant responses were indifferent to plastic type, with most studies conducted using polyethylene (PE) and polystyrene (PS) plastics, but soil fauna were frequently more sensitive to PS than to PE exposure. Plant species played a vital role in some parameters, with the effects of plastics being considerably greater on vegetable plants than on cereal plants.
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Affiliation(s)
- Yuxin Huo
- Biomedical Building, 3 Central Ave, School of Life and Environmental Sciences, University of Sydney, Eveleigh, Sydney, NSW, 2015, Australia.
| | - Feike A Dijkstra
- Biomedical Building, 3 Central Ave, School of Life and Environmental Sciences, University of Sydney, Eveleigh, Sydney, NSW, 2015, Australia
| | - Malcolm Possell
- Biomedical Building, 3 Central Ave, School of Life and Environmental Sciences, University of Sydney, Eveleigh, Sydney, NSW, 2015, Australia
| | - Balwant Singh
- Biomedical Building, 3 Central Ave, School of Life and Environmental Sciences, University of Sydney, Eveleigh, Sydney, NSW, 2015, Australia
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22
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Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential. THE ISME JOURNAL 2022; 16:1853-1863. [PMID: 35430593 PMCID: PMC9213548 DOI: 10.1038/s41396-022-01232-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/06/2022] [Accepted: 03/28/2022] [Indexed: 12/14/2022]
Abstract
Increasing wildfire severity, which is common throughout the western United States, can have deleterious effects on plant regeneration and large impacts on carbon (C) and nitrogen (N) cycling rates. Soil microbes are pivotal in facilitating these elemental cycles, so understanding the impact of increasing fire severity on soil microbial communities is critical. Here, we assess the long-term impact of high-severity fires on the soil microbiome. We find that high-severity wildfires result in a multi-decadal (>25 y) recovery of the soil microbiome mediated by concomitant differences in aboveground vegetation, soil chemistry, and microbial assembly processes. Our results depict a distinct taxonomic and functional successional pattern of increasing selection in post-fire soil microbial communities. Changes in microbiome composition corresponded with changes in microbial functional potential, specifically altered C metabolism and enhanced N cycling potential, which related to rates of potential decomposition and inorganic N availability, respectively. Based on metagenome-assembled genomes, we show that bacterial genomes enriched in our earliest site (4 y since fire) harbor distinct traits such as a robust stress response and a high potential to degrade pyrogenic, polyaromatic C that allow them to thrive in post-fire environments. Taken together, these results provide a biological basis for previously reported process rate measurements and explain the temporal dynamics of post-fire biogeochemistry, which ultimately constrains ecosystem recovery.
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Wong OWH, Lam AMW, Or BPN, Mo FYM, Shea CKS, Lai KYC, Ma SL, Hung SF, Chan S, Kwong TNY, Wong S, Leung PWL. Disentangling the relationship of gut microbiota, functional gastrointestinal disorders and autism: a case-control study on prepubertal Chinese boys. Sci Rep 2022; 12:10659. [PMID: 35739175 PMCID: PMC9225987 DOI: 10.1038/s41598-022-14785-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/10/2022] [Indexed: 12/19/2022] Open
Abstract
Emerging evidence of an altered gut microbiome in autism spectrum disorder (ASD) suggests a pathomechanism through the gut-brain axis despite the inconsistent microbiome profile reported across studies. One of the knowledge gaps in the existing ASD microbiota studies is the lack of systematic exploration of the role of comorbid functional gastrointestinal disorder (FGID) in the association of ASD and altered gut microbiome. Consequently, 92 ASD and 112 age-matched typically developing (TD) boys were profiled on general psychopathology, FGID status by Rome IV classification, and gut microbiota using 16S ribosomal RNA amplicon sequencing at the V4 hypervariable region. Compared to TD, a significant decrease in the within-sample abundance of taxa was observed in ASD, regardless of FGID status. The microbiota of ASD FGID+ and ASD FGID- clustered apart from the TD groups. The microbiota of ASD FGID+ also showed qualitative differences from that of ASD FGID- and had the highest-level Firmicutes: Bacteroidetes ratio, which was paralleled by elevated levels of anxiety and overall psychopathology. The altered gastrointestinal microbiota composition in ASD appeared to be independent of comorbid FGID. Further studies should address how FGID may mediate neuropsychiatric symptoms in ASD through inflammation along the microbiota-gut-brain axis.
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Affiliation(s)
- Oscar W H Wong
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China.
| | - Angela M W Lam
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China
| | - Brian P N Or
- Department of Psychiatry, Tai Po Hospital, Hong Kong, China
| | - Flora Y M Mo
- Department of Psychiatry, Alice Ho Miu Ling Nethersole Hospital, Hong Kong, China
| | - Caroline K S Shea
- Department of Psychiatry, Alice Ho Miu Ling Nethersole Hospital, Hong Kong, China
| | - Kelly Y C Lai
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China
| | - Suk Ling Ma
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China
| | - Se Fong Hung
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China
| | - Sandra Chan
- Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong, China
| | - Thomas N Y Kwong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Patrick W L Leung
- Department of Psychology, The Chinese University of Hong Kong, Hong Kong, China
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24
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Li P, Zhang J, Wang S, Zhang P, Chen W, Ding S, Xi J. Changes in the Distribution Preference of Soil Microbial Communities During Secondary Succession in a Temperate Mountain Forest. Front Microbiol 2022; 13:923346. [PMID: 35783407 PMCID: PMC9247583 DOI: 10.3389/fmicb.2022.923346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/02/2022] [Indexed: 11/18/2022] Open
Abstract
Soil microbes play a crucial role in a forest ecosystem. However, whether the distribution of bacteria and fungi in different forest succession stages is random or following ecological specialization remains to be further studied. In the present study, we characterized soil bacterial and fungal communities to determine their distribution preference, with different succession communities in a temperate mountain forest. The Kruskal–Wallis method was used to analyze structural differences between bacterial and fungal communities in different succession processes. The specificity of soil microbial distribution in a secondary forest was studied by network analysis. The torus-translation test was used to analyze the species distribution preference of soil microbes in different succession stages. Results showed that the species composition of soil bacteria and fungi differed significantly in different succession processes. The modularity index of fungi (0.227) was higher than that of bacteria (0.080). Fungi (54.47%) had specific preferences than bacteria (49.95%) with regard to forests in different succession stages. Our work suggests that the distribution pattern of most soil microbes in a temperate mountain forest was not random but specialized in temperate mountain forests. Different microbes showed different distribution preferences. Fungi were more sensitive than bacteria during secondary succession in a temperate mountain forest. In addition, microbe–environment relations varied during secondary succession. Our results provided new insight into the mechanism through which complex soil microbial communities responded to changes in forest community succession.
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Affiliation(s)
- Peikun Li
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Henan University, Ministry of Education, Kaifeng, China
- College of Geography and Environmental Science, Henan University, Kaifeng, China
| | - Jian Zhang
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Henan University, Ministry of Education, Kaifeng, China
- College of Geography and Environmental Science, Henan University, Kaifeng, China
| | - Senlin Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Panpan Zhang
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Henan University, Ministry of Education, Kaifeng, China
- College of Geography and Environmental Science, Henan University, Kaifeng, China
| | - Wenju Chen
- College of Resources and Environment Sciences, Henan Agricultural University, Zhengzhou, China
| | - Shengyan Ding
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Henan University, Ministry of Education, Kaifeng, China
- College of Geography and Environmental Science, Henan University, Kaifeng, China
- *Correspondence: Shengyan Ding,
| | - Jingjing Xi
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
- Jingjing Xi,
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25
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Izabel-Shen D, Li S, Luo T, Wang J, Li Y, Sun Q, Yu CP, Hu A. Repeated introduction of micropollutants enhances microbial succession despite stable degradation patterns. ISME COMMUNICATIONS 2022; 2:48. [PMID: 37938643 PMCID: PMC9723708 DOI: 10.1038/s43705-022-00129-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 05/28/2023]
Abstract
The increasing-volume release of micropollutants into natural surface waters has raised great concern due to their environmental accumulation. Persisting micropollutants can impact multiple generations of organisms, but their microbially-mediated degradation and their influence on community assembly remain understudied. Here, freshwater microbes were treated with several common micropollutants, alone or in combination, and then transferred every 5 days to fresh medium containing the same micropollutants to mimic the repeated exposure of microbes. Metabarcoding of 16S rRNA gene makers was chosen to study the succession of bacterial assemblages following micropollutant exposure. The removal rates of micropollutants were then measured to assess degradation capacity of the associated communities. The degradation of micropollutants did not accelerate over time but altered the microbial community composition. Community assembly was dominated by stochastic processes during early exposure, via random community changes and emergence of seedbanks, and deterministic processes later in the exposure, via advanced community succession. Early exposure stages were characterized by the presence of sensitive microorganisms such as Actinobacteria and Planctomycetes, which were then replaced by more tolerant bacteria such as Bacteroidetes and Gammaproteobacteria. Our findings have important implication for ecological feedback between microbe-micropollutants under anthropogenic climate change scenarios.
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Affiliation(s)
- Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Shuang Li
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Environmental Microbiology, UFZ, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Tingwei Luo
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yan Li
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Sun
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- Graduate Institute of Environmental Engineering, National Taiwan University, Taipei, 106, Taiwan
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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26
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Drivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet. NPJ Biofilms Microbiomes 2022; 8:36. [PMID: 35508464 PMCID: PMC9068720 DOI: 10.1038/s41522-022-00296-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 03/31/2022] [Indexed: 11/09/2022] Open
Abstract
It is difficult to disentangle the many variables (e.g. internal or external cues and random events) that shape the microbiota in the gastrointestinal tract of any living species. Ecological assembly processes applied to microbial communities can elucidate these drivers. In our study, farmed Atlantic cod (Gadus morhua) were fed a diet of 10% macroalgae supplement (Ulva rigida [ULVA] or Ascophyllum nodosum [ASCO] or a non-supplemented control diet [CTRL]) over 12 weeks. We determined the influence of ecological assembly processes using a suite of null-modelling tools. We observed dissimilarity in the abundance of common OTUs over time, which was driven by deterministic assembly. The CTRL samples showed selection as a critical assembly process. While dispersal limitation was a driver of the gut microbiome for fish fed the macroalgae supplemented diet at Week 12 (i.e., ASCO and ULVA). Fish from the ASCO grouping diverged into ASCO_N (normal) and ASCO_LG (lower growth), where ASCO_LG individuals found the diet unpalatable. The recruitment of new taxa overtime was altered in the ASCO_LG fish, with the gut microbiome showing phylogenetic underdispersion (nepotistic species recruitment). Finally, the gut microbiome (CTRL and ULVA) showed increasing robustness to taxonomic disturbance over time and lower functional redundancy. This study advances our understanding of the ecological assembly and succession in the hindgut of juvenile Atlantic cod across dietary treatments. Understanding the processes driving ecological assembly in the gut microbiome, in fish research specifically, could allow us to manipulate the microbiome for improved health or resilience to disease for improved aquaculture welfare and production.
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27
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Bintarti AF, Kearns PJ, Sulesky-Grieb A, Shade A. Abiotic Treatment to Common Bean Plants Results in an Altered Endophytic Seed Microbiome. Microbiol Spectr 2022; 10:e0021021. [PMID: 35377190 PMCID: PMC9045313 DOI: 10.1128/spectrum.00210-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 03/10/2022] [Indexed: 11/30/2022] Open
Abstract
There has been a growing interest in the seed microbiome due to its important role as an end and starting point of plant microbiome assembly that can have consequences for plant health. However, the effect of abiotic conditions on the seed microbial community remains unknown. We performed a pilot study in a controlled growth chamber to investigate how the endophytic seed microbiome of the common bean (Phaseolus vulgaris L. [var. Red Hawk]) was altered under abiotic treatments relevant for crop management with changing climate. Bean plants were subjected to one of three treatments: 66% water withholding to simulate mild drought, 50% Hoagland nutrient solution to simulate fertilization, or control with sufficient water and baseline nutrition. We performed 16S rRNA gene amplicon sequencing and Internal Transcribed Spacer 1 (ITS1) amplicon sequencing of the endophytic DNA to assess seed bacterial/archaeal and fungal community structure, respectively. We found that variability in the seed microbiome structure was high, while α-diversity was low, with tens of taxa present. Water withholding and nutrient addition significantly altered the seed microbiome structure for bacterial/archaeal communities compared to the control, and each treatment resulted in a distinct microbiome structure. Conversely, there were no statistically supported differences in the fungal microbiome across treatments. These promising results suggest that further investigation is needed to better understand abiotic or stress-induced changes in the seed microbiome, the mechanisms that drive those changes, and their implications for the health and stress responses of the next plant generation. IMPORTANCE Seed microbiome members initiate the assembly of plant-associated microbial communities, but the environmental drivers of endophytic seed microbiome composition are unclear. Here, we exposed plants to short-term drought and fertilizer treatments during early vegetative growth and quantified the microbiome composition of the seeds that were ultimately produced. We found that seeds produced by plants stressed by water limitation or receiving nutrient addition had statistically different endophytic bacterial/archaeal microbiome compositions from each other and from seeds produced by control plants. This work suggests that the abiotic experience of a parental plant can influence the composition of its seed microbiome, with unknown consequences for the next plant generation.
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Affiliation(s)
- A. Fina Bintarti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
- The Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
| | - Patrick J. Kearns
- The Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
| | - Abby Sulesky-Grieb
- The Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Ashley Shade
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
- The Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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28
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Feng X, Wang Q, Sun Y, Zhang S, Wang F. Microplastics change soil properties, heavy metal availability and bacterial community in a Pb-Zn-contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127364. [PMID: 34879561 DOI: 10.1016/j.jhazmat.2021.127364] [Citation(s) in RCA: 149] [Impact Index Per Article: 74.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/22/2021] [Accepted: 09/25/2021] [Indexed: 05/06/2023]
Abstract
Microplastics (MPs) co-occur widely with diverse contaminants in soils. However, few data are available on their impacts on soil chemical and microbial properties of heavy metal-contaminated soils. For the first time, we investigated the changes in chemical and microbial properties of a Pb-Zn-contaminated soil as induced by six different MPs, including polyethylene (PE), polystyrene (PS), polyamide (PA), polylactic acid (PLA), polybutylene succinate (PBS), and polyhydroxybutyrate (PHB), at two doses (0.2% and 2%, w/w). After 120 days of soil incubation, significant changes were observed in soil pH, dissolved organic carbon (DOC), NH4+-N, NO3--N, available P, the availability of Zn and Pb, and the activities of soil enzymes. Overall, MPs especially at the dose of 2% decreased the richness and diversity of bacterial communities and altered microbial community composition, causing special enrichments of specific taxa. MPs increased predicted functional genes involved in xenobiotics biodegradation and metabolism. Generally, impacts were dependent on MPs' type and dose. Changes in soil properties and heavy metal availability had significant correlations with bacterial community diversity and composition. Our findings imply that MPs co-occurring with heavy metals may change metal mobility, soil fertility, and microbial diversity and functions, thus causing a potential threat to soil ecosystem multifunctionality.
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Affiliation(s)
- Xueying Feng
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province, 266042, PR China
| | - Quanlong Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province, 266042, PR China
| | - Yuhuan Sun
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province, 266042, PR China
| | - Shuwu Zhang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province, 266042, PR China
| | - Fayuan Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province, 266042, PR China.
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29
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Potts L, Douglas A, Perez Calderon LJ, Anderson JA, Witte U, Prosser JI, Gubry-Rangin C. Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2300-2311. [PMID: 35103467 PMCID: PMC9007448 DOI: 10.1021/acs.est.1c05106] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.
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Affiliation(s)
- Lloyd
D. Potts
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Alex Douglas
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Luis J. Perez Calderon
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James A. Anderson
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Ursula Witte
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James I. Prosser
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Cécile Gubry-Rangin
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
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30
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Dong Y, Wu S, Fan H, Li X, Li Y, Xu S, Bai Z, Zhuang X. Ecological selection of bacterial taxa with larger genome sizes in response to polycyclic aromatic hydrocarbons stress. J Environ Sci (China) 2022; 112:82-93. [PMID: 34955225 DOI: 10.1016/j.jes.2021.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/24/2021] [Accepted: 04/25/2021] [Indexed: 05/15/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous priority pollutants that cause great damage to the natural environment and health. Average genome size in a community is critical for shedding light on microbiome's functional response to pollution stress within an environment. Here, microcosms under different concentrations were performed to evaluate the selection of PAHs stress on the average genome size in a community. We found the distinct communities of significantly larger genome size with the increase of PAHs concentration gradients in soils, and consistent trends were discovered in soils at different latitudes. The abundance of Proteobacteria and Deinococcus-Thermus with relatively larger genomes increased along with PAHs stress and well adapted to polluted environments. In contrast, the abundance of Patescibacteria with a highly streamlined and smaller genome decreased, implying complex interactions between environmental selection and functional fitness resulted in bacteria with larger genomes becoming more abundant. Moreover, we confirmed the increased capacity for horizontal transfer of degrading genes between communities by showing an increased connection number per node positively related to the nidA gene along the concentration gradients in the co-occurrence network. Our findings suggest PAHs tend to select bacterial taxa with larger genome sizes, with significant consequences for community stability and potential biodegradation strategies.
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Affiliation(s)
- Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yijing Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Sino-Danish Center, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengjun Xu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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31
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Sun Y, Duan C, Cao N, Li X, Li X, Chen Y, Huang Y, Wang J. Effects of microplastics on soil microbiome: The impacts of polymer type, shape, and concentration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150516. [PMID: 34592287 DOI: 10.1016/j.scitotenv.2021.150516] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 06/13/2023]
Abstract
Increasing research has recognized that the ubiquitous presence of microplastics in terrestrial environments is undeniable, which potentially alters the soil ecosystem properties and processes. The fact that microplastics with diverse characteristics enter into the soil may induce distinct effects on soil ecosystems. Our knowledge of the impacts of microplastics with different polymers, shapes, and concentrations on soil bacterial communities is still limited. To address this, we examined the effects of spherical microplastics (150 μm) with different polymers (i.e., polyethylene (PE), polystyrene (PS), and polypropylene (PP)) and four shapes of PP microplastics (i.e., fiber, film, foam, and particle) at a constant concentration (1%, w/w) on the soil bacterial community in an agricultural soil over 60 days. Treatments with different concentrations (0.01-20%, w/w) of PP microplastic particles (150 μm) were also included. The bacterial communities in PE and PP treatments showed a similar pattern but separated from those in PS-treated soils, indicating the polymer backbone structure is an important factor modulating the soil bacterial responses. Fiber, foam, and film microplastics significantly affected the soil bacterial composition as compared to the particle. The community dissimilarity of soil bacteria was significantly (R2 = 0.592, p < 0.001) correlated with the changes of microplastic concentration. The random forest model identified that certain bacteria belonging to Patescibacteria were closely linked to microplastic contamination. Additionally, analysis of the predicted function further showed that microplastics with different characteristics caused distinct effects on microbial community function. Our findings suggested that the idiosyncrasies of microplastics should not be neglected when studying their effects on terrestrial ecosystems.
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Affiliation(s)
- Yuanze Sun
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Chongxue Duan
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Na Cao
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xinfei Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaomin Li
- Institute of Quality Standard and Testing Technology for Agro-Products, The Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Yumei Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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32
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Chen G, Gu X, Liu Y, Wang W, Wang M. Different functional feeding groups of mangrove soil molluscs invoke unique co‐occurrence patterns in response to a climate extreme. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Guogui Chen
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University) Ministry of Education College of the Environment & Ecology Xiamen University Xiamen China
| | - Xuan Gu
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University) Ministry of Education College of the Environment & Ecology Xiamen University Xiamen China
| | - Yi Liu
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University) Ministry of Education College of the Environment & Ecology Xiamen University Xiamen China
| | - Wenqing Wang
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University) Ministry of Education College of the Environment & Ecology Xiamen University Xiamen China
| | - Mao Wang
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University) Ministry of Education College of the Environment & Ecology Xiamen University Xiamen China
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33
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Kim HS, Lee SH, Jo HY, Finneran KT, Kwon MJ. Diversity and composition of soil Acidobacteria and Proteobacteria communities as a bacterial indicator of past land-use change from forest to farmland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:148944. [PMID: 34298360 DOI: 10.1016/j.scitotenv.2021.148944] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/05/2021] [Accepted: 07/05/2021] [Indexed: 05/20/2023]
Abstract
The land-use change from natural to managed farmland ecosystems can undergo perturbations and significantly impact soil environment and communities. To understand how anthropogenic land-use alteration determines in-depth relationships among soil environmental factors and soil bacterial communities, high-resolution characterization was performed using soil samples (27 spots × 3 depths; top 10-20 cm, middle 90-100 cm, bottom 180-190 cm) from a natural forest and a 50 year-old farmland. The soil bacterial community abundance (number of OTU's per sample) and diversity (Faith's phylogenetic diversity) was significantly higher in the top layer of farmland soil than in forest soil. However, the differences in bacterial community abundance between farmland and forest decreased with depth, suggesting that the effect of fertilization was limited to top and middle layers. The phyla Acidobacteria and Proteobacteria were distributed distinctively during the land-use change. The subgroups Gp1-3 of Acidobacteria were more abundant in the forest samples (pH 3.5-5), while Gp4-7 and Gp10 were predominant in the farmland (pH 4.5-9.5). Members belonging to α-Proteobacteria and Xanthomonadales in γ-Proteobacteria were dominant in the forest, whereas β-, δ-, and γ-Proteobacteria were relatively abundant in the farmland. Both multivariate and correlation network analyses revealed that Acidobacteria and Proteobacteria communities were significantly affected by soil pH, as well as toxic metals from pesticides (Zn, Cr, Ni, Cu, Cd, As) and terminal electron acceptors (NO3, bioavailable Fe(III), SO4). In line with the long history of anthropogenic fertilization, the farmland site showed high abundance of membrane and ATP-binding cassette transporter genes, suggesting the key for uptake of nutrients and for protection against toxic metals and environmental stresses. This study provides new insights into the use of both Acidobacteria and Proteobacteria community structures as a bacterial indicator for land-use change.
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Affiliation(s)
- Han-Suk Kim
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Sang-Hoon Lee
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul 02841, South Korea
| | - Ho Young Jo
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Kevin T Finneran
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC 29643, USA
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea.
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Nikolova C, Ijaz UZ, Gutierrez T. Exploration of marine bacterioplankton community assembly mechanisms during chemical dispersant and surfactant-assisted oil biodegradation. Ecol Evol 2021; 11:13862-13874. [PMID: 34707823 PMCID: PMC8525123 DOI: 10.1002/ece3.8091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 11/07/2022] Open
Abstract
Assembly processes in marine microbial communities amended with crude oil and chemical dispersant are poorly understood and even more so when biosurfactants are used. We set up a microcosm experiment in which microbiome structure was analyzed using 16S rRNA gene amplicon sequencing and six null models to better understand and quantify the mechanisms and patterns controlling the assembly of a marine crude oil degrading microbial community in the presence of chemical dispersant or rhamnolipid biosurfactant. Although each null model quantifies different aspects of the community assembly, there was a general agreement that neither purely stochastic nor purely deterministic processes dominated the microbial communities, and their influence was variable over time. Determinism was dominant in the early phase of incubation, while stochasticity was prevalent in the middle and late stages. There was faster recruitment of phylogenetically distant species in the dispersant-amended community compared to oil-only or rhamnolipid-amended communities. This analysis provides important insights of how chemical dispersants and rhamnolipid influence microbial communities' dynamics and identified which groups may be excluded-an important consideration for biodegradation process and oil spill response.
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Affiliation(s)
- Christina Nikolova
- Institute of Mechanical, Process and Energy EngineeringSchool of Engineering and Physical SciencesHeriot‐Watt UniversityEdinburghUK
| | | | - Tony Gutierrez
- Institute of Mechanical, Process and Energy EngineeringSchool of Engineering and Physical SciencesHeriot‐Watt UniversityEdinburghUK
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35
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Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Metagenomic Analysis of the Microbial Community in the Underground Coal Fire Area (Kemerovo Region, Russia) Revealed Predominance of Thermophilic Members of the Phyla Deinococcus-Thermus, Aquificae, and Firmicutes. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721050088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Abstract
Underground burning of coal seams accompanied by release of gases leads to development of local thermal ecosystems. We investigated the microbial community of the ground heated to 72°C in the release area of hot gases resulting from underground combustion of coal mining waste at the Bungurskiy-Severny coal deposit in the Kemerovo region of Russia. Analysis of the composition of the microbial community by 16S rRNA gene profiling revealed predominance of thermophilic bacteria of the phyla Deinococcus-Thermus, Aquificae, and Firmicutes. As a result of metagenomic analysis, 18 genomes of the main members of the microbial community were assembled, including the complete genomes of Hydrogenobacter thermophiles, a member of the candidate genus UBA11096 of the phylum Aquificae (RBS10-58), Thermoflexus hugenholtzii, and Thermus antranikianii. Analysis of the RBS10-58 genome indicates that this bacterium can autotrophically fix carbon in the reductive tricarboxylic acid cycle and obtain energy via oxidation of hydrogen and sulfur compounds with oxygen or nitrate as electron acceptors. Genome analysis of the two dominant Firmicutes species, Hydrogenibacillus schlegelii and an uncultured member of the class Thermaerobacteria, showed that these bacteria could grow aerobically by oxidizing hydrogen and carbon monoxide. Overall, the community was dominated by aerobic bacteria capable of growing autotrophically and obtaining energy via oxidation of the main components of coal gases, hydrogen and carbon monoxide. Thermus antranikianii, which makes up about a half of the microbial community, probably uses organic matter produced by autotrophic members of Firmicutes and Aquificae.
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36
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Lee SH, Kim TS, Park HD. Transient-rare Bacterial Taxa Are Assembled Neutrally across Temporal Scales. Microbes Environ 2021; 36. [PMID: 33563869 PMCID: PMC7966942 DOI: 10.1264/jsme2.me20110] [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] [Indexed: 12/02/2022] Open
Abstract
Despite the importance of microbial communities in ecosystem functions, the mechanisms underlying the assembly of rare taxa over time are poorly understood. It remains largely unknown whether rare taxa exhibit similar assembly processes to common taxa in local communities. We herein retrieved the 16S rRNA sequences of bacteria collected bimonthly for 2 years from the Pohang wastewater treatment plant. The transient-rare taxa showed different abundance distributions from the common taxa. Transient-rare taxon assemblages also exhibited higher temporal variations than common taxon assemblages, suggesting the distinct ecological patterns of the two assemblages. A multivariate analysis revealed that environmental parameters accounted for 25.3 and 61.6% of temporal variations in the transient-rare and common taxon assemblages, respectively. The fitting of all observed taxa to a neutral community model revealed that 96.4% of the transient-rare taxa (relative abundance, 71.4%) and 73.3% of the common taxa (relative abundance, 45.6%) followed the model, suggesting that stochastic mechanisms were more important than deterministic ones in the assembly of the transient-rare taxa. Collectively, the present results indicate that the transient-rare bacterial taxa at the Pohang wastewater treatment plant differed from the common taxa in ecological patterns, suggesting that dispersal is a key process in their assembly.
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Affiliation(s)
- Sang-Hoon Lee
- School of Civil, Environmental and Architectural Engineering, Korea University
| | - Taek-Seung Kim
- School of Civil, Environmental and Architectural Engineering, Korea University
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University
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37
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Dong Y, Wu S, Deng Y, Wang S, Fan H, Li X, Bai Z, Zhuang X. Distinct Functions and Assembly Mechanisms of Soil Abundant and Rare Bacterial Taxa Under Increasing Pyrene Stresses. Front Microbiol 2021; 12:689762. [PMID: 34276621 PMCID: PMC8283415 DOI: 10.3389/fmicb.2021.689762] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/20/2021] [Indexed: 01/23/2023] Open
Abstract
Elucidating the relative importance of species interactions and assembly mechanisms in regulating bacterial community structure and functions, especially the abundant and rare subcommunities, is crucial for understanding the influence of environmental disturbance in shaping ecological functions. However, little is known about how polycyclic aromatic hydrocarbon (PAH) stress alters the stability and functions of the abundant and rare taxa. Here, we performed soil microcosms with gradient pyrene stresses as a model ecosystem to explore the roles of community assembly in determining structures and functions of the abundant and rare subcommunities. The dose–effect of pyrene significantly altered compositions of abundant and rare subcommunities. With increasing pyrene stresses, diversity increased in abundant subcommunities, while it decreased in the rare. Importantly, the abundant taxa exhibited a much broader niche width and environmental adaptivity than the rare, contributing more to pyrene biodegradation, whereas rare taxa played a key role in improving subcommunity resistance to stress, potentially promoting community persistence and stability. Furthermore, subcommunity co-occurrence network analysis revealed that abundant taxa inclined to occupy the core and central position in adaptation to the pyrene stresses. Stochastic processes played key roles in the abundant subcommunity rather than the rare subcommunity. Overall, these findings extend our understanding of the ecological mechanisms and interactions of abundant and rare taxa in response to pollution stress, laying a leading theoretical basis that abundant taxa are core targets for biostimulation in soil remediation.
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Affiliation(s)
- Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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38
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Rong L, Zhao L, Zhao L, Cheng Z, Yao Y, Yuan C, Wang L, Sun H. LDPE microplastics affect soil microbial communities and nitrogen cycling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145640. [PMID: 33582358 DOI: 10.1016/j.scitotenv.2021.145640] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/05/2021] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Microplastics (MPs) are a contaminant of increasing concern in the environment. However, the impacts of MPs on soil ecosystems and biogeochemical processes like nitrogen cycle have not been well elucidated. In this study, we designed an indoor microcosm experiment to investigate the effects of exposure to low density polyethylene (LDPE) MPs on soil bacterial community and nitrogen cycling function over a 90-day incubation. Next-generation sequencing of the 16S rRNA genes revealed that both 2% and 7% LDPE MPs exposure slightly affected the soil bacterial diversity. Further analysis at the genus level showed differential tolerance to LDPE MPs, the genera Pedomicrobium, Steroidobacter, Pseudonocardia, Nitrospira and Turicibacter were enriched in the soil with 2% (w/w) LDPE MPs amendment, while the genera Pedomicrobium, Mycobacterium and Hyphomicrobium were significantly enriched in the soil with 7% (w/w) LDPE MPs amendment on days 15 and 30. Co-occurrence network analysis further suggested that LDPE MPs changed bacterial network complexity and modularity and Acidobacteria formed intimate associations with each other in responding to LDPE MPs exposure. Additionally, LDPE MPs in soil increased the abundance of nifH, AOBamoA and nirK genes involved in nitrogen cycling in different incubation phases compared to the control. The abundance of AOAamoA genes decreased on day 15 and then increased. Conversely, the abundance of nirS genes increased during the first 15 days and then decreased. These results suggested that both 2% and 7% LDPE MPs impact soil bacterial network structure and alters functional groups involved in soil nitrogen cycling processing.
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Affiliation(s)
- Lili Rong
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Longfei Zhao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Leicheng Zhao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Zhipeng Cheng
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yiming Yao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Chaolei Yuan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Lei Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Hongwen Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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39
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Xie G, Kong X, Kang J, Su N, Luo G, Fei J. Community-level dormancy potential regulates bacterial beta-diversity succession during the co-composting of manure and crop residues. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145506. [PMID: 33571759 DOI: 10.1016/j.scitotenv.2021.145506] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/17/2021] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to disclose the bacterial diversity succession during the co-composting of manure and crop residues and to provide new insight into the role of community-level dormancy potential in diversity succession. Illumina sequencing and PICRUSt-estimated metagenomes were used for this purpose. The bacterial richness and phylogenetic diversity decreased in the early and middle stages of composting and were maintained to a stable status in the late stage. Both composting phases and raw materials impacted the aforementioned alpha diversity significantly, while the composting phases had a greater (80%-94%) impact than the raw materials (1%-18%). Bacterial beta-diversity succession exhibited selectivity as the composting proceeded, and the dominant taxa changed into salt- and heat-resistant genera such as Bacillus, Glycomyces, and Halocella. Meanwhile, Georgenia, Actinomadura, and Ruminofilibacter were identified as the dominant predictor taxa of bacterial community succession in composting. Roughly, the abundance of genes underlying dormancy strategies, including sporulation factors (spo0A gene), toxin-antitoxin systems (dinJ/yafP, mazF/E, hipA/O, and relA/E genes), and resuscitation-promoting factors (rpfC gene), increased as composting proceeded and reached the highest in the thermophilic or maturation phases. Co-occurring relationships between bacterial communities and genes underlying dormancy strategies in different composting phases comprised multiple associations dominated by positive edges (50%-97%). The stability in genes underlying dormancy strategies and aggregate dormancy potential had a positive linear correlation with that in bacterial beta diversity (R2 = 0.26-0.42; P < 0.05), but not related significantly to that in richness and phylogenetic diversity. This study highlighted the importance of understanding how community-level dormancy strategies mediated microbial succession in composting to better predict compost maturity and product quality.
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Affiliation(s)
- Guixian Xie
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Xiaoliang Kong
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Jialu Kang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Ning Su
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Gongwen Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China.
| | - Jiangchi Fei
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
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40
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Gao GF, Peng D, Wu D, Zhang Y, Chu H. Increasing Inundation Frequencies Enhance the Stochastic Process and Network Complexity of the Soil Archaeal Community in Coastal Wetlands. Appl Environ Microbiol 2021; 87:e02560-20. [PMID: 33741614 PMCID: PMC8208137 DOI: 10.1128/aem.02560-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 03/07/2021] [Indexed: 01/03/2023] Open
Abstract
Coastal wetlands are experiencing frequent flooding because of global climate changes, such as the rising sea level. Despite the key role of archaea in soil biogeochemical cycles, the assembly processes and co-occurrence patterns of archaeal communities in coastal wetlands in response to increasing inundation frequencies remain elusive. In this study, we established an in situ mesocosm with an inundation frequency gradient to investigate the response of soil archaeal community toward increasing inundation frequencies in monocultures of Spartina alterniflora and a mangrove species, Kandelia obovata Both neutral community model and null model analyses suggested that stochastic processes are dominant in governing the archaeal community assembly and that the stochastic processes are enhanced with increasing inundation frequencies. Increasing inundation frequencies significantly increased the community niche width. Moreover, archaeal community in S. alterniflora soil displayed lower niche overlap and higher stochasticity than in K. obovata soil. Co-occurrence network analysis revealed that the network complexity increases with increase in the inundation frequencies. Soil water content is the most decisive factor influencing the archaeal communities. Overall, we found that increasing inundation frequencies enhance the stochastic processes and network complexity of the soil archaeal community in coastal wetlands. This study could enhance our understanding on the response of soil archaeal communities in coastal wetlands toward global change.IMPORTANCE Coastal wetlands, subjected to regular disturbances by periodic tides, are highly productive and important in the regulation of climate change. However, the assembly mechanisms and co-occurrence patterns of soil archaeal communities in coastal areas remain poorly known, especially for their responses to increasing inundation frequencies. In this study, we aimed at unraveling these uncertainties by studying typical estuarine ecosystems in southern China. We show that increasing inundation frequencies enhance the stochastic processes and network complexity of the soil archaeal community. This study offers a new path for an improved understanding of archaeal community assembly and species coexistence in coastal environments, with a special focus on the role of inundation frequency.
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Affiliation(s)
- Gui-Feng Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Dan Peng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Di Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yihui Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
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41
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Thatikayala D, Min B. Copper ferrite supported reduced graphene oxide as cathode materials to enhance microbial electrosynthesis of volatile fatty acids from CO 2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 768:144477. [PMID: 33736314 DOI: 10.1016/j.scitotenv.2020.144477] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/23/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Copper ferrite/reduced graphene oxide (CF/rGO) nanocomposites (NCs) was synthesized using the bio-combustion method and applied as a cathode catalyst in the microbial reduction of CO2 to volatile fatty acids (VFAs) in a single chamber microbial electrosynthesis system (MES). The synthesized NCs exhibited a porous network-like structure with a high surface area of CF/rGO (158.22 m2/g), which was 2.24 folds higher than that of CF. The Cyclic Voltammetry (CV) and Electrochemical Impedance Spectroscopy (EIS) analysis for CF/rGO/Carbon cloth (Cc) revealed a high reduction current density of -7.3 A/m2 and a low charge transfer resistance of 2.8 Ω. The isobutyrate and acetate in MES-2 (Cu/rGO/Cc) were produced at 35.37 g/m2/d, which was 1.53 folds higher than that of MES-1 (bare Cc: 23.10 g/m2/d). The columbic efficiency (77.78%) and total VFA concentration (1941.13 ± 83 mg COD/L) were noted to be 1.97 and 1.6 folds higher for MES-2 than MES-1, respectively. The Tafel plot drawn from the CV curves exhibited an exchange current density value of MES-2 that was 3.46 A/m2, and this value was 1.19 and 33.92 folds higher than that of MES-1 and abiotic CF/rGO/Cc, respectively. Field emission scanning electron microscopy (FESEM) observations revealed enhanced rod-shaped bacteria had grown on the cathode suggesting excellent biocompatible and multi-length scale porosity of CF/rGO catalysts for enhanced colonization of microbes. The phyla Proteobacteria (Betaproteobacteria), Bacteroidetes, and Firmicutes were highly abundant as the dominant microbial communities on the cathode, which might played a major role in bioelectrochemical CO2 reduction to VFAs. The results from this study clearly demonstrate that the CF/rGO/Cc electrode could serve as a conductive element between microbes and bactericidal electrodes with excellent electrochemical properties to enable performance of the MES.
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Affiliation(s)
- Dayakar Thatikayala
- Department of Environment Science and Engineering, Kyung Hee University, Yongin, Republic of Korea
| | - Booki Min
- Department of Environment Science and Engineering, Kyung Hee University, Yongin, Republic of Korea.
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42
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Rosier CL, Polson SW, D’Amico V, Kan J, Trammell TLE. Urbanization pressures alter tree rhizosphere microbiomes. Sci Rep 2021; 11:9447. [PMID: 33941814 PMCID: PMC8093231 DOI: 10.1038/s41598-021-88839-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 04/13/2021] [Indexed: 02/02/2023] Open
Abstract
The soil microbial community (SMC) provides critical ecosystem services including organic matter decomposition, soil structural formation, and nutrient cycling. Studies suggest plants, specifically trees, act as soil keystone species controlling SMC structure via multiple mechanisms (e.g., litter chemistry, root exudates, and canopy alteration of precipitation). Tree influence on SMC is shaped by local/regional climate effects on forested environments and the connection of forests to surrounding landscapes (e.g., urbanization). Urban soils offer an ideal analog to assess the influence of environmental conditions versus plant species-specific controls on SMC. We used next generation high throughput sequencing to characterize the SMC of specific tree species (Fagus grandifolia [beech] vs Liriodendron tulipifera [yellow poplar]) across an urban-rural gradient. Results indicate SMC dissimilarity within rural forests suggests the SMC is unique to individual tree species. However, greater urbanization pressure increased SMC similarity between tree species. Relative abundance, species richness, and evenness suggest that increases in similarity within urban forests is not the result of biodiversity loss, but rather due to greater overlap of shared taxa. Evaluation of soil chemistry across the rural-urban gradient indicate pH, Ca+, and organic matter are largely responsible for driving relative abundance of specific SMC members.
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Affiliation(s)
- Carl L. Rosier
- grid.33489.350000 0001 0454 4791Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716 USA
| | - Shawn W. Polson
- grid.33489.350000 0001 0454 4791Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19713 USA ,grid.33489.350000 0001 0454 4791Department of Computer and Information Sciences, University of Delaware, Newark, DE 19716 USA
| | - Vincent D’Amico
- grid.33489.350000 0001 0454 4791US Forest Service, Northern Research Station, Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE 19716 USA
| | - Jinjun Kan
- grid.274177.00000 0000 9615 2850Department of Microbiology, Stroud Water Research Center, Avondale, PA 19311 USA
| | - Tara L. E. Trammell
- grid.33489.350000 0001 0454 4791Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716 USA
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43
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Kadnikov VV, Mardanov AV, Beletsky AV, Grigoriev MA, Karnachuk OV, Ravin NV. Thermophilic Chloroflexi Dominate in the Microbial Community Associated with Coal-Fire Gas Vents in the Kuznetsk Coal Basin, Russia. Microorganisms 2021; 9:microorganisms9050948. [PMID: 33924824 PMCID: PMC8146126 DOI: 10.3390/microorganisms9050948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 01/12/2023] Open
Abstract
Thermal ecosystems associated with areas of underground burning coal seams are rare and poorly understood in comparison with geothermal objects. We studied the microbial communities associated with gas vents from the coal-fire in the mining wastes in the Kemerovo region of the Russian Federation. The temperature of the ground heated by the hot coal gases and steam coming out to the surface was 58 °C. Analysis of the composition of microbial communities revealed the dominance of Ktedonobacteria (the phylum Chloroflexi), known to be capable of oxidizing hydrogen and carbon monoxide. Thermophilic hydrogenotrophic Firmicutes constituted a minor part of the community. Among the well-known thermophiles, members of the phyla Aquificae, Deinococcus-Thermus and Bacteroidetes were also found. In the upper ground layer, Acidobacteria, Verrucomicrobia, Actinobacteria, Planctomycetes, as well as Proteobacteria of the alpha and gamma classes, typical of soils, were detected; their relative abundancies decreased with depth. The phylum Verrucomicrobia was dominated by Candidatus Udaeobacter, aerobic heterotrophs capable of generating energy through the oxidation of hydrogen present in the atmosphere in trace amounts. Archaea made up a small part of the communities and were represented by thermophilic ammonium-oxidizers. Overall, the community was dominated by bacteria, whose cultivated relatives are able to obtain energy through the oxidation of the main components of coal gases, hydrogen and carbon monoxide, under aerobic conditions.
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Affiliation(s)
- Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (A.V.M.); (A.V.B.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (A.V.M.); (A.V.B.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (A.V.M.); (A.V.B.)
| | - Mikhail A. Grigoriev
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia; (M.A.G.); (O.V.K.)
| | - Olga V. Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia; (M.A.G.); (O.V.K.)
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (A.V.M.); (A.V.B.)
- Correspondence:
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44
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Lee JY, Jacob KM, Kashefi K, Reguera G. Oral seeding and niche-adaptation of middle ear biofilms in health. Biofilm 2021; 3:100041. [PMID: 33665609 PMCID: PMC7822943 DOI: 10.1016/j.bioflm.2020.100041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
The entrenched dogma of a sterile middle ear mucosa in health is incongruent with its periodic aeration and seeding with saliva aerosols. To test this, we sequenced 16S rRNA-V4 amplicons from otic secretions collected at the nasopharyngeal orifice of the tympanic tube and, as controls, oropharyngeal and buccal samples. The otic samples harbored a rich diversity of oral keystone genera and similar functional traits but were enriched in anaerobic genera in the Bacteroidetes (Prevotella and Alloprevotella), Fusobacteria (Fusobacterium and Leptotrichia) and Firmicutes (Veillonella) phyla. Facultative anaerobes in the Streptococcus genus were also abundant in the otic and oral samples but corresponded to distinct, and sometimes novel, cultivars, consistent with the ecological diversification of the oral migrants once in the middle ear microenvironment. Neutral community models also predicted a large contribution of oral dispersal to the otic communities and the positive selection of taxa better adapted to growth and reproduction under limited aeration. These results challenge the traditional view of a sterile middle ear in health and highlight hitherto unknown roles for oral dispersal and episodic ventilation in seeding and diversifying otic biofilms. The middle ear mucosa harbors a rich bacterial community in health. Oral migration is the primary mechanism for seeding otic biofilms. Periodic aeration of the middle ear enriches for anaerobic taxa and promotes the ecological diversification of oral migrants. Our study challenges the entrenched dogma of a sterile middle ear in health.
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Affiliation(s)
- Joo-Young Lee
- Department of Microbiology and Molecular Genetics, Michigan State University, MI, USA
| | - Kristin M Jacob
- Department of Microbiology and Molecular Genetics, Michigan State University, MI, USA
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, MI, USA
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, MI, USA
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45
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Hall JPJ, Harrison E, Pärnänen K, Virta M, Brockhurst MA. The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer. Front Microbiol 2020; 11:1846. [PMID: 32849443 PMCID: PMC7419628 DOI: 10.3389/fmicb.2020.01846] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022] Open
Abstract
Carriage of resistance genes can underpin bacterial survival, and by spreading these genes between species, mobile genetic elements (MGEs) can potentially protect diversity within microbial communities. The spread of MGEs could be affected by environmental factors such as selection for resistance, and biological factors such as plasmid host range, with consequences for individual species and for community structure. Here we cultured a focal bacterial strain, Pseudomonas fluorescens SBW25, embedded within a soil microbial community, with and without mercury selection, and with and without mercury resistance plasmids (pQBR57 or pQBR103), to investigate the effects of selection and resistance gene introduction on (1) the focal species; (2) the community as a whole; (3) the spread of the introduced mer resistance operon. We found that P. fluorescens SBW25 only escaped competitive exclusion by other members of community under mercury selection, even when it did not begin with a mercury resistance plasmid, due to its propensity to acquire resistance from the community by horizontal gene transfer. Mercury pollution had a significant effect on community structure, decreasing alpha diversity within communities while increasing beta diversity between communities, a pattern that was not affected by the introduction of mercury resistance plasmids by P. fluorescens SBW25. Nevertheless, the introduced merA gene spread to a phylogenetically diverse set of recipients over the 5 weeks of the experiment, as assessed by epicPCR. Our data demonstrates how the effects of MGEs can be experimentally assessed for individual lineages, the wider community, and for the spread of adaptive traits.
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Affiliation(s)
- James P J Hall
- Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, The University of Liverpool, Liverpool, United Kingdom.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.,Department of Biology, University of York, York, United Kingdom
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | | - Marko Virta
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
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46
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Abstract
Soil microbial community assembly is crucial for understanding the mechanisms of microbial communities that regulate ecosystem-level functioning. The relative contributions of stochastic and deterministic processes to microbial community assembly remain poorly defined, and major questions exist concerning the soil organic carbon (SOC) dynamics of microbial community assembly in deep soil. Here, the bacterial community assembly processes were explored across five soil profile depths (up to 80 cm) during a 15-year field experiment involving four fertilization regimes. We found that the bacterial community assembly was initially governed by deterministic selection in topsoil but was progressively structured by increasing stochastic dispersal with depth. The migration rate (m) and β-null deviation pattern supported the hypothesis of a relatively greater influence of dispersal in deep soil, which was correlated with bacterial community assembly by stochastic processes. These changes in the entire community assembly reflected consistent assembly processes of the two most dominant phyla, Acidobacteria and Chloroflexi Structural equation modeling showed that soil features (pH and total phosphorus) and bacterial interactions (competition and network complexity) were significantly related to bacterial community assembly in the 0-to-10-cm and 10-to-20-cm layers. Partial Mantel tests, structural equation modeling, and random forest modeling consistently indicated a strong and significant correlation between bacterial community assemblages and SOC dynamics, implying that bacterial assembly processes would potentially suppress SOC metabolism and mineralization when the contributions of stochastic dispersal to communities increased in deeper layers. Our results have important implications for integrating bacterial community assembly processes into the predictions of SOC dynamics.IMPORTANCE We have provided a framework to better understand the mechanisms governing the balance between stochastic and deterministic processes and to integrate the shifts in community assembly processes with microbial carbon metabolism. Our study reinforced that environmental filtering and bacterial cooccurrence patterns influence the stochastic/deterministic continuum of soil bacterial community assembly and that stochasticity may act through deeper soil layers to influence carbon metabolism. Delineating theoretically the potential linkages between community assembly and SOC dynamics across a broad range of microbial systems represents an interesting topic for future research.
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47
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Westerholm M, Liu T, Schnürer A. Comparative study of industrial-scale high-solid biogas production from food waste: Process operation and microbiology. BIORESOURCE TECHNOLOGY 2020; 304:122981. [PMID: 32088624 DOI: 10.1016/j.biortech.2020.122981] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 06/10/2023]
Abstract
Anaerobic high-solid treatment (HST) for processing food waste and biogas production is a viable technology with considerable commercial potential. In this study, we examined and compared mesophilic and thermophilic industrial-scale plug-flow digesters. The HSTs demonstrated reasonable biogas yields from food waste (0.4-0.6 Nm3 CH4/kg volatile solids). However, during operation at thermophilic conditions ammonia inhibition (~2 g NH3-N/L) and acid accumulation (6-14 g/L) caused severe process disturbance. Microbial community structures diverged between the processes, with temperature appearing to be a strong driver. A unique feature of the thermophilic HSTs was high abundance of the uncultivated Clostridia group MBA03 and temperature fluctuations in one mesophilic HST were linked to drastically decreased abundance of methanogens and relative abundance of Cloacimonetes. The process data obtained in this study clearly demonstrate both potential and challenges in HST of food waste but also possibilities for management approaches to tackle process imbalance and restore process function.
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Affiliation(s)
- M Westerholm
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala BioCenter, Box 7025, SE-750 07 Uppsala, Sweden; Biogas Research Center, Linköping University, SE-581 83 Linköping, Sweden.
| | - T Liu
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala BioCenter, Box 7025, SE-750 07 Uppsala, Sweden
| | - A Schnürer
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala BioCenter, Box 7025, SE-750 07 Uppsala, Sweden; Biogas Research Center, Linköping University, SE-581 83 Linköping, Sweden; Department of Thematic Studies Environmental Change, Linköping University, SE-581 83 Linköping, Sweden
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48
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Sorensen JW, Shade A. Dormancy dynamics and dispersal contribute to soil microbiome resilience. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190255. [PMID: 32200738 PMCID: PMC7133531 DOI: 10.1098/rstb.2019.0255] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In disturbance ecology, stability is composed of resistance to change and resilience towards recovery after the disturbance subsides. Two key microbial mechanisms that can support microbiome stability include dormancy and dispersal. Specifically, microbial populations that are sensitive to disturbance can be re-seeded by local dormant pools of viable and reactivated cells, or by immigrants dispersed from regional metacommunities. However, it is difficult to quantify the contributions of these mechanisms to stability without, first, distinguishing the active from inactive membership, and, second, distinguishing the populations recovered by local resuscitation from those recovered by dispersed immigrants. Here, we investigate the contributions of dormancy dynamics (activation and inactivation), and dispersal to soil microbial community resistance and resilience. We designed a replicated, 45-week time-series experiment to quantify the responses of the active soil microbial community to a thermal press disturbance, including unwarmed control mesocosms, disturbed mesocosms without dispersal, and disturbed mesocosms with dispersal after the release of the stressor. Communities changed in structure within one week of warming. Though the disturbed mesocosms did not fully recover within 29 weeks, resuscitation of thermotolerant taxa was key for community transition during the press, and both resuscitation of opportunistic taxa and immigration contributed to community resilience. Also, mesocosms with dispersal were more resilient than mesocosms without. This work advances the mechanistic understanding of how microbiomes respond to disturbances in their environment. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
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Affiliation(s)
- Jackson W Sorensen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, USA
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49
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Chen H, Wang Y, Sun X, Peng Y, Xiao L. Mixing effect of polylactic acid microplastic and straw residue on soil property and ecological function. CHEMOSPHERE 2020; 243:125271. [PMID: 31760289 DOI: 10.1016/j.chemosphere.2019.125271] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 10/28/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
Microplastics have become a contaminant of increasing concern in soils. Although biodegradable plastics were considered as alternatives of traditional plastics, some evidence showed that biodegradable plastics might produce more microplastics. Until now, the effect of biodegradable microplastics on soil functions and processes, as well as microbial communities is uncertain. Based on high throughput sequencing, enzymatic activity assay and dynamic analysis of soil carbon and nitrogen, we investigated the effects of biodegradable polylactic acid microplastics (PLA MPs) on soil microbiota and related ecological processes under conditions of high or low carbon content. The results showed that PLA MPs had no significant effect on the overall diversity and composition of bacterial communities or related ecosystem functions and processes. However, co-occurrence network analysis revealed that PLA MPs impacted the interactions between constituent species, which might have legacy effect on soil bacterial communities and functions. Our data also revealed that PLA MPs could trade off the priming effect of carbon source. Our results provided an integrated picture in understanding the effects of PLA MPs on soil microbes, properties and ecological functions, which will help to further understand the effects of MPs on terrestrial ecosystems.
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Affiliation(s)
- Huiping Chen
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Yuhuang Wang
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Xi Sun
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Yuke Peng
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Lin Xiao
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China.
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50
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Eckert EM, Quero GM, Di Cesare A, Manfredini G, Mapelli F, Borin S, Fontaneto D, Luna GM, Corno G. Antibiotic disturbance affects aquatic microbial community composition and food web interactions but not community resilience. Mol Ecol 2019; 28:1170-1182. [PMID: 30697889 DOI: 10.1111/mec.15033] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/13/2018] [Accepted: 01/14/2019] [Indexed: 01/17/2023]
Abstract
Notwithstanding the fundamental role that environmental microbes play for ecosystem functioning, data on how microbes react to disturbances are still scarce, and most factors that confer stability to microbial communities are unknown. In this context, antibiotic discharge into the environment is considered a worldwide threat for ecosystems with potential risks to human health. We therefore tested resilience of microbial communities challenged by the presence of an antibiotic. In a continuous culture experiment, we compared the abundance, composition and diversity of microbial communities undisturbed or disturbed by the constant addiction of tetracycline in low (10 µg/L) or intermediate (100 µg/L) concentration (press disturbance). Further, the bacterial communities in the three treatments had to face the sudden pulse disturbance of adding an allochthonous bacterium (Escherichia coli). Tetracycline, even at low concentrations, affected microbial communities by changing their phylogenetic composition and causing cell aggregation. This, however, did not coincide with a reduced microbial diversity, but was mainly caused by a shift in dominance of specific bacterial families. Moreover, the less disturbed community (10 µg/L tetracycline) was sometimes more similar to the control and sometimes more similar to heavily disturbed community (100 µg/L tetracycline). All in all, we could not see a pattern where the communities disturbed with antibiotics were less resilient to a second disturbance introducing E. coli, but they seemed to be able to buffer the input of the allochthonous strain in a similar manner as the control.
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Affiliation(s)
- Ester M Eckert
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Grazia M Quero
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn (SZN), Napoli, Italy
| | - Andrea Di Cesare
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy.,Department of Environmental and Life Sciences (DISTAV), University of Genoa, Genova, Italy
| | - Giuliana Manfredini
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milano, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milano, Italy
| | - Diego Fontaneto
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Gian Marco Luna
- National Research Council, Istituto per le Risorse Biologiche e le Biotecnologie Marine (CNR-IRBIM), Ancona, Italy
| | - Gianluca Corno
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
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