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Liu Y, Wang F, Wang Z, Xiang L, Fu Y, Zhao Z, Kengara FO, Mei Z, He C, Bian Y, Naidu R, Jiang X. Soil properties and organochlorine compounds co-shape the microbial community structure: A case study of an obsolete site. ENVIRONMENTAL RESEARCH 2024; 240:117589. [PMID: 37926227 DOI: 10.1016/j.envres.2023.117589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023]
Abstract
Organochlorine compounds (OCs) such as chlorobenzenes (CB) are persistent organic pollutants that are ubiquitous in soils at organochlorine pesticides (OCP) production sites. Long-term contamination with OCs might alter the soil microbial structure and further affect soil functions. However, the effects of OCs regarding the shaping of microbial community structures in the soils of OCs-contaminated sites remain obscure, especially in the vertical soil profile where pollutants are highly concealed. Hence this paper explored the status and causes of OCs pollution (CB, hexachlorocyclohexane (HCH), and dichlorodiphenyltrichloroethane (DDT)) in an obsolete site, and its combined effects with soil properties (pH, available phosphorus (AP), dissolved organic carbon (DOC), etc) on microbial community structure. The mean total concentration of OCs in the subsoils was up to 996 times higher than that in the topsoils, with CB constituting over 90% of OCs in the subsoil. Historical causes, anthropogenic effects, soil texture, and the nature of OCs contributed to the differences in the spatial distribution of OCs. Redundancy analysis revealed that both the soil properties and OCs were important factors in shaping microbial composition and diversity. Variation partitioning analysis further indicated that soil properties had a greater impact on microbial community structure than OCs. Significant differences in microbial composition between topsoils and subsoils were observed through linear discriminant analysis effect size (LEfSe) analysis, primarily driven by different pollutant conditions. Additionally, co-occurrence network analysis indicated that heavily contaminated subsoils exhibited closer and more intricate bacterial community interactions compared to lightly contaminated topsoils. This work reveals the impact of environmental factors in co-shaping the structure of soil microbial communities. These findings advance our understanding of the intricate interplay among organochlorine pollutants, soil properties, and microbial communities, and provides valuable insights into devising effective management strategies in OCs-contaminated soils.
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Affiliation(s)
- Yu Liu
- Chinese Academy of Science State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- Chinese Academy of Science State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ziquan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Leilei Xiang
- Chinese Academy of Science State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhao Fu
- Chinese Academy of Science State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiliang Zhao
- Chinese Academy of Science State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Zhi Mei
- Chinese Academy of Science State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao He
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yongrong Bian
- Chinese Academy of Science State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), University of Newcastle, Callaghan, NSW 2308, Australia; Crc for Contamination Assessment and Remediation of the Environment (crcCARE), University of Newcastle, Callaghan, NSW 2308, Australia
| | - Xin Jiang
- Chinese Academy of Science State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Yin Y, Wang X, Hu Y, Li F, Cheng H. Insights on the assembly processes and drivers of soil microbial communities in different depth layers in an abandoned polymetallic mining district. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:132043. [PMID: 37453349 DOI: 10.1016/j.jhazmat.2023.132043] [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: 04/21/2023] [Revised: 07/02/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Soil microbes, which play crucial roles in maintaining soil functions and restoring degraded lands, are impacted by heavy metal pollution. This study investigated the vertical distribution of bacterial communities along the soil profiles across four types of areas (heavy metal pollution level: tailings heap area > phytoremediation area > natural restoration area > original forest area) in an abandoned polymetallic mining district by 16S rRNA sequencing, and aimed to disentangle the assembly mechanisms and key drivers of the vertical variation in bacterial community structure. Bacterial diversity and composition were found to vary remarkably between the depth layers in all types of areas, with heterogeneous selection dominated the vertical distribution pattern of soil bacterial communities. Pearson correlation analysis and partial Mantel test revealed that soil nutrients mainly shaped the vertical distribution of bacterial microbiota along soil profiles in the original forest and natural restoration areas. Ni, As, and bioavailable As were the key drivers regulating the vertical variation of bacterial assemblages in the phytoremediation area, whereas Pb, pH, soil organic carbon, and available nitrogen were crucial drivers in the tailings heap area. These findings reveal the predominant assembly mechanisms and drivers governing the vertical distribution of soil bacterial microbiota and indicate the efficiency of phytoremediation and ecological restoration on ameliorating edaphic micro-ecosystems in heavy metal-contaminated areas.
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Affiliation(s)
- Yue Yin
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Xiaojie Wang
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yuanan Hu
- MOE Laboratory of Groundwater Circulation and Evolution, School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Fadong Li
- State Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
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He L, Sun X, Li S, Zhou W, Chen Z, Bai X. The vertical distribution and control factor of microbial biomass and bacterial community at macroecological scales. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161754. [PMID: 36709888 DOI: 10.1016/j.scitotenv.2023.161754] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/04/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Microorganisms exist throughout the soil profile and those microorganisms living in deeper soil horizons likely play key roles in regulating biogeochemical processes. However, the vertical differentiations of microbes along soil depth and their global biogeographical patterns remain poorly understood. Herein, we conducted a global meta-analysis to clarify the vertical changes of microbial biomass, diversity, and microbial relative abundance across the soil profiles. Data was collected from 43 peer-reviewed articles of 110 soil profiles (467 observations in total) from around the world. We found soil microbial biomass and bacterial diversity decreased with depth in soils. Among examined edaphic factors, the depth variation in soil pH exhibited significant negative associations with the depth change in microbial biomass and bacterial Shannon index, while soil total organic carbon (TOC) and total nitrogen (TN) exhibited significant positive associations. For the major bacteria phyla, the relative abundances of Proteobacteria and Bacteroidetes decreased with soil depth, while Chloroflexi, Gemmatimonadetes, and Nitrospirae increased. We found both parallels and differences in the biogeographical patterns of microbial attribute of topsoil vs. subsoil. Microbial biomass was significantly controlled by the soil nutrient concentrations in both topsoil and subsoil compared with climatic factors, while bacterial Shannon index was significantly controlled by the edaphic factors and across latitudes or climatic factors. Moreover, mean annual precipitation can also be used as a predictor of microbial biomass in subsoil which is different from topsoil. Collectively, our results provide a novel integrative view of how microbial biomass and bacterial community response to soil depth change and clarify the controlling factors of the global distribution patterns of microbial biomass and diversity, which are critical to enhance ecosystem simulation models and for formulating sustainable ecosystem management and conservation policies.
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Affiliation(s)
- Libing He
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Suyan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Wenzhi Zhou
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Zhe Chen
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xueting Bai
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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4
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Zhao Z, Oury BM, Xia L, Qin Z, Pan X, Qian J, Luo F, Wu Y, Liu L, Wang W. The ecological response and distribution characteristics of microorganisms and polycyclic aromatic hydrocarbons in a retired coal gas plant post-thermal remediation site. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159314. [PMID: 36220477 DOI: 10.1016/j.scitotenv.2022.159314] [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: 07/15/2022] [Revised: 09/16/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Thermal remediation is one of the most common approaches of removing organic pollutants in the retired contamination sites. However, little is known about the performance of bacterial community characteristics after in situ thermal remediation. In this study, the ecological response and spatial distributional characteristics of microorganisms and polycyclic aromatic hydrocarbons (PAHs) were investigated using a high throughput sequencing method in a retired coal gas plant site after in situ thermal remediation in Nanjing, China. Combination of Venn, clustering-correlation heatmap and two - factor correlation network analysis revealed that, microbial communities were obviously affected and classified by soil depths, temperature, and contamination level, respectively. The common and endemic microorganisms of each group were identified. The relative abundances of Thermaerobacter, Calditerricola, Brevibacillus, Ralstonia and Rhodococcus (aerobic bacteria) gradually declined with the increase of soil depth, while those of Bacillus, Fictibacillus, Paenibacillus, Rheinheimera presented opposite tendency. Some thermophilic degradation bacteria of PAHs, including Thermaerobacter, Calditerricola, Bacillus, Rhodococcus, unclassified_p__Firmicutes, Arthrobacter and Deinococcus, were identified and increased in the abundance at heavily polluted sites. Additionally, Proteobacteria, Bacteroidota, Deinococcota, Chloroflexi, Acidobacteriota, and Actinobacteriota showed negative response to the increase of soil depth, temperature and pollution level, while Firmicutes presented a positive response. This implied that Firmicutes has better stress resistance and adaptability to thermal remediation condition. The key environmental factors affecting microorganism composition and distribution were Temperature, Total nitrogen, Oxidation-Reduction Potential, Organic matters, and PAHs concentrations, which explains the dominant driving mechanism of soil depth, temperature, and contamination level on microbial characteristics in thermal remediation site. Our study could contribute to a better understanding of the resilience and adaptation mechanisms of microbial community at the contaminated site after the in situ thermal remediation.
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Affiliation(s)
- Zhenhua Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA.
| | - Barry Mody Oury
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Liling Xia
- Nanjing Vocational University of Industry Technology, Nanjing 210016, China.
| | - Zhirui Qin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Xiangyu Pan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Jichan Qian
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Fangzhou Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Yong Wu
- Nanjing Qingzhan Environmental Engineering CO. Ltd, China
| | - Luqi Liu
- SUMEC Complete Equipment & Engineering CO. LTD, Nanjing 210018, China
| | - Wei Wang
- SUMEC Complete Equipment & Engineering CO. LTD, Nanjing 210018, China
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5
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Wu W, Dijkstra P, Hungate BA, Shi L, Dippold MA. In situ diversity of metabolism and carbon use efficiency among soil bacteria. SCIENCE ADVANCES 2022; 8:eabq3958. [PMID: 36332015 PMCID: PMC9635821 DOI: 10.1126/sciadv.abq3958] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
The central carbon (C) metabolic network harvests energy to power the cell and feed biosynthesis for growth. In pure cultures, bacteria use some but not all of the network's major pathways, such as glycolysis and pentose phosphate and Entner-Doudoroff pathways. However, how these pathways are used in microorganisms in intact soil communities is unknown. Here, we analyzed the incorporation of 13C from glucose isotopomers into phospholipid fatty acids. We showed that groups of Gram-positive and Gram-negative bacteria in an intact agricultural soil used different pathways to metabolize glucose. They also differed in C use efficiency (CUE), the efficiency with which a substrate is used for biosynthesis. Our results provide experimental evidence for diversity among microbes in the organization of their central carbon metabolic network and CUE under in situ conditions. These results have important implications for our understanding of how community composition affects soil C cycling and organic matter formation.
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Affiliation(s)
- Weichao Wu
- Biogeochemistry of Agroecosystem, University of Goettingen, Goettingen, Germany
- Department of Environmental Science, Stockholm University, Stockholm, Sweden
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Science, Shanghai Ocean University, Shanghai, China
| | - Paul Dijkstra
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Lingling Shi
- Key Laboratory of Economics Plants and Biotechnology, Institute of Botany, Chinese Academy of Sciences, Kunming, China
- World Agroforestry Centre, China and East-Asia Office, Kunming, China
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Michaela A. Dippold
- Biogeochemistry of Agroecosystem, University of Goettingen, Goettingen, Germany
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
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6
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Ravinath R, Das AJ, Usha T, Ramesh N, Middha SK. Targeted metagenome sequencing reveals the abundance of Planctomycetes and Bacteroidetes in the rhizosphere of pomegranate. Arch Microbiol 2022; 204:481. [PMID: 35834016 DOI: 10.1007/s00203-022-03100-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
Agricultural productivity of pomegranate can be enhanced by identifying the crop-associated microbial diversity in the rhizosphere region with respect to plant growth promoters and other beneficial organisms. Traditional culture methods have limitations in microbial screening as only 1-2% of these organisms can be cultured. In the present study, 16S rRNA amplicon-based metagenomics approach using MinION Oxford Nanopore platform was employed to explore the microbial diversity in the rhizosphere of pomegranate Bhagwa variety, across variable soil depths from 0 to 5 cms (R2), 5-10 cms (R4) and 10-15 cms (R6), using bulk soil as the control. Across all the three layers, significant variations in pH, nitrogen content and total fungal count were observed. 16S rRNA analysis showed the abundance of planctomycetes, Pirellula staleyi, followed by bacteroidetes, Flavisolibacter LC59 and Niastella koreensis across the various soil depths in the rhizospheric soil samples. Pathway prediction analysis indicated arginine and proline metabolism (gamma-glutamyl putrescine oxidase) and hydrogen sulfide biosynthesis as the most abundant pathway hits. Comparative abundance analysis across layers showed the R6 layer with the maximum microbial diversity in terms of highest dimension of variation (79.2%) followed by R4 and R2 layers (p < 0.01). Our analysis shows the significant influence of root zone in shaping microbial diversity. This study has reported the presence of Planctomycetes, Pirellula staleyi for the first time in the pomegranate field.
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Affiliation(s)
- Renuka Ravinath
- School of Applied Sciences, REVA University, Rukmini Knowledge Park, Bangalore, 560064, Karnataka, India
| | - Anupam J Das
- School of Applied Sciences, REVA University, Rukmini Knowledge Park, Bangalore, 560064, Karnataka, India
- Basesolve Informatics Private Limited, Ellisbridge, Ahmedabad, 380006, Gujarat, India
| | - Talambedu Usha
- Department of Biotechnology, Maharani Lakshmi Ammani College for Women, Bangalore, 560012, Karnataka, India
| | - Nijalingappa Ramesh
- School of Applied Sciences, REVA University, Rukmini Knowledge Park, Bangalore, 560064, Karnataka, India
| | - Sushil Kumar Middha
- Department of Biotechnology, Maharani Lakshmi Ammani College for Women, Bangalore, 560012, Karnataka, India.
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Naylor D, McClure R, Jansson J. Trends in Microbial Community Composition and Function by Soil Depth. Microorganisms 2022; 10:microorganisms10030540. [PMID: 35336115 PMCID: PMC8954175 DOI: 10.3390/microorganisms10030540] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 12/18/2022] Open
Abstract
Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.
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Alves RJE, Callejas IA, Marschmann GL, Mooshammer M, Singh HW, Whitney B, Torn MS, Brodie EL. Kinetic Properties of Microbial Exoenzymes Vary With Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile. Front Microbiol 2021; 12:735282. [PMID: 34917043 PMCID: PMC8669745 DOI: 10.3389/fmicb.2021.735282] [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: 07/02/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
Current knowledge of the mechanisms driving soil organic matter (SOM) turnover and responses to warming is mainly limited to surface soils, although over 50% of global soil carbon is contained in subsoils. Deep soils have different physicochemical properties, nutrient inputs, and microbiomes, which may harbor distinct functional traits and lead to different SOM dynamics and temperature responses. We hypothesized that kinetic and thermal properties of soil exoenzymes, which mediate SOM depolymerization, vary with soil depth, reflecting microbial adaptation to distinct substrate and temperature regimes. We determined the Michaelis-Menten (MM) kinetics of three ubiquitous enzymes involved in carbon (C), nitrogen (N) and phosphorus (P) acquisition at six soil depths down to 90 cm at a temperate forest, and their temperature sensitivity based on Arrhenius/Q10 and Macromolecular Rate Theory (MMRT) models over six temperatures between 4–50°C. Maximal enzyme velocity (Vmax) decreased strongly with depth for all enzymes, both on a dry soil mass and a microbial biomass C basis, whereas their affinities increased, indicating adaptation to lower substrate availability. Surprisingly, microbial biomass-specific catalytic efficiencies also decreased with depth, except for the P-acquiring enzyme, indicating distinct nutrient demands at depth relative to microbial abundance. These results suggested that deep soil microbiomes encode enzymes with intrinsically lower turnover and/or produce less enzymes per cell, reflecting distinct life strategies. The relative kinetics between different enzymes also varied with depth, suggesting an increase in relative P demand with depth, or that phosphatases may be involved in C acquisition. Vmax and catalytic efficiency increased consistently with temperature for all enzymes, leading to overall higher SOM-decomposition potential, but enzyme temperature sensitivity was similar at all depths and between enzymes, based on both Arrhenius/Q10 and MMRT models. In a few cases, however, temperature affected differently the kinetic properties of distinct enzymes at discrete depths, suggesting that it may alter the relative depolymerization of different compounds. We show that soil exoenzyme kinetics may reflect intrinsic traits of microbiomes adapted to distinct soil depths, although their temperature sensitivity is remarkably uniform. These results improve our understanding of critical mechanisms underlying SOM dynamics and responses to changing temperatures through the soil profile.
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Affiliation(s)
- Ricardo J Eloy Alves
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ileana A Callejas
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Civil and Environmental Engineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Gianna L Marschmann
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Maria Mooshammer
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Hans W Singh
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Bizuayehu Whitney
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Margaret S Torn
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Energy and Resources Group, University of California, Berkeley, Berkeley, CA, United States
| | - Eoin L Brodie
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
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9
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Hu X, Liu X, Qiao L, Zhang S, Su K, Qiu Z, Li X, Zhao Q, Yu C. Study on the spatial distribution of ureolytic microorganisms in farmland soil around tailings with different heavy metal pollution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 775:144946. [PMID: 33618300 DOI: 10.1016/j.scitotenv.2021.144946] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/02/2021] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
Ureolytic microorganisms, a kind of microorganism which can secrete urease and decompose urea, have great potential in remediation of soil heavy metals based on microbial induced carbonate precipitation. However, the horizontal and vertical distribution of ureolytic microbial community in heavy metals contaminated soils is poorly understood. In this study, urease genes in agricultural soils surrounding tailings were first investigated using metagenomic in two dimensions: heavy metal pollution (Low-L, Middle-M, High-H) and soil depth (0-20 cm, 20-40 cm, 40-60 cm, 60-80 cm, 80-100 cm). Results showed that the effect of heavy metal concentration on ureolytic microorganisms was indeed significant, while the changes of ureolytic microorganisms with increasing soil depth varied in the vertical direction at the same level of heavy metal contamination. H site had the highest diversity of ureolytic microorganisms except for the topsoil. And at the same heavy metal contamination level, the ureolytic microbial diversity was lower in deeper soils. Proteobacteria, Actinobacteria and Thaumarchaeota (Archaea) were the dominant phyla of ureolytic microorganisms in all three sites, accounting for more than 80% of the total. However, the respond to the heavy metal concentrations of three phyla were different, which were increasing, decreasing and essentially unchanged, respectively. Besides, other environmental factors such as SOM and pH had different effects on ureolytic microorganisms, with Proteobacteria being positively correlated and Actinobacteria being the opposite. Another phenomenon was that Actinobacteria and Verrucomicrobia were biomarkers of group L, which could significantly explain the difference with the other two sites. These results provided valuable information for further research on the response mechanism and remediation of heavy metal pollution by ureolytic microbial system.
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Affiliation(s)
- Xuesong Hu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Xiaoxia Liu
- Beijing Station of Agro-Environmental Monitoring, Test and Supervision Center of Agro-Environmental Quality, MOA, 100032 Beijing, China
| | - Longkai Qiao
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Shuo Zhang
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Kaiwen Su
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Ziliang Qiu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Xianhong Li
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Qiancheng Zhao
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Caihong Yu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China.
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10
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Diverse Understory Vegetation Alleviates Nitrogen Competition with Crop Trees in Poplar Plantations. FORESTS 2021. [DOI: 10.3390/f12060705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Understory vegetation plays a crucial role in nutrient turnover and cycling in plantations, but it also competes for nutrients with crop trees when only a single species is present due to its specific nutrient requirements. However, it remains unclear whether this competition can be alleviated when the species richness of understory vegetation increases. In this study, we tested different gradients of understory vegetation species richness, including understory vegetation removal (UR), the retention of a single main understory vegetation species (RS), and the retention of natural diverse understory vegetation (RD) as part of a poplar (Populus deltoides ‘Nanlin-3804′) plantation, to study their effects on poplar growth, and to evaluate nitrogen (N) usage and how this was affected by the interactions between the poplar and understory vegetation. The results showed a generally lower periodic growth, and a significant decline in the foliar chlorophyll content and glutamine synthetase activity of poplar under treatment with RS and RD compared to those under UR treatment conducted in July 2019, which clearly indicated N competition between the understory vegetation and poplar trees. However, no significant difference was detected in the foliar chlorophyll content and glutamine synthetase activity of poplar under RD and RS treatment; only the nitrate reductase activity in poplar leaves under RD treatment declined significantly, by 22.25%, in June 2019. On the contrary, the diameter at breast height (DBH) of the poplar under RD treatment showed an increase of 34.69% from July to August 2019, compared with that under RS treatment. Furthermore, the increase in the species richness of understory vegetation resulted in an increase in the δ15N values in the poplar leaves, which was strongly regulated by the NH4+-N pool in the 10–20 cm soil layer, indicating the effective coordination of N utilization between poplar and understory vegetation when diversified understory plant species were present. These findings demonstrate the essential role of understory vegetation species diversity in alleviating N competition with crop trees, and provide guidance for understory vegetation management in poplar plantations.
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Frey B, Walthert L, Perez-Mon C, Stierli B, Köchli R, Dharmarajah A, Brunner I. Deep Soil Layers of Drought-Exposed Forests Harbor Poorly Known Bacterial and Fungal Communities. Front Microbiol 2021; 12:674160. [PMID: 34025630 PMCID: PMC8137989 DOI: 10.3389/fmicb.2021.674160] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/12/2021] [Indexed: 12/31/2022] Open
Abstract
Soil microorganisms such as bacteria and fungi play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of the soil microbiome to a depth of 2 m in Swiss drought-exposed forests of European beech and oaks on calcareous bedrock. We aimed to disentangle the effects of soil depth, tree (beech, oak), and substrate (soil, roots) on microbial abundance, diversity, and community structure. With increasing soil depth, organic carbon, nitrogen, and clay content decreased significantly. Similarly, fine root biomass, microbial biomass (DNA content, fungal abundance), and microbial alpha-diversity decreased and were consequently significantly related to these physicochemical parameters. In contrast, bacterial abundance tended to increase with soil depth, and the bacteria to fungi ratio increased significantly with greater depth. Tree species was only significantly related to the fungal Shannon index but not to the bacterial Shannon index. Microbial community analyses revealed that bacterial and fungal communities varied significantly across the soil layers, more strongly for bacteria than for fungi. Both communities were also significantly affected by tree species and substrate. In deep soil layers, poorly known bacterial taxa from Nitrospirae, Chloroflexi, Rokubacteria, Gemmatimonadetes, Firmicutes and GAL 15 were overrepresented. Furthermore, archaeal phyla such as Thaumarchaeota and Euryarchaeota were more abundant in subsoils than topsoils. Fungal taxa that were predominantly found in deep soil layers belong to the ectomycorrhizal Boletus luridus and Hydnum vesterholtii. Both taxa are reported for the first time in such deep soil layers. Saprotrophic fungal taxa predominantly recorded in deep soil layers were unknown species of Xylaria. Finally, our results show that the microbial community structure found in fine roots was well represented in the bulk soil. Overall, we recorded poorly known bacterial and archaeal phyla, as well as ectomycorrhizal fungi that were not previously known to colonize deep soil layers. Our study contributes to an integrated perspective on the vertical distribution of the soil microbiome at a fine spatial scale in drought-exposed forests.
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Affiliation(s)
- Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Lorenz Walthert
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Roger Köchli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Alexander Dharmarajah
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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Sun Q, Guo S, Wang R, Song J. Responses of bacterial communities and their carbon dynamics to subsoil exposure on the Loess Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:144146. [PMID: 33298321 DOI: 10.1016/j.scitotenv.2020.144146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
Subsoil exposure due to factors including erosion and terracing, evidently decreases soil organic carbon storage and productivity, but the responses of bacterial communities and their carbon dynamics remain unclear. Soils from 0-20 cm, 20-60 cm and 60-100 cm were collected from three 100 cm profiles in bare land on the Loess Plateau, and incubated in buried pots for a year (July 2016 to July 2017) to simulate subsoil exposure, with ongoing monitoring of the microbial mineralization rate of soil organic carbon (Kc), using Li-Cor 8100. At the end of the incubation period, the exposed soil and the in situ control soil were sampled to investigate changes in bacterial community composition, as represented by 16S rRNA, and the activities of enzymes involved in soil carbon cycling. Both copiotrophic (Actinobacteria and Alphaproteobacteria) and oligotrophic (Thermoleophilia) groups were stimulated in the exposed vs. control soil at 20-60 and 60-100 cm. The exposed vs. control soil from 60 to 100 cm produced the greatest bacterial responses, such as greater diversity and altered keystone groups (Thermoleophilia vs. unidentified Acidobacteria). Enzyme activities were greater in the exposed vs. control soil at both 20-60 cm (β-D-xylosidase and cellobiohydrolase) and 60-100 cm (β-D-xylosidase and β-D-glucosidase). The exposed soil from 20-60 cm and 60-100 cm had lower Kc and Q10 values than those at 0-20 cm. Our findings revealed the existence of bacterial depth-specific responses to subsoil exposure, and highlight the effect of anthropogenic soil redistribution on soil carbon flux and its potential responses to future climate change.
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Affiliation(s)
- Qiqi Sun
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shannxi 712100, PR China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shannxi 712100, PR China; Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, PR China
| | - Shengli Guo
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shannxi 712100, PR China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shannxi 712100, PR China
| | - Rui Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shannxi 712100, PR China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shannxi 712100, PR China.
| | - Jinming Song
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, PR China.
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