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Hao Y, Sun A, Lu C, Su JQ, Chen QL. Protists and fungi: Reinforcing urban soil ecological functions against flash droughts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175274. [PMID: 39117190 DOI: 10.1016/j.scitotenv.2024.175274] [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: 04/23/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
Rising instances of flash droughts are contributing to notable variability in soil moisture across terrestrial ecosystems. These phenomena challenge urban ecosystem services, yet the reaction of soil ecological functions (SEFs) to such events is poorly understood. This study investigates the responses of SEFs (about nutrient metabolism capacity and potential) and the microbiome under two specific scenarios: a flooding-drought sequence and a direct drought condition. Using quantitative microbial element cycling analysis, high-throughput sequencing, and enzyme activity measurements, we found that unlike in forests, the microbial composition in urban soils remained unchanged during flash drought conditions. However, SEFs were affected in both settings. Correlation analysis and Mantel test showed that forest soils exhibited more complex interactions among soil moisture, properties, and microbial communities. Positive linear correlation revealed that bacteria were the sole drivers of SEFs. Interestingly, while multi-threshold results suggested bacterial α diversity impeded the maximization of SEFs in urban soils, fungi and protists had a beneficial impact. Cross-domain network of urban soils had higher number of nodes and edges, but lower average degree and robustness than forest soils. Mantel test revealed that fungi and protist had significant correlations with bacterial composition in forest soils, but not in urban soils. In the urban network, the degree and eigenvector centrality of bacterial, fungal and protistan ASVs were significantly lower compared to those in the forest. These results suggest that the lower robustness of the microbial network in urban soils is attributed to limited interactions among fungi, consumer protists, and bacteria, contributing to the failure of microbial-driven ecological functions. Overall, our findings emphasize the critical role of fungi and protists in shielding urban soils from drought-induced disturbances and in enhancing the resistance of urban ecological functions amidst environmental changes.
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Affiliation(s)
- Yilong Hao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Anqi Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Changyi Lu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
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2
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Zeng Q, Lam K, Salcedo A, Tikekar RV, Micallef SA, Blaustein RA. Effects of Organic Soil Amendments on Antimicrobial-Resistant Bacteria in Urban Agriculture Environments. J Food Prot 2024; 87:100344. [PMID: 39147100 DOI: 10.1016/j.jfp.2024.100344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 08/06/2024] [Accepted: 08/09/2024] [Indexed: 08/17/2024]
Abstract
Biological soil amendments of animal origin (BSAAOs) are widely used in urban agriculture to improve soil quality. Although BSAAO use is regulated due to risks for introducing foodborne pathogens, effects on antimicrobial-resistant (AMR) bacteria are not well established. Here, we aimed to explore the impacts of BSAAOs on levels of resident AMR bacteria in leafy vegetable production environments (i.e., kale, lettuce, chard, cabbage) across urban farms and community gardens in the greater Washington D.C. area (n = 7 sites). Leaf tissue (LT), root zone soil (RZS; amended soil in crop beds), and bulk soil (BS; site perimeter) were collected and analyzed for concentrations of total heterotrophic bacteria (THB), ampicillin (Amp) or tetracycline (Tet) resistant THB, and coliforms. As expected, amended plots harbored significantly higher concentrations of THB than bulk soil (P < 0.001). The increases in total bacteria associated with reduced fractions of Tet-resistant bacteria (P = 0.008), as well as case-specific trends for reduced fractions of Amp-resistant bacteria and coliforms. Site-to-site variation in concentrations of AMR bacteria in soil and vegetable samples reflected differences in land history and crop management, while within-site variation was associated with specific amendment sources, as well as vegetable type and cultivar. Representative isolates of the AMR bacteria and coliforms were further screened for multidrug resistance (MDR) phenotypes, and a high frequency was observed for the former. In amended soils, as the soil pH (range 6.56-7.80) positively correlated with the fraction of Tet-resistant bacteria (rho = 0.529; P < 0.001), crop management strategies targeting pH may have applications to control related risks. Overall, our findings demonstrate that soil amendments promote soil bacteria concentrations and have important implications for limiting the spread of AMR bacteria, at least in the urban landscape.
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Affiliation(s)
- Qingyue Zeng
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, United States
| | - Kevin Lam
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, United States
| | - Autumn Salcedo
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, United States
| | - Rohan V Tikekar
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, United States
| | - Shirley A Micallef
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, United States; Centre for Food Safety and Security Systems, University of Maryland, College Park, Maryland, United States
| | - Ryan A Blaustein
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, United States.
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3
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Wang M, Li D, Liu X, Chen C, Frey B, Sui X, Li MH. Global hierarchical meta-analysis to identify the factors for controlling effects of antibiotics on soil microbiota. ENVIRONMENT INTERNATIONAL 2024; 192:109038. [PMID: 39357259 DOI: 10.1016/j.envint.2024.109038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 09/16/2024] [Accepted: 09/26/2024] [Indexed: 10/04/2024]
Abstract
It is widely known that antibiotics can affect the structure and function of soil microbial communities, but the specific degree of impact and controlled factors on different indicators remain inconclusive. We conducted a multiple hierarchical mixed effects meta-analysis on 2564 observations that were extracted from 60 publications, to comprehensively assess the impact of antibiotics on soil microbiota. The results showed that antibiotics had significant negative effects on soil microbial biomass, α-diversity and soil enzyme activity. Under neutral initial soil, when soil was derived from agricultural land or had a fine-textured, the negative impacts of antibiotics on soil microbial community were exacerbated. Both single and mixed additions of antibiotics had significant inhibitory effects on soil microbial enzyme activities. The Random Forest model predicted the following key moderators involved in the effects of antibiotics on the soil microbiome, and antibiotics type, soil texture were key moderators on the severity of soil microbial biomass changes. Soil texture, temperature and single or combined application constitute of antibiotics were the main drivers of effects on soil enzyme activities. The reported results can be helpful to assess the ecological risk of antibiotics in a soil environment and provides a scientific basis for the rational of antibiotics use in the soil environment.
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Affiliation(s)
- Mingyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, PR China
| | - Detian Li
- Griffith School of Environment and Science and the Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Xiangyu Liu
- Griffith School of Environment and Science and the Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Chengrong Chen
- Griffith School of Environment and Science and the Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Beat Frey
- Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, PR China.
| | - Mai-He Li
- Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland; Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, PR China; School of Life Science, Hebei University, Baoding, PR China.
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4
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Zheng F, Gao J, Tang M, Zhou T, Zhu D, Yang X, Chen B. Urbanization reduces the stability of soil microbial community by reshaping the diversity and network complexity. CHEMOSPHERE 2024; 364:143177. [PMID: 39182733 DOI: 10.1016/j.chemosphere.2024.143177] [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: 06/27/2024] [Revised: 08/12/2024] [Accepted: 08/22/2024] [Indexed: 08/27/2024]
Abstract
Rapid urbanization considerably alters soil environment, biodiversity, and stability of terrestrial ecosystems. Soil microbial community, a key component of global biodiversity, plays a pivotal role in ecosystem stability and is highly vulnerable to urbanization. However, effects of urbanization on the diversity, stability, and network structure of soil microbial community remain poorly understood. Herein, we investigated the diversity and stability of soil microbial communities, including bacteria, fungi, and protists, across three regions with different levels of urbanization-urban, suburb, and ecoregion-using high-throughput sequencing techniques. Our results revealed that urbanization led to a notable decrease in the alpha diversity of soil microbial community, causing a significant reduction in soil stability, as assessed by the average variation degree (AVD). The loss of stability was linked to the diminished alpha diversity of the soil fungal and protistan communities, along with weakened interactions among bacteria, fungi, and protists. Notably, the majority of keystone species identified through network analysis were classified as bacteria (Proteobacteria) and displayed a strong positive correlation with the environmental factors influencing AVD. This highlights that the variability of bacteria and the immutability of fungi and protists are important to sustain soil microbial stability. Furthermore, structural equation models indicated that protistan diversity primarily drove soil microbial stability across all regions studied. In the suburban and ecoregion areas, soil microbial stability was directly influenced by the soil properties, bacterial diversity, and keystone species, as well as indirectly affected by heavy metals. These results underscore how urbanization can reduce the stability of soil microbial community via declined diversity and network complexity, whereas the establishment of ecoregions maybe contribute to preserve the diversity and stability of soil microbial community.
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Affiliation(s)
- Fei Zheng
- College of Life Sciences, Hebei University, Baoding, 071002, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Jingwei Gao
- College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Mingyang Tang
- College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Tao Zhou
- College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Bing Chen
- College of Life Sciences, Hebei University, Baoding, 071002, China.
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5
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Wiener EA, Ewald JM, LeFevre GH. Fungal diversity and key functional gene abundance in Iowa bioretention cells: implications for stormwater remediation potential. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2024. [PMID: 39192758 DOI: 10.1039/d4em00275j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Stormwater bioretention cells are green stormwater infrastructure systems that can help mitigate flooding and remove contaminants. Plants and bacteria improve nutrient removal and degrade organic contaminants; however, the roles of fungi in bioretention cells are less known. Although mycorrhizal fungi aid in plant growth/improve nutrient uptake, there is a notable lack of research investigating fungal diversity in bioretention cells. Other types of fungi could benefit bioretention cells (e.g., white rot fungi degrade recalcitrant contaminants). This study addresses the knowledge gap of fungal function and diversity within stormwater bioretention cells. We collected multiple soil samples from 27 different bioretention cells in temperate-climate eastern Iowa USA, characterized soil physicochemical parameters, sequenced the internal transcribed spacer (ITS) amplicon to identify fungal taxa from extracted DNA, and measured functional gene abundances for two fungal laccases (Cu1, Cu1A) and a fungal nitrite reductase gene (nirKf). Fungal biodegradation functional genes were present in bioretention soils (mean copies per g: 7.4 × 105nirKf, 3.2 × 106Cu1, 4.0 × 108Cu1A), with abundance of fungal laccase and fungal nitrite reductase genes significantly positively correlated with soil pH and organic matter (Pearson's R: >0.39; rho < 0.05). PERMANOVA analysis determined soil characteristics were not significant explanatory variables for community composition (beta diversity). In contrast, planting specifications significantly impacted fungal diversity; the presence/absence of a few planting types and predominant vegetation type in the cell explained 89% of variation in fungal diversity. These findings further emphasize the importance of plants and media as key design parameters for bioretention cells, with implications for fungal bioremediation of captured stormwater contaminants.
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Affiliation(s)
- Erica A Wiener
- Department of Civil & Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA 52242, USA.
- IIHR-Hydroscience &Engineering, 100 C. Maxwell Stanley Hydraulics Laboratory, Iowa City, IA 52242, USA
| | - Jessica M Ewald
- Department of Civil & Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA 52242, USA.
- IIHR-Hydroscience &Engineering, 100 C. Maxwell Stanley Hydraulics Laboratory, Iowa City, IA 52242, USA
| | - Gregory H LeFevre
- Department of Civil & Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA 52242, USA.
- IIHR-Hydroscience &Engineering, 100 C. Maxwell Stanley Hydraulics Laboratory, Iowa City, IA 52242, USA
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Yang L, Chen H, Gao H, Wang Y, Chen T, Svartengren M, Norbäck D, Wei J, Zheng X, Zhang L, Lu C, Yu W, Wang T, Ji JS, Meng X, Zhao Z, Zhang X. Prenatal and postnatal early life exposure to greenness and particulate matter of different size fractions in relation to childhood rhinitis - A multi-center study in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 938:173402. [PMID: 38797418 DOI: 10.1016/j.scitotenv.2024.173402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/18/2024] [Accepted: 05/19/2024] [Indexed: 05/29/2024]
Abstract
The impact of early life exposure to residential greenness on childhood rhinitis and its interaction with particulate matter (PM) of different size fractions remain inconsistent. Herein, we recruited 40,486 preschool children from randomly selected daycare centers in 7 cities in China from 2019 to 2020, and estimated exposure to residential greenness by the normalized difference vegetation index (NDVI) with a 500 m buffer. Exposure to ambient PM (PM1, PM2.5, and PM10) was evaluated using a satellite-based prediction model (daily, at a resolution of 1 km × 1 km). By mixed-effect logistic regression, NDVI values during pregnancy, in the first (0-1 year old) and the second (1-2 years old) year of life were negatively associated with lifetime rhinitis (LR) and current rhinitis (CR) (P < 0.001). PM in the same time windows was associated with increased risks of LR and CR in children, with smaller size fraction of PM showing greater associations. The negative associations between prenatal and postnatal NDVI and LR and CR in preschool children remained robust after adjusting for concomitant exposure to PM, whereas the associations of postnatal NDVI and rhinitis showed significant interactions with PM. At lower levels of PM, postnatal NDVI remained negatively associated with rhinitis and was partly mediated by PM (10.0-40.9 %), while at higher levels of PM, the negative associations disappeared or even turned positive. The cut-off levels of PM were identified for each size fraction of PM. In conclusion, prenatal exposure to greenness had robust impacts in lowering the risk of childhood rhinitis, while postnatal exposure to greenness depended on the co-exposure levels to PM. This study revealed the complex interplay of greenness and PM on rhinitis in children. The exposure time window in prenatal or postnatal period and postnatal concomitant PM levels played important roles in influencing the associations between greenness, PM and rhinitis.
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Affiliation(s)
- Liu Yang
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China
| | - Han Chen
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment (Fudan University), Fudan University, Shanghai 200032, China
| | - Huiyu Gao
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China
| | - Ying Wang
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China
| | - Tianyi Chen
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment (Fudan University), Fudan University, Shanghai 200032, China
| | - Magnus Svartengren
- Department of Occupational and Environmental Medicine, Uppsala University Hospital, 751 85 Uppsala, Sweden
| | - Dan Norbäck
- Department of Occupational and Environmental Medicine, Uppsala University Hospital, 751 85 Uppsala, Sweden
| | - Jing Wei
- Department of Atmospheric and Oceanic Science, Earth System Science Interdisciplinary Center, University of Maryland, College Park, MD, USA
| | - Xiaohong Zheng
- School of Energy & Environment, Southeast University, Nanjing 210096, China
| | - Ling Zhang
- Department of Environmental Hygiene and Occupational Medicine, School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Chan Lu
- Department of Occupational and Environmental Health, School of Public Health, Xiangya Medical College, Central South University, Changsha 410078, China
| | - Wei Yu
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Chongqing University, Chongqing 400030, China
| | - Tingting Wang
- School of Nursing & Health Management, Shanghai University of Medicine & Health Sciences, Shanghai 201318, China
| | - John S Ji
- Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - Xia Meng
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment (Fudan University), Fudan University, Shanghai 200032, China; Key Laboratory of Public Health Safety of the Ministry of Education, Shanghai Typhoon Institute/CMA, Shanghai Key Laboratory of Meteorology and Health, Shanghai 200030, China; IRDR International Center of Excellence on Risk Interconnectivity and Governance on Weather/Climate Extremes Impact and Public Health, Fudan University, Shanghai 200438, China.
| | - Zhuohui Zhao
- Department of Environmental Health, School of Public Health, NHC Key Laboratory of Health Technology Assessment (Fudan University), Fudan University, Shanghai 200032, China; Key Laboratory of Public Health Safety of the Ministry of Education, Shanghai Typhoon Institute/CMA, Shanghai Key Laboratory of Meteorology and Health, Shanghai 200030, China; IRDR International Center of Excellence on Risk Interconnectivity and Governance on Weather/Climate Extremes Impact and Public Health, Fudan University, Shanghai 200438, China.
| | - Xin Zhang
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China.
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Chen Y, Tao S, Ma J, Qu Y, Sun Y, Wang M, Cai Y. New insights into assembly processes and driving factors of urban soil microbial community under environmental stress in Beijing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174551. [PMID: 38972416 DOI: 10.1016/j.scitotenv.2024.174551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/21/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
Rapid urbanization leads to drastic environmental changes, directly or indirectly affecting the structure and function of soil microbial communities. However, the ecological response of soil microbes to environmental stresses has not yet been fully explored. In this study, we used high-throughput sequencing to analyze the assembly mechanism and driving factors of soil microbial community under environmental stresses. The results indicated that environmental stresses significantly affected soil properties and the levels of beryllium, cobalt, antimony, and vanadium contamination in soil generally increased from the suburban areas toward the city core. The composition and distribution of soil microbial communities demonstrated clear differences under different levels of environmental stress, but there was no significant difference in microbial diversity. Random forest and partial least squares structural equation modeling results suggested that multiple factors influenced microbial diversity, but antimony was the key driver. The influence of environmental stress led to deterministic processes dominating microbial community assembly processes, which promoted the regional homogenization of soil microbes. Therefore, this study provides new insights into urban soil microbial management under environmental stresses.
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Affiliation(s)
- Ying Chen
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Shiyang Tao
- South China Institute of Environmental Science, Ministry of Ecological Environment, Guangzhou 510655, China
| | - Jin Ma
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Yajing Qu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yi Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Meiying Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yuxuan Cai
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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8
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Xu Z, Zhao S. Fine-grained urban landscape mapping reveals broad-scale homogeneity in urban environments. Sci Bull (Beijing) 2024; 69:1802-1805. [PMID: 38641512 DOI: 10.1016/j.scib.2024.03.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Affiliation(s)
- Zhiyu Xu
- College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Shuqing Zhao
- School of Ecology, Hainan University, Haikou 570228, China.
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9
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Monaco P, Baldoni A, Naclerio G, Scippa GS, Bucci A. Impact of Plant-Microbe Interactions with a Focus on Poorly Investigated Urban Ecosystems-A Review. Microorganisms 2024; 12:1276. [PMID: 39065045 PMCID: PMC11279295 DOI: 10.3390/microorganisms12071276] [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: 05/16/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
The urbanization process, which began with the Industrial Revolution, has undergone a considerable increase over the past few decades. Urbanization strongly affects ecological processes, often deleteriously, because it is associated with a decrease in green spaces (areas of land covered by vegetation), loss of natural habitats, increased rates of species extinction, a greater prevalence of invasive and exotic species, and anthropogenic pollutant accumulation. In urban environments, green spaces play a key role by providing many ecological benefits and contributing to human psychophysical well-being. It is known that interactions between plants and microorganisms that occur in the rhizosphere are of paramount importance for plant health, soil fertility, and the correct functioning of plant ecosystems. The growing diffusion of DNA sequencing technologies and "omics" analyses has provided increasing information about the composition, structure, and function of the rhizomicrobiota. However, despite the considerable amount of data on rhizosphere communities and their interactions with plants in natural/rural contexts, current knowledge on microbial communities associated with plant roots in urban soils is still very scarce. The present review discusses both plant-microbe dynamics and factors that drive the composition of the rhizomicrobiota in poorly investigated urban settings and the potential use of beneficial microbes as an innovative biological tool to face the challenges that anthropized environments and climate change impose. Unravelling urban biodiversity will contribute to green space management, preservation, and development and, ultimately, to public health and safety.
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Affiliation(s)
- Pamela Monaco
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (A.B.); (G.N.); (G.S.S.)
| | | | | | | | - Antonio Bucci
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (A.B.); (G.N.); (G.S.S.)
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10
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He K, Han R, Wang Z, Xiao Z, Hao Y, Dong Z, Xu Q, Li G. Soil source, not the degree of urbanization determines soil physicochemical properties and bacterial composition in Ningbo urban green spaces. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172550. [PMID: 38643872 DOI: 10.1016/j.scitotenv.2024.172550] [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: 03/07/2024] [Revised: 04/07/2024] [Accepted: 04/16/2024] [Indexed: 04/23/2024]
Abstract
Urban green spaces provide multiple ecosystem services and have great influences on human health. However, the compositions and properties of urban soil are not well understood yet. In this study, soil samples were collected from 45 parks in Ningbo to investigate the relationships among soil physicochemical properties, heavy metals and bacterial communities. The results showed that soil dissolved organic matter (DOM) was of high molecular weight, high aromaticity, and low degree of humification. The contents of heavy metals were all below the China's national standard safety limit (GB 3660-2018). The bioavailability of heavy metals highly correlated with soil pH, the content of DOC, the fluorescent component, the degree of humification and the source of DOM. The most abundant genera were Gemmatimonadaceae_uncultured, Xanthobacteraceae_uncultured, and Acidothermus in all samples, which were related to nitrogen cycle and bioavailability of heavy metals. Soil pH, bioavailability of Zn, Cd, and Pb (CaCl2 extracted) were the main edaphic factors influencing bacterial community composition. It should be noted that there was no significant impact of urbanization on soil physicochemical properties and bacterial composition, but they were determined by the source of soil in urban green spaces. However, with the passage of time, the effect of urbanization on urban green spaces cannot be ignored. Overall, this study provided new insight for understanding the linkage among soil physicochemical properties, heavy metals, and bacterial communities in urban green spaces.
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Affiliation(s)
- Kaiwen He
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruixia Han
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhe Wang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zufei Xiao
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yilong Hao
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuozhen Dong
- Agricultural Technology Management and Service Station of Haishu District in Ningbo, Ningbo 315012, China
| | - Qiao Xu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Li S, Yan X, Abdullah Al M, Ren K, Rensing C, Hu A, Tsyganov AN, Mazei Y, Smirnov A, Mazei N, Yang J. Ecological and evolutionary processes involved in shaping microbial habitat generalists and specialists in urban park ecosystems. mSystems 2024; 9:e0046924. [PMID: 38767347 PMCID: PMC11237591 DOI: 10.1128/msystems.00469-24] [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: 03/31/2024] [Accepted: 04/17/2024] [Indexed: 05/22/2024] Open
Abstract
Microbiomes are integral to ecological health and human well-being; however, their ecological and evolutionary drivers have not been systematically investigated, especially in urban park ecosystems. As microbes have different levels of tolerance to environmental changes and habitat preferences, they can be categorized into habitat generalists and specialists. Here, we explored the ecological and evolutionary characteristics of both prokaryotic and microeukaryotic habitat generalists and specialists from six urban parks across five habitat types, including moss, soil, tree hole, water, and sediment. Our results revealed that different ecological and evolutionary processes maintained and regulated microbial diversity in urban park ecosystems. Under ecological perspective, community assembly of microbial communities was mainly driven by stochastic processes; however, deterministic processes were higher for habitat specialists than generalists. Microbial interactions were highly dynamic among habitats, and habitat specialists played key roles as module hubs in intradomain networks. In aquatic interdomain networks, microeukaryotic habitat specialists and prokaryotic habitat specialists played crucial roles as module hubs and connectors, respectively. Furthermore, analyzing evolutionary characteristics, our results revealed that habitat specialists had a much higher diversification potential than generalists, while generalists showed shorter phylogenetic branch lengths as well as larger genomes than specialists. This study broadens our understanding of the ecological and evolutionary features of microbial habitat generalists and specialists in urban park ecosystems across multi-habitat. IMPORTANCE Urban parks, as an important urban greenspace, play essential roles in ecosystem services and are important hotspots for microbes. Microbial diversity is driven by different ecological and evolutionary processes, while little is currently known about the distinct roles of ecological and evolutionary features in shaping microbial diversity in urban park ecosystems. We explored the ecological and evolutionary characteristics of prokaryotic and microeukaryotic habitat generalists and specialists in urban park ecosystems based on a representative set of different habitats. We found that different ecological and evolutionary drivers jointly maintained and regulated microbial diversity in urban park microbiomes through analyzing the community assembly process, ecological roles in hierarchical interaction, and species diversification potential. These findings significantly advance our understanding regarding the mechanisms governing microbial diversity in urban park ecosystems.
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Affiliation(s)
- Shuzhen Li
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Xue Yan
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mamun Abdullah Al
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Kexin Ren
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Christopher Rensing
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Institute of Environmental Microbiology, College of Resources and the Environment, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | | | - Yuri Mazei
- Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Smirnov
- Department of Invertebrate Zoology, Faculty of Biolog, St. Petersburg University, St Petersburg, Russia
| | | | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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12
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Brüssow F, Bruessow F, Brüssow H. The role of the plant microbiome for forestry, agriculture and urban greenspace in times of environmental change. Microb Biotechnol 2024; 17:e14482. [PMID: 38858806 PMCID: PMC11164675 DOI: 10.1111/1751-7915.14482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 06/12/2024] Open
Abstract
This Lilliput article provides a literature overview on ecological effects of the plant microbiome with a focus on practical application in forestry, agriculture and urban greenspace under the spectre of climate change. After an overview of the mostly bacterial microbiome of the model plant Arabidopsis thaliana, worldwide data from forests reveal ecological differentiation with respect to major guilds of predominantly fungal plant root symbionts. The plant-microbiome association forms a new holobiont, an integrated unit for ecological adaptation and evolutionary selection. Researchers explored the impact of the microbiome on the capacity of plants to adapt to changing climate conditions. They investigated the impact of the microbiome in reforestation programs, after wildfire, drought, salination and pollution events in forestry, grasslands and agriculture. With increasing temperatures plant populations migrate to higher latitudes and higher altitudes. Ecological studies compared the dispersal capacity of plant seeds with that of soil microbes and the response of soil and root microbes to experimental heating of soils. These studies described a succession of microbiome associations and the kinetics of a release of stored soil carbon into the atmosphere enhancing global warming. Scientists explored the impact of synthetic microbial communities (SynComs) on rice productivity or tea quality; of whole soil addition in grassland restoration; or single fungal inoculation in maize fields. Meta-analyses of fungal inoculation showed overall a positive effect, but also a wide variation in effect sizes. Climate change will be particularly prominent in urban areas ("urban heat islands") where more than half of the world population is living. Urban landscape architecture will thus have an important impact on human health and studies started to explore the contribution of the microbiome from urban greenspace to ecosystem services.
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Affiliation(s)
- Felix Brüssow
- La Comète, Paysage, Architecture et TerritoireGenèveSwitzerland
| | | | - Harald Brüssow
- Laboratory of Gene Technology, Department of BiosystemsKU LeuvenLeuvenBelgium
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13
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Nair GR, Kooverjee BB, de Scally S, Cowan DA, Makhalanyane TP. Changes in nutrient availability substantially alter bacteria and extracellular enzymatic activities in Antarctic soils. FEMS Microbiol Ecol 2024; 100:fiae071. [PMID: 38697936 PMCID: PMC11107947 DOI: 10.1093/femsec/fiae071] [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: 09/06/2023] [Revised: 03/07/2024] [Accepted: 05/01/2024] [Indexed: 05/05/2024] Open
Abstract
In polar regions, global warming has accelerated the melting of glacial and buried ice, resulting in meltwater run-off and the mobilization of surface nutrients. Yet, the short-term effects of altered nutrient regimes on the diversity and function of soil microbiota in polyextreme environments such as Antarctica, remains poorly understood. We studied these effects by constructing soil microcosms simulating augmented carbon, nitrogen, and moisture. Addition of nitrogen significantly decreased the diversity of Antarctic soil microbial assemblages, compared with other treatments. Other treatments led to a shift in the relative abundances of these microbial assemblages although the distributional patterns were random. Only nitrogen treatment appeared to lead to distinct community structural patterns, with increases in abundance of Proteobacteria (Gammaproteobateria) and a decrease in Verrucomicrobiota (Chlamydiae and Verrucomicrobiae).The effects of extracellular enzyme activities and soil parameters on changes in microbial taxa were also significant following nitrogen addition. Structural equation modeling revealed that nutrient source and extracellular enzyme activities were positive predictors of microbial diversity. Our study highlights the effect of nitrogen addition on Antarctic soil microorganisms, supporting evidence of microbial resilience to nutrient increases. In contrast with studies suggesting that these communities may be resistant to change, Antarctic soil microbiota responded rapidly to augmented nutrient regimes.
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Affiliation(s)
- Girish R Nair
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa
- Centre for Epidemic Response and Innovation, School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Bhaveni B Kooverjee
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Storme de Scally
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Thulani P Makhalanyane
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa
- Centre for Epidemic Response and Innovation, School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
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14
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Li X, Qin H, Tang N, Li X, Xing W. Microplastics enhance the invasion of exotic submerged macrophytes by mediating plant functional traits, sediment properties, and microbial communities. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134032. [PMID: 38492389 DOI: 10.1016/j.jhazmat.2024.134032] [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: 01/23/2024] [Revised: 02/25/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
Plant invasions and microplastics (MPs) have significantly altered the structure and function of aquatic habitats worldwide, resulting in severe damage to aquatic ecosystem health. However, the effects of MPs on plant invasion and the underlying mechanisms remain largely unknown. In this study, we conducted mesocosm experiments over a 90-day period to assess the effects of polystyrene microplastics on the invasion of exotic submerged macrophytes, sediment physicochemical properties, and sediment bacterial communities. Our results showed that PS-MPs significantly promoted the performance of functional traits and the invasive ability of exotic submerged macrophytes, while native plants remained unaffected. Moreover, PS-MPs addition significantly decreased sediment pH while increasing sediment carbon and nitrogen content. Additionally, MPs increased the diversity of sediment bacterial community but inhibited its structural stability, thereby impacting sediment bacterial multifunctionality to varying degrees. Importantly, we identified sediment properties, bacterial composition, and bacterial multifunctionality as key mediators that greatly enhance the invasion of exotic submerged macrophytes. These findings provide compelling evidence that the increase in MPs may exacerbate the invasion risk of exotic submerged macrophytes through multiple pathways. Overall, this study enhances our understanding of the ecological impacts of MPs on aquatic plant invasion and the health of aquatic ecosystems.
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Affiliation(s)
- Xiaowei Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Hongjie Qin
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Na Tang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xiaolu Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Wei Xing
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Wuhan 430074, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
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15
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Mo L, Zanella A, Squartini A, Ranzani G, Bolzonella C, Concheri G, Pindo M, Visentin F, Xu G. Anthropogenic vs. natural habitats: Higher microbial biodiversity pays the trade-off of lower connectivity. Microbiol Res 2024; 282:127651. [PMID: 38430888 DOI: 10.1016/j.micres.2024.127651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/23/2024] [Accepted: 02/16/2024] [Indexed: 03/05/2024]
Abstract
Climate change and anthropogenic disturbances are known to influence soil biodiversity. The objectives of this study were to compare the community composition, species coexistence patterns, and ecological assembly processes of soil microbial communities in a paired setting featuring a natural and an anthropogenic ecosystem facing each other at identical climatic, pedological, and vegetational conditions. A transect gradient from forest to seashore allowed for sampling across different habitats within both sites. The field survey was carried out at two adjacent strips of land within the Po River delta lagoon system (Veneto, Italy) one of which is protected within a natural preserve and the other has been converted for decades into a tourist resort. The anthropogenic pressure interestingly led to an increase in the α-diversity of soil microbes but was accompanied by a reduction in β-diversity. The community assembly mechanisms of microbial communities differentiate in natural and anthropic ecosystems: for bacteria, in natural ecosystems deterministic variables and homogeneous selection play a main role (51.92%), while stochastic dispersal limitation (52.15%) is critical in anthropized ecosystems; for fungi, stochastic dispersal limitation increases from 38.1% to 66.09% passing from natural to anthropized ecosystems. We are on calcareous sandy soils and in more natural ecosystems a variation of topsoil pH favors the deterministic selection of bacterial communities, while a divergence of K availability favors stochastic selection. In more anthropized ecosystems, the deterministic variable selection is influenced by the values of SOC. Microbial networks in the natural system exhibited higher numbers of nodes and network edges, as well as higher averages of path length, weighted degree, clustering coefficient, and density than its equivalent sites in the more anthropically impacted environment. The latter on the other hand presented a stronger modularity. Although the influence of stochastic processes increases in anthropized habitats, niche-based selection also proves to impose constraints on communities. Overall, the functionality of the relationships between groups of microorganisms co-existing in communities appeared more relevant to the concept of functional biodiversity in comparison to the plain number of their different taxa. Fewer but functionally more organized lineages displayed traits underscoring a better use of the resources than higher absolute numbers of taxa when those are not equally interconnected in their habitat exploitation. However, considering that network complexity can have important implications for microbial stability and ecosystem multifunctionality, the extinction of complex ecological interactions in anthropogenic habitats may impair important ecosystem services that soils provide us.
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Affiliation(s)
- Lingzi Mo
- School of Geography and Remote Sensing, Guangzhou University, Guangzhou, Guangdong 510006, China.
| | - Augusto Zanella
- Department Land Environment Agriculture and Forestry, University of Padua, Viale dell'Università 16, Legnaro 35020, Italy.
| | - Andrea Squartini
- Department Agronomy, Food, Natural Resources, Animals, Environment, University of Padua, Viale dell'Università 16, Legnaro 35020, Italy.
| | - Giulia Ranzani
- Department Land Environment Agriculture and Forestry, University of Padua, Viale dell'Università 16, Legnaro 35020, Italy.
| | - Cristian Bolzonella
- Department Land Environment Agriculture and Forestry, University of Padua, Viale dell'Università 16, Legnaro 35020, Italy.
| | - Giuseppe Concheri
- Department Agronomy, Food, Natural Resources, Animals, Environment, University of Padua, Viale dell'Università 16, Legnaro 35020, Italy.
| | - Massimo Pindo
- Fondazione Edmund Mach, San Michele all'Adige 38098, Italy.
| | - Francesca Visentin
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy.
| | - Guoliang Xu
- School of Geography and Remote Sensing, Guangzhou University, Guangzhou, Guangdong 510006, China.
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16
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Li J, Chen C, Ji L, Wen S, Peng J, Yang L, He G. Urbanization-driven forest soil greenhouse gas emissions: Insights from the role of soil bacteria in carbon and nitrogen cycling using a metagenomic approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171364. [PMID: 38438026 DOI: 10.1016/j.scitotenv.2024.171364] [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: 10/03/2023] [Revised: 02/07/2024] [Accepted: 02/27/2024] [Indexed: 03/06/2024]
Abstract
Increasing population densities and urban sprawl have induced greenhouse gas (GHG) emissions from the soil, and the soil microbiota of urban forests play a critical role in the production and consumption of GHGs, supporting green development. However, the function and potential mechanism of soil bacteria in GHG emissions from forests during urbanization processes need to be better understood. Here, we measured the fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in Cinnamomum camphora forest soils along an urbanization gradient. 16S amplicon and metagenomic sequencing approaches were employed to examine the structure and potential functions of the soil bacterial community involved in carbon (C) and nitrogen (N) cycling. In this study, the CH4 and CO2 emissions from urban forest soils (sites U and G) were significantly greater than those from suburban soils (sites S and M). The N2O emissions in the urban center (site U) were 24.0 % (G), 13.8 % (S), and 13.5 % (M) greater than those at the other three sites. These results were related to the increasing bacterial alpha diversity, interactions, and C and N cycling gene abundances (especially those involved in denitrification) in urban forest soils. Additionally, the soil pH and metal contents (K, Ca, Mg) affected key bacterial populations (such as Methylomirabilota, Acidobacteriota, and Proteobacteria) and indicators (napA, nosZ, nrfA, nifH) involved in reducing N2O emissions. The soil heavy metal contents (Fe, Cr, Pb) were the main contributors to CH4 emissions, possibly by affecting methanogens (Desulfobacterota) and methanotrophic bacteria (Proteobacteria, Actinobacteriota, and Patescibacteria). Our study provides new insights into the benefits of conservation-minded urban planning and close-to-nature urban forest management and construction, which are conducive to mitigating GHG emissions and supporting urban sustainable development by mediating the core bacterial population.
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Affiliation(s)
- Jing Li
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Chuxiang Chen
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Li Ji
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China.
| | - Shizhi Wen
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Jun Peng
- Hunan Geological Experiment and Testing Center, Changsha, 290 Middle Chengnan Road, 410007, PR China
| | - Lili Yang
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Gongxiu He
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China.
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17
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Xia N, Du E, Wu X, Tang Y, Guo H, Wang Y. Distinct latitudinal patterns and drivers of topsoil nitrogen and phosphorus across urban forests in eastern China. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e2951. [PMID: 38357775 DOI: 10.1002/eap.2951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/07/2023] [Indexed: 02/16/2024]
Abstract
Nitrogen (N) and phosphorus (P) are the two most important macronutrients supporting forest growth. Unprecedented urbanization has created growing areas of urban forests that provide key ecosystem services for city dwellers. However, the large-scale patterns of soil N and P content remain poorly understood in urban forests. Based on a systematic soil survey in urban forests from nine large cities across eastern China, we examined the spatial patterns and key drivers of topsoil (0-20 cm) total N content, total P content, and N:P ratio. Topsoil total N content was found to change significantly with latitude in the form of an inverted parabolic curve, while total P content showed an opposite latitudinal pattern. Variance partition analysis indicated that regional-scale patterns of topsoil total N and P contents were dominated by climatic drivers and partially regulated by time and pedogenic drivers. Conditional regression analyses showed a significant increase in topsoil total N content with lower mean annual temperature (MAT) and higher mean annual precipitation (MAP), while topsoil total P content decreased significantly with higher MAP. Topsoil total N content also increased significantly with the age of urban park and varied with pre-urban soil type, while no such effects were found for topsoil total P content. Moreover, topsoil N:P ratio showed a latitudinal pattern similar to that of topsoil total N content and also increased significantly with lower MAT and higher MAP. Our findings demonstrate distinct latitudinal trends of topsoil N and P contents and highlight a dominant role of climatic drivers in shaping the large-scale patterns of topsoil nutrients in urban forests.
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Affiliation(s)
- Nan Xia
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
- School of Natural Resources, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Enzai Du
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
- School of Natural Resources, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Xinhui Wu
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
- School of Natural Resources, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Yang Tang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
- School of Natural Resources, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Hongbo Guo
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
- School of Natural Resources, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Yang Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
- School of Natural Resources, Faculty of Geographical Science, Beijing Normal University, Beijing, China
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18
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Zhao X, Wang J, Liu Q, Du W, Yang S, Cai P, Ni J. Multifunctionality promotes the prosperity of riverine planktonic diatoms in plateau. ENVIRONMENTAL RESEARCH 2024; 246:118148. [PMID: 38191040 DOI: 10.1016/j.envres.2024.118148] [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: 10/25/2023] [Revised: 12/20/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024]
Abstract
Interpreting the biogeographic distribution and underlying mechanisms of functional traits not only contributes to revealing the spatiotemporal dynamics of species biodiversity but also helps to maintain ecological stability during environmental variations. However, little is known about the functional profiles of diatom communities over large river systems. Herein, we provided the first blueprints about the spatiotemporal distributions and driving forces of functional traits for both planktonic and sedimentary diatoms over the 6030 km continuum of the Yangtze River, with the help of the high-throughput sequencing and functional identification. By investigating the 28 functional traits affiliated into five categories, we found that planktonic diatom functions showed clearer landform-heterogeneity patterns (ANOSIM R = 0.336) than sedimentary functions (ANOSIM R = 0.172) along the river, represented by life-forms and ecological-guilds prominent in water-plateau as well as cell-sizes and life-forms particularly in sediment-plateau. Planktonic diatom functions also displayed higher richness and network complexity in plateau (richness: 58.70 ± 9.30, network edges: 65) than in non-plateau regions (23.82 ± 13.16, 16), promoting the stability and robustness of diatom functions against the high-radiation and low-temperature plateau environment. Environmental selection (mainly exerted by PAR, UV, and Tw) played crucial roles in determining the functional variations of planktonic diatoms (explaining 80.5%) rather than sedimentary diatoms (14.5%) between plateau and non-plateau regions. Meanwhile, planktonic diatom traits within life-forms were identified to be well responsive to the ecological environment quality (r = 0.56-0.60, P < 0.001) in the Yangtze. This study provided comprehensive insights into the multifunctionality of diatoms and their responses to environmental disturbance and environment quality, which helps to develop effective strategies for maintaining ecological stability in changing river environments.
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Affiliation(s)
- Xiaohui Zhao
- School of Water Resources and Hydropower Engineering, Xi'an University of Technology, Xi'an, 710048, PR China
| | - Jiawen Wang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China; College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China.
| | - Qingxiang Liu
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China
| | - Wenran Du
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China; College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China
| | - Shanqing Yang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China
| | - Pinggui Cai
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China; College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, PR China
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19
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Liu L, Wang H, Guo Y, Yan Q, Chen J. Human-induced homogenization of microbial taxa and function in a subtropical river and its impacts on community stability. WATER RESEARCH 2024; 252:121198. [PMID: 38295455 DOI: 10.1016/j.watres.2024.121198] [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: 07/12/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/02/2024]
Abstract
Combination of taxa and function can provide a more comprehensive picture on human-induced microbial homogenization. Here, we obtained 2.58 billion high-throughput sequencing reads and 479 high-quality metagenome-assembled genomes (MAGs) of planktonic microbial communities in a subtropical river for 5 years. We found the microbial taxa homogenization and functional homogenization were uncoupled. Although human activities in downstream sites significantly decreased the taxonomic diversity of non-abundant ASV communities (16S rRNA gene amplicon sequence variants), they did not significantly decrease the taxonomic diversity of abundant ASV and total observed MAG communities. However, the total observed MAG communities in downstream sites tended to homogenize into some specific taxa which encode human-activity-related functional genes, such as nutrient cycles, greenhouse gas emission, antibiotic and arsenic resistance. Those specific MAGs with high taxonomic diversity caused the weak heterogenization of total observed MAG communities in downstream sites. Moreover, functional homogenization promoted the synchrony among downstream MAGs, and these MAGs constructed some specific network modules might to synergistically execute or resist the human-activity-related functions. High synchrony also led to the tandem effects among MAGs and thus decreased community stability. Overall, our findings revealed the links of microbial taxa, functions and stability under human activity impacts, and provided a strong evidence to encourage us re-thinking biotic homogenization based on microbial taxa and their functional attributes.
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Affiliation(s)
- Lemian Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Institute of Natural Products and Traditional Chinese Medicine Modernization, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China.
| | - Hongwei Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Institute of Natural Products and Traditional Chinese Medicine Modernization, Fuzhou University, Fuzhou 350108, China
| | - Yisong Guo
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Institute of Natural Products and Traditional Chinese Medicine Modernization, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China
| | - Qi Yan
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Institute of Natural Products and Traditional Chinese Medicine Modernization, Fuzhou University, Fuzhou 350108, China
| | - Jianfeng Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Institute of Natural Products and Traditional Chinese Medicine Modernization, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China.
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20
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Luo S, Chen R, Han J, Zhang W, Petropoulos E, Liu Y, Feng Y. Urban green space area mitigates the accumulation of heavy metals in urban soils. CHEMOSPHERE 2024; 352:141266. [PMID: 38316278 DOI: 10.1016/j.chemosphere.2024.141266] [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: 09/27/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
Despite that the heavy metals in urban soils pose a threat to public health, the critical factors that influence their concentrations in urban soils are not well understood. In this study, we conducted a survey of surface soil samples from urban green spaces in Shanghai, to analyze the concentrations of the key heavy metals. The results showed that Zn was the most abundant metal with an average concentration of 122.99 mg kg-1, followed by Pb (32.72 mg kg-1) and Cd (0.23 mg kg-1). All concentrations were found to be below the risk screening values defined by the National Environmental Quality Standards for soils of development land in China (GB36600-2018), indicating no current risk in Shanghai. However, there was a clear accumulation of heavy metals, as the mean concentrations were significantly higher than the background values. Furthermore, we explored the relationships between key heavy metals with population density, GDP and green space area. Both Spearman correlation and Random Forest analysis indicated that per capita green space area (pGSA) and population density were the most crucial factors influencing the status of heavy metals in urban soils, unlike edaphic factors e.g. SOM content in farmland soils. Specifically, there was a significantly positive linear correlation between heavy metal concentrations and population density, with correlation coefficients ranging from 0.3 to 0.4. However, the correlation with pGSA was found to be non-linear. The nonlinear regression analysis revealed threshold values between heavy metals concentrations and pGSA (e.g Zn 22.22 m2, Pb 24.92 m2, and Cd 25.92 m2), with a sharp reduction in heavy metal concentrations below the threshold and a slow reduction above the threshold. It suggests that an increase in per capita green space area can mitigate the accumulation of heavy metals caused by growing population density, but the effect is limited after the threshold. Our findings not only provide insights into the distribution patterns of heavy metals in the urban soils at the local scale, but also contribute to the urban greening at the global scale and offer guidance for city planning in the face of increasing population densities over the coming decades.
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Affiliation(s)
- Shuhong Luo
- Shanghai Wildlife and Protected Natural Areas Research Center, Shanghai, 202150, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruirui Chen
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China.
| | - Jigang Han
- Shanghai Wildlife and Protected Natural Areas Research Center, Shanghai, 202150, China; Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, National Forestry and Grassland Innovation Alliance on Afforestation and Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, 200232, China.
| | - Weiwei Zhang
- School of Resources and Materials, Northeastern University at Qinhuangdao, Qinhuangdao, 066004, China
| | - Evangelos Petropoulos
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK; Stantec, UK, Newcastle upon Tyne, NE1 3DY, UK
| | - Yun Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Youzhi Feng
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
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21
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Fickling NW, Abbott CA, Brame JE, Cando‐Dumancela C, Liddicoat C, Robinson JM, Breed MF. Light-dark cycles may influence in situ soil bacterial networks and diurnally-sensitive taxa. Ecol Evol 2024; 14:e11018. [PMID: 38357595 PMCID: PMC10864733 DOI: 10.1002/ece3.11018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 02/16/2024] Open
Abstract
Soil bacterial taxa have important functional roles in ecosystems (e.g. nutrient cycling, soil formation, plant health). Many factors influence their assembly and regulation, with land cover types (e.g. open woodlands, grasslands), land use types (e.g. nature reserves, urban green space) and plant-soil feedbacks being well-studied factors. However, changes in soil bacterial communities in situ over light-dark cycles have received little attention, despite many plants and some bacteria having endogenous circadian rhythms that could influence soil bacterial communities. We sampled surface soils in situ across 24-h light-dark cycles (at 00:00, 06:00, 12:00, 18:00) at two land cover types (remnant vegetation vs. cleared, grassy areas) and applied 16S rRNA amplicon sequencing to investigate changes in bacterial communities. We show that land cover type strongly affected soil bacterial diversity, with soils under native vegetation expressing 15.4%-16.4% lower alpha diversity but 4.9%-10.6% greater heterogeneity than soils under cleared vegetation. In addition, we report time-dependent and site-specific changes in bacterial network complexity and between 598-922 ASVs showing significant changes in relative abundance across times. Native site node degree (bacterial interactions) at the phylum level was 16.0% higher in the early morning than in the afternoon/evening. Our results demonstrate for the first time that light-dark cycles have subtle yet important effects on soil bacterial communities in situ and that land cover influences these dynamics. We provide a new view of soil microbial ecology and suggest that future studies should consider the time of day when sampling soil bacteria.
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Affiliation(s)
- Nicole W. Fickling
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Catherine A. Abbott
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Joel E. Brame
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | | | - Craig Liddicoat
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Jake M. Robinson
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Martin F. Breed
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
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22
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Banerjee S, Zhao C, Garland G, Edlinger A, García-Palacios P, Romdhane S, Degrune F, Pescador DS, Herzog C, Camuy-Velez LA, Bascompte J, Hallin S, Philippot L, Maestre FT, Rillig MC, van der Heijden MGA. Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe. Nat Commun 2024; 15:327. [PMID: 38184663 PMCID: PMC10771452 DOI: 10.1038/s41467-023-44073-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024] Open
Abstract
Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.
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Affiliation(s)
- Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA.
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland.
| | - Cheng Zhao
- ETH Zurich, Institute for Environmental Decisions, 8092, Zurich, Switzerland
| | - Gina Garland
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
| | - Anna Edlinger
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
- Wageningen Environmental Research, Wageningen University & Research, Droevendaalsesteeg 3, 6708 PB, Wageningen, The Netherlands
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
- University of Zurich, Department of Plant and Microbial Biology, 8057, Zurich, Switzerland
| | - Sana Romdhane
- University Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, Dijon, France
| | - Florine Degrune
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, 14195, Berlin, Germany
| | - David S Pescador
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28940, Madrid, Spain
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933, Móstoles, Spain
| | - Chantal Herzog
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
| | - Lennel A Camuy-Velez
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Jordi Bascompte
- University of Zurich, Department of Evolutionary Biology and Environmental Studies, 8057, Zurich, Switzerland
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 750 07, Uppsala, Sweden
| | - Laurent Philippot
- University Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, Dijon, France
| | - Fernando T Maestre
- Departamento de Ecología, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente del Raspeig, Alicante, Spain
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente, del Raspeig, Alicante, Spain
| | - Matthias C Rillig
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Marcel G A van der Heijden
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland.
- University of Zurich, Department of Plant and Microbial Biology, 8057, Zurich, Switzerland.
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23
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Shangguan HY, Geisen S, Li ZP, Yao HF, Li G, Breed MF, Scheu S, Sun X. Urban greenspaces shape soil protist communities in a location-specific manner. ENVIRONMENTAL RESEARCH 2024; 240:117485. [PMID: 37907164 DOI: 10.1016/j.envres.2023.117485] [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: 08/05/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/02/2023]
Abstract
The impacts of urbanization on aboveground biodiversity are well studied, and its impact on soil microorganisms are also receiving increased attention. However, the impact of urbanization on the soil protists are hardly investigated. Here, we studied how urbanization and distinct urban greenspaces affect protist communities. We used amplicon sequencing of the18 S rRNA gene of samples from five types of urban greenspaces (parks, greenbelts, industrial areas, residential areas and hospital lawns), neighboring natural forests and agricultural ecosystems in Ningbo, China. We found that urban greenspaces harbored higher protist α-diversity than forests, while protist β-diversity increased from agricultural systems to urban greenspaces to forests. Among the studied driving factors, soil bacterial α- and β-diversity best predicted phagotrophic protist α- and β-diversity in urban greenspaces, while differences in α- and β-diversity of phototrophic protists were best explained by soil carbon-to-nitrogen ratio and fungal β-diversity, respectively. Abiotic factors i.e., total phosphorus and carbon-to-nitrogen ratio, best predicted the α- and β-diversity of protist parasites in urban greenspaces, respectively. The results revealed that the composition and drivers of protist communities vary between functional groups and urban ecosystems. Overall, our findings contribute to a better understanding of drivers of soil protist communities and indicate that soil protist communities and associated soil functions could be managed in predictable ways in urban greenspaces.
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Affiliation(s)
- Hua-Yuan Shangguan
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB Wageningen, the Netherlands
| | - Zhi-Peng Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Hai-Feng Yao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Martin F Breed
- College of Science & Engineering, Flinders University, Bedford Park 5042 SA, Australia
| | - Stefan Scheu
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany; Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Xin Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
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24
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Robinson JM, Hodgson R, Krauss SL, Liddicoat C, Malik AA, Martin BC, Mohr JJ, Moreno-Mateos D, Muñoz-Rojas M, Peddle SD, Breed MF. Opportunities and challenges for microbiomics in ecosystem restoration. Trends Ecol Evol 2023; 38:1189-1202. [PMID: 37648570 DOI: 10.1016/j.tree.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Microbiomics is the science of characterizing microbial community structure, function, and dynamics. It has great potential to advance our understanding of plant-soil-microbe processes and interaction networks which can be applied to improve ecosystem restoration. However, microbiomics may be perceived as complex and the technology is not accessible to all. The opportunities of microbiomics in restoration ecology are considerable, but so are the practical challenges. Applying microbiomics in restoration must move beyond compositional assessments to incorporate tools to study the complexity of ecosystem recovery. Advances in metaomic tools provide unprecedented possibilities to aid restoration interventions. Moreover, complementary non-omic applications, such as microbial inoculants and biopriming, have the potential to improve restoration objectives by enhancing the establishment and health of vegetation communities.
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Affiliation(s)
- Jake M Robinson
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia; The Aerobiome Innovation & Research Hub, Flinders University, Bedford Park, SA 5042, Australia.
| | - Riley Hodgson
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Siegfried L Krauss
- Kings Park Science, Department of Biodiversity, Conservation, and Attractions, Fraser Avenue, Kings Park, WA 6005, Australia; Environmental and Conservation Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Craig Liddicoat
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia; School of Public Health, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Ashish A Malik
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Belinda C Martin
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia; Ooid Scientific, North Lake, WA 6162, Australia
| | - Jakki J Mohr
- College of Business, University of Montana, Missoula, MT, USA
| | - David Moreno-Mateos
- School of Geography and the Environment, University of Oxford, South Parks Road. Oxford OX1 3QY, UK; Department of Landscape Architecture, Graduate School of Design, Harvard University, Quincy Street. Cambridge, MA 02138, USA; Basque Center for Climate Change - BC3, Ikerbasque Foundation for Science. Edificio Sede 1, Parque Cientifico UPV, 04940 Leioa, Spain
| | - Miriam Muñoz-Rojas
- Departamento de Biologia Vegetal y Ecologia. Universidad de Sevilla, 41004 Sevilla, Spain; Centre for Ecosystem Science, School of Biological, Earth, and Environmental Sciences, University of New South Wales (UNSW) Sydney, Sydney, NSW 2052, Australia
| | - Shawn D Peddle
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
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25
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Yao H, Li Z, Geisen S, Qiao Z, Breed MF, Sun X. Degree of urbanization and vegetation type shape soil biodiversity in city parks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:166437. [PMID: 37604369 DOI: 10.1016/j.scitotenv.2023.166437] [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: 03/30/2023] [Revised: 07/28/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Urbanization negatively impacts aboveground biodiversity, such as bird and insect communities. City parks can reduce these negative impacts by providing important habitat. However, it remains poorly understood how the degree of urbanization and vegetation types within city parks (e.g., lawns, woodland) impact soil biodiversity. Here we investigated the impact of the degree of urbanization (urban vs. suburban) and vegetation type (lawn, shrub-lawn, tree-lawn and tree-shrub mixtures) on soil biodiversity in parkland systems. We used eDNA metabarcoding to characterize soil biodiversity of bacteria, fungi, protists, nematodes, meso- and macrofauna across park vegetation types in urban and suburban regions in Xiamen, China. We observed a strong effect of the degree of urbanization on the richness of different soil biota groups, with higher species richness of protists and meso/macrofauna in urban compared to suburban areas, while the richness of bacteria and fungi did not differ, and the difference of nematode richness depended on vegetation type. At the functional level, increased degree of urbanization associated with greater species richness of bacterivores, plant pathogens and animal parasites. These urbanization effects were at least partly modulated by higher soil phosphorous levels in urban compared to suburban sites. Also, the vegetation type impacted soil biodiversity, particularly fungal richness, with the richness of pathogenic and saprotrophic fungi increasing from lawn to tree-shrub mixtures. Tree-shrub mixtures also had the highest connectedness between biotas and lowest variation in the soil community structure. Overall, we show that soil biodiversity is strongly linked to the degree of urbanization, with overall richness increasing with urbanization, especially in bacterivores, plant pathogens and animal parasites. Targeted management of vegetation types in urban areas should provide a useful way to help mitigate the negative effect of urbanization on soil biodiversity.
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Affiliation(s)
- Haifeng Yao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Zhipeng Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Stefan Geisen
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, 6700 ES Wageningen, the Netherlands.
| | - Zhihong Qiao
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia.
| | - Xin Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
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26
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Liu H, Han H, Zhang C, Yu X, Nie W, Shao Q, Yang P, Li X, Yang Y, Cao H. Patterns of bacterial distance decay and community assembly in different land-use types as influenced by tillage management and soil layers. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 266:115595. [PMID: 37839185 DOI: 10.1016/j.ecoenv.2023.115595] [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: 05/05/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
Land use and cover change are major factors driving global change and greatly impact terrestrial organisms, especially soil microbial diversity. Little is known, however, about bacterial diversity, distribution patterns and assembly processes across different land use types. In this study, therefore, we conducted a large-scale field survey of 48 sampling sites, encompassing different land use types in Xuancheng city, China, with different degrees of soil disturbance and different soil horizons. The distance-decay relationships (DDRs), assembly processes and the spatial patterns of soil bacterial communities were investigated based on high-throughput sequencing data. We found that the DDRs might be weakened by anthropogenic disturbances, which were not observed in tilled soils, while a decreasing trend was observed along the soil horizon in untilled soils. The relative importance of environmental factors and geographic distance varied with soil tillage. Specifically, bacterial communities in tilled soils were driven by non-spatially autocorrelated environmental factors, while untilled soils were more susceptible to geographic distance. In addition, the heterogeneity of soil properties, as well as the differences in soil bacterial niche width and niche overlap, determined the assembly processes of the bacterial community, resulting in opposite trends along the soil layers in tilled and untilled soils. These findings expand the current understanding of the biogeography of soil bacterial communities across different land use types.
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Affiliation(s)
- Hao Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and rural affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Heming Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and rural affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Cunzhi Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and rural affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaowei Yu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and rural affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenfang Nie
- Center for Plantation Management Services, Agricultural and Rural Bureau, Xuancheng 242000, China
| | - Qiuyun Shao
- Center for Plantation Management Services, Agricultural and Rural Bureau, Xuancheng 242000, China
| | - Ping Yang
- Center for Plantation Management Services, Agricultural and Rural Bureau, Xuancheng 242000, China
| | - Xiang Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yang Yang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and rural affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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27
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Liu J, Guo Y, Gu H, Liu Z, Hu X, Yu Z, Li Y, Li L, Sui Y, Jin J, Liu X, Adams JM, Wang G. Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes. THE ISME JOURNAL 2023; 17:1872-1883. [PMID: 37607984 PMCID: PMC10579271 DOI: 10.1038/s41396-023-01496-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023]
Abstract
The microbiome function responses to land use change are important for the long-term prediction and management of soil ecological functions under human influence. However, it has remains uncertain how the biogeographic patterns of soil functional composition change when transitioning from natural steppe soils (NS) to agricultural soils (AS). We collected soil samples from adjacent pairs of AS and NS across 900 km of Mollisol areas in northeast China, and the soil functional composition was characterized using shotgun sequencing. AS had higher functional alpha-diversity indices with respect to KO trait richness and a higher Shannon index than NS. The distance-decay slopes of functional gene composition were steeper in AS than in NS along both spatial and environmental gradients. Land-use conversion from steppe to farmland diversified functional gene profiles both locally and spatially; it increased the abundances of functional genes related to labile carbon, but decreased those related to recalcitrant substrate mobilization (e.g., lignin), P cycling, and S cycling. The composition of gene functional traits was strongly driven by stochastic processes, while the degree of stochasticity was higher in NS than in AS, as revealed by the neutral community model and normalized stochasticity ratio analysis. Alpha-diversity of core functional genes was strongly related to multi-nutrient cycling in AS, suggesting a key relationship to soil fertility. The results of this study challenge the paradigm that the conversion of natural to agricultural habitat will homogenize soil properties and biology while reducing local and regional gene functional diversity.
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Affiliation(s)
- Junjie Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Yaping Guo
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, P R China
| | - Haidong Gu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Zhuxiu Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Xiaojing Hu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Zhenhua Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Yansheng Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Lujun Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Yueyu Sui
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Xiaobing Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Jonathan M Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, P R China.
| | - Guanghua Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China.
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Du S, Li XQ, Feng J, Huang Q, Liu YR. Soil core microbiota drive community resistance to mercury stress and maintain functional stability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 894:165056. [PMID: 37348729 DOI: 10.1016/j.scitotenv.2023.165056] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
Soil microbial communities have resistance to environmental stresses and thus can maintain ecosystem functions such as decomposition, nutrient provisioning, and plant pathogen control. However, predominant factors driving community resistance of soil microbiome to heavy metal pollution stresses and ecosystem functional stability are still unclear, limiting our ability to forecast how soil pollution might affect ecosystem sustainability. Here, we conducted microcosm experiments to estimate the importance of soil microbiome in predicting community resistance to heavy metal mercury (Hg) stress in paired paddy and upland fields. We found that community resistance of soil microbiome was strongly correlated with ecosystem functional stability, so were the individual groups of organisms such as bacteria, saprotrophic fungi, and phototrophic protists. The core phylotypes within soil microbiome had a major contribution to community resistance, which was essential for the maintenance of functional stability. Co-occurrence network further confirmed that community resistances of main ecological clusters were positively correlated with ecosystem functional stability. Together, our results provide new insights into the link between community resistance and functional stability, and highlight the importance of core microbiota in driving community resistance to environmental stresses and maintain functional stability.
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Affiliation(s)
- Shuai Du
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin-Qi Li
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiao Feng
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China.
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29
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Zhou Y, Zhou S. Role of microplastics in microbial community structure and functions in urban soils. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132141. [PMID: 37506647 DOI: 10.1016/j.jhazmat.2023.132141] [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: 05/27/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 07/30/2023]
Abstract
Evidence from the laboratory suggests that microplastics (MPs) can harm soil microorganisms, affecting the structures and functions of microbial communities. The impact of soil MPs on microbes in actual urban environments with high human activity levels, however, has not been well reported. To investigate the MP effect on urban soil microorganisms under complex scenarios, we analyzed 42 soil samples from standardized plots of 7 urban functional zones. We report that urban green spaces are important for studying microbial diversity in the study area, and they also contribute to the global homogenization of soil microbes and genes. Bacterial communities in soils enriched with various MPs showed greater differences in OTUs than fungi. Compared to low-MP soils, most ARGs and nutrient cycling genes had similar or slightly lower abundances in soils with high levels of MPs. The coupling of pollutant factors with MPs as independent variables had significant explanatory power for both positive and negative correlations in PLS-PM analysis. Specifically, PET and PP MPs explained 3.54% and 6.03%, respectively, of the microbial community and functional genes. This study fills knowledge gaps on the effects of MPs on urban soil microbial communities in real environments, facilitating better management of urban green spaces.
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Affiliation(s)
- Yujie Zhou
- School of Geographic Sciences, Nanjing University of Information Science & Technology, Nanjing 210044, China; School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing 210046, China.
| | - Shenglu Zhou
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing 210046, China.
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30
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Liu YR, Guo L, Yang Z, Xu Z, Zhao J, Wen SH, Delgado-Baquerizo M, Chen L. Multidimensional Drivers of Mercury Distribution in Global Surface Soils: Insights from a Global Standardized Field Survey. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12442-12452. [PMID: 37506289 DOI: 10.1021/acs.est.3c04313] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Soil stores a large amount of mercury (Hg) that has adverse effects on human health and ecosystem safety. Significant uncertainties still exist in revealing environmental drivers of soil Hg accumulation and predicting global Hg distribution owing to the lack of field data from global standardized analyses. Here, we conducted a global standardized field survey and explored a holistic understanding of the multidimensional environmental drivers of Hg accumulation in global surface soils. Hg content in surface soils from our survey ranges from 3.8 to 618.2 μg kg-1 with an average of 74.0 μg kg-1 across the globe. Atmospheric Hg deposition, particularly vegetation-induced elemental Hg0 deposition, is the major source of surface soil Hg. Soil organic carbon serves as the major substrate for sequestering Hg in surface soils and is significantly influenced by agricultural management, litterfall, and elevation. For human activities, changing land-use could be a more important contributor than direct anthropogenic emissions. Our prediction of a new global Hg distribution highlights the hot spots (high Hg content) in East Asia, the Northern Hemispheric temperate/boreal regions, and tropical areas, while the cold spots (low Hg content) are in arid regions. The holistic understanding of multidimensional environmental drivers helps to predict the Hg distribution in global surface soils under a changing global environment.
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Affiliation(s)
- Yu-Rong Liu
- College of Resources and Environment and State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Long Guo
- College of Resources and Environment and State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziming Yang
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
| | - Zeng Xu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Jiating Zhao
- Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Shu-Hai Wen
- College of Resources and Environment and State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla 41012, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla 41013, Spain
| | - Long Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai 200241, China
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31
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Voor T, Pärtel M, Peet A, Saare L, Hyöty H, Knip M, Davison J, Zobel M, Tillmann V. Atopic sensitization in childhood depends on the type of green area around the home in infancy. Clin Exp Allergy 2023; 53:850-853. [PMID: 37038920 DOI: 10.1111/cea.14317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 04/12/2023]
Affiliation(s)
- Tiia Voor
- Children's Clinic of Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Aleksandr Peet
- Children's Clinic of Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Liisa Saare
- Children's Clinic of Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
| | - Mikael Knip
- Pediatric Research Centre, New Children's Hospital, Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Vallo Tillmann
- Children's Clinic of Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
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32
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Christel A, Dequiedt S, Chemidlin-Prevost-Bouré N, Mercier F, Tripied J, Comment G, Djemiel C, Bargeot L, Matagne E, Fougeron A, Mina Passi JB, Ranjard L, Maron PA. Urban land uses shape soil microbial abundance and diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163455. [PMID: 37062324 DOI: 10.1016/j.scitotenv.2023.163455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/03/2023]
Abstract
Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered - public leisure, traffic, and urban agriculture - sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.
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Affiliation(s)
- Amélie Christel
- AgroParisTech, 75732 Paris, France; Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Florian Mercier
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Julie Tripied
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Gwendoline Comment
- Platforme GenoSol, INRAE-Université de Bourgogne, CMSE, 21000 Dijon, France
| | - Christophe Djemiel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Eric Matagne
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - Agnès Fougeron
- Jardin de l'Arquebuse Mairie de Dijon, CS 73310, 21033 Dijon Cedex, France
| | | | - Lionel Ranjard
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France.
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Philpott M, Liew ECY, van der Merwe MM, Mertin A, French K. The Influence of Cone Age and Urbanisation on the Diversity and Community Composition of Culturable Seed Fungal Endophytes within Native Australian Banksia ericifolia L.f. subsp. ericifolia. J Fungi (Basel) 2023; 9:706. [PMID: 37504695 PMCID: PMC10381327 DOI: 10.3390/jof9070706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Seed fungal endophytes play a crucial role in assisting the overall health and success of their host plant; however, little is known about the factors that influence the diversity and composition of these endophytes, particularly with respect to how they change over time and within urban environments. Using culturing techniques, morphological analyses, and Sanger sequencing, we identified the culturable seed fungal endophytes of Banksia ericifolia at two urban and two natural sites in Sydney, New South Wales, Australia. A total of 27 Operational Taxonomic Units were obtained from 1200 seeds. Older cones were found to contain, on average, more colonised endophytes than younger cones. Species richness was also significantly influenced by cone age, with older cones being more speciose. Between urban and natural sites, the overall community composition did not change, although species richness and diversity were greatest at urban sites. Understanding how these endophytes vary in time and space may help provide an insight into the transmission pathways used and the potential role they play within the development and survival of the seed. This knowledge may also be crucial for restoration purposes, especially regarding the need to consider endophyte viability in ex situ seed collection and storage in seed-banking practices.
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Affiliation(s)
- Merize Philpott
- Centre for Sustainable Ecosystems Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Edward C Y Liew
- Research Centre for Ecosystem Resilience, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW 2000, Australia
| | - Marlien M van der Merwe
- Research Centre for Ecosystem Resilience, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW 2000, Australia
| | - Allison Mertin
- Research Centre for Ecosystem Resilience, The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW 2000, Australia
| | - Kristine French
- Centre for Sustainable Ecosystems Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
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34
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Thompson GL, Bray N, Groffman PM, Kao-Kniffin J. Soil microbiomes in lawns reveal land-use legacy impacts on urban landscapes. Oecologia 2023:10.1007/s00442-023-05389-8. [PMID: 37286887 DOI: 10.1007/s00442-023-05389-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023]
Abstract
Land-use change is highly dynamic globally and there is great uncertainty about the effects of land-use legacies on contemporary environmental performance. We used a chronosequence of urban grasslands (lawns) that were converted from agricultural and forested lands from 10 to over 130 years prior to determine if land-use legacy influences components of soil biodiversity and composition over time. We used historical aerial imagery to identify sites in Baltimore County, MD (USA) with agricultural versus forest land-use history. Soil samples were taken from these sites as well as from existing well-studied agricultural and forest sites used as historical references by the National Science Foundation Long-Term Ecological Research Baltimore Ecosystem Study program. We found that the microbiomes in lawns of agricultural origin were similar to those in agricultural reference sites, which suggests that the ecological parameters on lawns and reference agricultural systems are similar in how they influence soil microbial community dynamics. In contrast, lawns that were previously forest showed distinct shifts in soil bacterial composition upon recent conversion but reverted back in composition similar to forest soils as the lawns aged over decades. Soil fungal communities shifted after forested land was converted to lawns, but unlike bacterial communities, did not revert in composition over time. Our results show that components of bacterial biodiversity and composition are resistant to change in previously forested lawns despite urbanization processes. Therefore land-use legacy, depending on the prior use, is an important factor to consider when examining urban ecological homogenization.
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Affiliation(s)
- Grant L Thompson
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Natalie Bray
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Peter M Groffman
- Advanced Science Research Center at the Graduate Center, Environmental Sciences Initiative, City University of New York, New York, NY, 10031, USA
- Cary Institute of Ecosystem Studies, Millbrook, NY, 12545, USA
| | - Jenny Kao-Kniffin
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
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35
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Romero F, Hilfiker S, Edlinger A, Held A, Hartman K, Labouyrie M, van der Heijden MGA. Soil microbial biodiversity promotes crop productivity and agro-ecosystem functioning in experimental microcosms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 885:163683. [PMID: 37142020 DOI: 10.1016/j.scitotenv.2023.163683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/06/2023]
Abstract
Soil biota contribute substantially to multiple ecosystem functions that are key for geochemical cycles and plant performance. However, soil biodiversity is currently threatened by land-use intensification, and a mechanistic understanding of how soil biodiversity loss interacts with the myriad of intensification elements (e.g., the application of chemical fertilizers) is still unresolved. Here we experimentally simplified soil biological communities in microcosms to test whether changes in the soil microbiome influenced soil multifunctionality including crop productivity (leek, Allium porrum). Additionally, half of microcosms were fertilized to further explore how different levels of soil biodiversity interact with nutrient additions. Our experimental manipulation achieved a significant reduction of soil alpha-diversity (45.9 % reduction in bacterial richness, 82.9 % reduction in eukaryote richness) and resulted in the complete removal of key taxa (i.e., arbuscular mycorrhizal fungi). Soil community simplification led to an overall decrease in ecosystem multifunctionality; particularly, plant productivity and soil nutrient retention capacity were reduced with reduced levels of soil biodiversity. Ecosystem multifunctionality was positively correlated with soil biodiversity (R = 0.79). Mineral fertilizer application had little effect on multifunctionality compared to soil biodiversity reduction, but it reduced leek nitrogen uptake from decomposing litter by 38.8 %. This suggests that natural processes and organic nitrogen acquisition are impaired by fertilization. Random forest analyses revealed a few members of protists (i.e., Paraflabellula), Actinobacteria (i.e., Micolunatus), and Firmicutes (i.e., Bacillus) as indicators of ecosystem multifunctionality. Our results suggest that preserving the diversity of soil bacterial and eukaryotic communities within agroecosystems is crucial to ensure the provisioning of multiple ecosystem functions, particularly those directly related to essential ecosystem services such as food provision.
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Affiliation(s)
- Ferran Romero
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland.
| | - Sarah Hilfiker
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Anna Edlinger
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Alain Held
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Kyle Hartman
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Maëva Labouyrie
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland; Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland; European Commission, Joint Research Centre Ispra (JRC Ispra), Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Marcel G A van der Heijden
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland; Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland.
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36
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Zhu W, Liu X, Zhang J, Zhao H, Li Z, Wang H, Chen R, Wang A, Li X. Response of coral bacterial composition and function to water quality variations under anthropogenic influence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 884:163837. [PMID: 37137368 DOI: 10.1016/j.scitotenv.2023.163837] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/06/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023]
Abstract
Microbial communities play key roles in the adaptation of corals living in adverse environments, as the microbiome flexibility can enhance environmental plasticity of coral holobiont. However, the ecological association of coral microbiome and related function to locally deteriorating water quality remains underexplored. In this work, we used 16S rRNA gene sequencing and quantitative microbial element cycling (QMEC) to investigate the seasonal changes of bacterial communities, particularly their functional genes related to carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycle, of the scleractinian coral Galaxea fascicularis from nearshore reefs exposed anthropogenic influence. We used nutrient concentrations as the indicator of anthropogenic activities in coastal reefs, and found a higher nutrient pressure in spring than summer. The bacterial diversity, community structure and dominant bacteria of coral shifted significantly due to seasonal variations dominated by nutrient concentrations. Additionally, the network structure and nutrient cycling gene profiles in summer under low nutrient stress was distinct from that under poor environmental conditions in spring, with lower network complexity and abundance of CNPS cycling genes in summer compared with spring. We further identified significant correlations between microbial community (taxonomic composition and co-occurrence network) and geochemical functions (abundance of multiple functional genes and functional community). Nutrient enrichment was proved to be the most important environmental fluctuation in controlling the diversity, community structure, interactional network and functional genes of the coral microbiome. These results highlight that seasonal shifts in coral-associated bacteria due to anthropogenic activities alter the functional potentials, and provide novel insight about the mechanisms of coral adaptation to locally deteriorating environments.
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Affiliation(s)
- Wentao Zhu
- College of Ecology and Environment, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Xiangbo Liu
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Junling Zhang
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - He Zhao
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Zhuoran Li
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Hao Wang
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Rouwen Chen
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Aimin Wang
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Xiubao Li
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China.
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37
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Li S, Ren K, Yan X, Tsyganov AN, Mazei Y, Smirnov A, Mazei N, Zhang Y, Rensing C, Yang J. Linking biodiversity and ecological function through extensive microeukaryotic movement across different habitats in six urban parks. IMETA 2023; 2:e103. [PMID: 38868434 PMCID: PMC10989963 DOI: 10.1002/imt2.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/08/2023] [Accepted: 03/22/2023] [Indexed: 06/14/2024]
Abstract
Highly diverse but divergent microeukaryotes dwell in all types of habitats in urban park ecosystems. Extensive microbial migration occurs between both terrestrial and aquatic habitats. Microbial movement is beneficial to the maintenance of biodiversity and the exchange of functional guilds.
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Affiliation(s)
- Shuzhen Li
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
| | - Kexin Ren
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
| | - Xue Yan
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Yuri Mazei
- Lomonosov Moscow State UniversityMoscowRussia
- Faculty of BiologyShenzhen MSU‐BIT UniversityShenzhenChina
- A. N. Severtsov Institute of Ecology and EvolutionRussian Academy of SciencesMoscowRussia
| | - Alexey Smirnov
- Department of Invertebrate Zoology, Faculty of BiologySt. Petersburg UniversitySt. PetersburgRussia
| | | | - Yiyue Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Christopher Rensing
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
- Institute of Environmental Microbiology, College of Resources and the EnvironmentFujian Agriculture & Forestry UniversityFuzhouChina
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
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Rillig MC, van der Heijden MG, Berdugo M, Liu YR, Riedo J, Sanz-Lazaro C, Moreno-Jiménez E, Romero F, Tedersoo L, Delgado-Baquerizo M. Increasing the number of stressors reduces soil ecosystem services worldwide. NATURE CLIMATE CHANGE 2023; 13:478-483. [PMID: 37193246 PMCID: PMC7614524 DOI: 10.1038/s41558-023-01627-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/09/2023] [Indexed: 05/18/2023]
Abstract
Increasing the number of environmental stressors could decrease ecosystem functioning in soils. Yet this relationship has never been globally assessed outside laboratory experiments. Here, using two independent global standardized field surveys, and a range of natural and human factors, we test the relationship between the number of environmental stressors exceeding different critical thresholds and the maintenance of multiple ecosystem services across biomes. Our analysis shows that, multiple stressors, from medium levels (>50%), negatively and significantly correlates with impacts on ecosystem services, and that multiple stressors crossing a high-level critical threshold (over 75% of maximum observed levels), reduces soil biodiversity and functioning globally. The number of environmental stressors >75% threshold was consistently seen as an important predictor of multiple ecosystem services, therefore improving prediction of ecosystem functioning. Our findings highlight the need to reduce the dimensionality of the human footprint on ecosystems to conserve biodiversity and function.
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Affiliation(s)
| | - Marcel G.A. van der Heijden
- Agroscope, Plant-Soil Interactions Group, 8046 Zurich, Switzerland
- University of Zurich, Department of Plant and Microbial Biology, 8057 Zurich, Switzerland
| | - Miguel Berdugo
- Institute of Integrative Biology, Department of Environment Systems Science, ETH Zürich, 8092 Zürich, Switzerland
- Complutense University of Madrid, Department of Biodiversity, Ecology and Evolution, Madrid, Spain
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Judith Riedo
- Agroscope, Plant-Soil Interactions Group, 8046 Zurich, Switzerland
| | - Carlos Sanz-Lazaro
- Multidisciplinary Institute for Environmental Studies (MIES), Universidad de Alicante, P.O. Box 99, E-03080 Alicante, Spain
- Department of Ecology, University of Alicante, PO Box 99, E-03080 Alicante, Spain
| | - Eduardo Moreno-Jiménez
- Freie Universität Berlin, Institute of Biology, Berlin, Germany
- Department of Agricultural and Food Chemistry, Faculty of Sciences, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ferran Romero
- Agroscope, Plant-Soil Interactions Group, 8046 Zurich, Switzerland
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, 14a Ravila, 50411 Tartu, Estonia
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, 41013 Sevilla, Spain
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Mollashahi H, Szymura M, Perera PCD, Szymura TH. The effect of grassland type and proximity to the city center on urban soil and vegetation coverage. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:599. [PMID: 37081193 PMCID: PMC10119043 DOI: 10.1007/s10661-023-11210-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
Urban soils with associated vegetation are important components of urban ecosystems, providing multiple regulating and supporting ecosystem services. This study aimed to analyze the differences in the soil chemistry and vegetation of urban grasslands considering urbanization gradient and urban grassland type (UGT). We hypothesized that the chemical properties of soil, such as metal content, as well as vegetation traits, differ according to grassland type (lawns, grasslands in parks, grasslands on river embankments, and roadsides) and the location of grassland patches (city center versus peripheries). Our samples included 94 UGT patches which each patch represented by four square sampling plots sized 1 m2. The results showed high differentiation of measured traits unrelated to UGT and location. The exception was K content, with a relatively high concentration in lawns, and some metals (Cd, Cu, Pb, Zn), with higher concentrations in the city center than in the peripheries. We found two grassland patches located in the city center where the concentrations of Pb, Zn, and Cu exceeded the level authorized by Polish standards. In the case of vegetation traits, the variability was not structured considering the UGT and location of the patches, except for bare soil cover, which was higher in lawns in the city center compared to embankments in the peripheries. We observed correlations between vegetation traits and soil chemical properties. The vascular plant species richness decreased when N, P, and C content, along with an increase in grass cover and a decrease in herbs.
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Affiliation(s)
- Hassanali Mollashahi
- Institute of Agroecology and Plant Production, Wrocław University of Environmental and Life Sciences, Grunwaldzki Sq 24a, Norwida St. 25, 50-363, Wroclaw, Poland.
| | - Magdalena Szymura
- Institute of Agroecology and Plant Production, Wrocław University of Environmental and Life Sciences, Grunwaldzki Sq 24a, Norwida St. 25, 50-363, Wroclaw, Poland
| | - Peliyagodage Chathura Dineth Perera
- Institute of Agroecology and Plant Production, Wrocław University of Environmental and Life Sciences, Grunwaldzki Sq 24a, Norwida St. 25, 50-363, Wroclaw, Poland
| | - Tomasz H Szymura
- Department of Ecology, Biogeochemistry and Environmental Protection, University of Wrocław, Wrocław, Poland
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40
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De León LF, Silva B, Avilés-Rodríguez KJ, Buitrago-Rosas D. Harnessing the omics revolution to address the global biodiversity crisis. Curr Opin Biotechnol 2023; 80:102901. [PMID: 36773576 DOI: 10.1016/j.copbio.2023.102901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 02/12/2023]
Abstract
Human disturbances are altering global biodiversity in unprecedented ways. We identify three fundamental challenges underpinning our understanding of global biodiversity (namely discovery, loss, and preservation), and discuss how the omics revolution (e.g. genomics, transcriptomics, proteomics, metabolomics, and meta-omics) can help address these challenges. We also discuss how omics tools can illuminate the major drivers of biodiversity loss, including invasive species, pollution, urbanization, overexploitation, and climate change, with a special focus on highly diverse tropical environments. Although omics tools are transforming the traditional toolkit of biodiversity research, their application to addressing the current biodiversity crisis remains limited and may not suffice to offset current rates of biodiversity loss. Despite technical and logistical challenges, omics tools need to be fully integrated into global biodiversity research, and better strategies are needed to improve their translation into biodiversity policy and practice. It is also important to recognize that although the omics revolution can be considered the biologist's dream, socioeconomic disparity limits their application in biodiversity research.
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Affiliation(s)
- Luis F De León
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
| | - Bruna Silva
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kevin J Avilés-Rodríguez
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA; Department of Biology, Fordham University, Bronx, NY, USA
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41
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Liu YR, van der Heijden MGA, Riedo J, Sanz-Lazaro C, Eldridge DJ, Bastida F, Moreno-Jiménez E, Zhou XQ, Hu HW, He JZ, Moreno JL, Abades S, Alfaro F, Bamigboye AR, Berdugo M, Blanco-Pastor JL, de Los Ríos A, Duran J, Grebenc T, Illán JG, Makhalanyane TP, Molina-Montenegro MA, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Rey A, Rodríguez A, Siebe C, Teixido AL, Casado-Coy N, Trivedi P, Torres-Díaz C, Verma JP, Mukherjee A, Zeng XM, Wang L, Wang J, Zaady E, Zhou X, Huang Q, Tan W, Zhu YG, Rillig MC, Delgado-Baquerizo M. Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide. Nat Commun 2023; 14:1706. [PMID: 36973286 PMCID: PMC10042830 DOI: 10.1038/s41467-023-37428-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Soil contamination is one of the main threats to ecosystem health and sustainability. Yet little is known about the extent to which soil contaminants differ between urban greenspaces and natural ecosystems. Here we show that urban greenspaces and adjacent natural areas (i.e., natural/semi-natural ecosystems) shared similar levels of multiple soil contaminants (metal(loid)s, pesticides, microplastics, and antibiotic resistance genes) across the globe. We reveal that human influence explained many forms of soil contamination worldwide. Socio-economic factors were integral to explaining the occurrence of soil contaminants worldwide. We further show that increased levels of multiple soil contaminants were linked with changes in microbial traits including genes associated with environmental stress resistance, nutrient cycling, and pathogenesis. Taken together, our work demonstrates that human-driven soil contamination in nearby natural areas mirrors that in urban greenspaces globally, and highlights that soil contaminants have the potential to cause dire consequences for ecosystem sustainability and human wellbeing.
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Affiliation(s)
- Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Marcel G A van der Heijden
- Plant-Soil Interactions, Agroscope, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Judith Riedo
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Carlos Sanz-Lazaro
- Multidisciplinary Institute for Environmental Studies (MIES), University of Alicante, P.O. Box 99, Alicante, E-03080, Spain
- Department of Ecology, University of Alicante, PO Box 99, Alicante, E-03080, Spain
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Felipe Bastida
- CEBAS-CSIC. Department of Soil and Water Conservation. Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Eduardo Moreno-Jiménez
- Department of Agricultural and Food Chemistry, Faculty of Sciences, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Institute of Biology, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, 14195, Germany
| | - Xin-Quan Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hang-Wei Hu
- Faculty of Science, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - Ji-Zheng He
- Faculty of Science, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - José L Moreno
- CEBAS-CSIC. Department of Soil and Water Conservation. Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Sebastian Abades
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
| | - Fernando Alfaro
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
- Instituto de Ecología y Biodiversidad (IEB), Santiago, 7800003, CP, Chile
| | - Adebola R Bamigboye
- Natural History Museum (Botany Unit), Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Miguel Berdugo
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología, Universidad Complutense de Madrid, C/Jose Antonio Novais 12, Madrid, 28040, Spain
| | | | - Asunción de Los Ríos
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Serrano 115 bis, 28006, Madrid, Spain
| | - Jorge Duran
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Tine Grebenc
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Javier G Illán
- Department of Entomology, Washington State University, Pullman, WA, 99164 USA, USA
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, DSI/NRF SARChI Chair in Marine Microbiomics, University of Pretoria, Pretoria, 0028, South Africa
| | - Marco A Molina-Montenegro
- Centre for Integrative Ecology, ICB, Universidad de Talca, Talca, Chile
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901, MG, Brazil
| | - Tina U Nahberger
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Gabriel F Peñaloza-Bojacá
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Serrano 115 bis, 28006, Madrid, Spain
| | - César Plaza
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F, 04510, CP, México
| | - Ana Rey
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Serrano 115 bis, 28006, Madrid, Spain
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
| | - Alexandra Rodríguez
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Christina Siebe
- Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Av. Fernando Corrêa, 2367, Boa Esperança, Cuiabá, 78060-900, MT, Brazil
| | - Alberto L Teixido
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, 80523, CO, USA
| | - Nuria Casado-Coy
- Multidisciplinary Institute for Environmental Studies (MIES), University of Alicante, P.O. Box 99, Alicante, E-03080, Spain
| | - Pankaj Trivedi
- Grupo de Biodiversidad y Cambio Global (BCG), Departamento de Ciencias. Básicas, Universidad del Bío-Bío, Campus Fernando May, Chillán, Chile
| | - Cristian Torres-Díaz
- Plant-Microbes Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Jay Prakash Verma
- Institute of Grassland Science/School of Life Science, Northeast Normal University, and Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, Jilin, China
| | - Arpan Mukherjee
- Institute of Grassland Science/School of Life Science, Northeast Normal University, and Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, Jilin, China
| | - Xiao-Min Zeng
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ling Wang
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Negev, 8531100, Israel
| | - Jianyong Wang
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Negev, 8531100, Israel
| | - Eli Zaady
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xiaobing Zhou
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Wuhan, 430000, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenfeng Tan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yong-Guan Zhu
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Sevilla, E-41012, Spain
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, 14195, Germany
| | - Manuel Delgado-Baquerizo
- Unidad Asociada CSIC-UPO (BioFun)., Universidad Pablo de Olavide, Sevilla, 41013, Spain.
- CEAZA, Universidad Católica del Norte, Coquimbo, Chile.
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Grierson J, Flies EJ, Bissett A, Ammitzboll H, Jones P. Which soil microbiome? Bacteria, fungi, and protozoa communities show different relationships with urban green space type and use-intensity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160468. [PMID: 36464041 DOI: 10.1016/j.scitotenv.2022.160468] [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: 09/14/2022] [Revised: 11/20/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Exposure to diverse microbial communities early in life can help support healthy human immune function. Soil microbiomes in public and private urban green spaces are potentially important sources of contact with diverse microbiomes for much of the global population. However, we lack understanding of how soil microbial communities vary across and within urban green spaces, and whether these patterns vary across microbial kingdoms; closing this knowledge gap may help us optimise green spaces' capacities to provide this ecosystem service. Here we explore the diversity and community compositions of soil microbiomes across urban green space types in Tasmania, Australia. Specifically, we analysed soil bacterial, fungal, and protozoan diversity and composition across private backyards and public parks. Within parks, we conducted separate sampling for areas of high and low intensity use. We found that: (i) bacteria, fungi, and protozoa showed different patterns of variation, (ii) bacterial alpha-diversity was lowest in low-intensity use areas of parks, (iii) there was relatively little variation in the community composition across backyards, and high and low intensity-use park areas and (iv) neither human-associated bacteria, nor potential microbial community function of bacteria and fungi differed significantly across green space types. To our knowledge, this is the first urban soil microbiome analysis which analyses these three soil microbial kingdoms simultaneously across public and private green space types and within public spaces according to intensity of use. These findings demonstrate how green space type and use intensity may impact on soil microbial diversity and composition, and thus may influence our opportunity to gain healthy exposure to diverse environmental microbiomes.
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Affiliation(s)
- Jessica Grierson
- Menzies Institute for Medical Research, University of Tasmania, Hobart 7001, Australia; School of Natural Sciences, University of Tasmania, Hobart 7001, Australia; Healthy Landscapes Research Group, University of Tasmania, Hobart 7001, Australia.
| | - Emily J Flies
- School of Natural Sciences, University of Tasmania, Hobart 7001, Australia; Healthy Landscapes Research Group, University of Tasmania, Hobart 7001, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, CSIRO, Hobart, TAS 7000, Australia
| | - Hans Ammitzboll
- School of Natural Sciences, University of Tasmania, Hobart 7001, Australia
| | - Penelope Jones
- Menzies Institute for Medical Research, University of Tasmania, Hobart 7001, Australia; School of Natural Sciences, University of Tasmania, Hobart 7001, Australia; Healthy Landscapes Research Group, University of Tasmania, Hobart 7001, Australia
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Lv Z, Xu M, Liu Y, Rønn R, Rensing C, Liu S, Gao S, Liao H, Liu YR, Chen W, Zhu YG, Huang Q, Hao X. Phagotrophic Protists Modulate Copper Resistance of the Bacterial Community in Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:3590-3601. [PMID: 36811608 DOI: 10.1021/acs.est.2c07136] [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] [Indexed: 06/18/2023]
Abstract
Protist predation is a crucial biotic driver modulating bacterial populations and functional traits. Previous studies using pure cultures have demonstrated that bacteria with copper (Cu) resistance exhibited fitness advantages over Cu-sensitive bacteria under the pressure of protist predation. However, the impact of diverse natural communities of protist grazers on bacterial Cu resistance in natural environments remains unknown. Here, we characterized the communities of phagotrophic protists in long-term Cu-contaminated soils and deciphered their potential ecological impacts on bacterial Cu resistance. Long-term field Cu pollution increased the relative abundances of most of the phagotrophic lineages in Cercozoa and Amoebozoa but reduced the relative abundance of Ciliophora. After accounting for soil properties and Cu pollution, phagotrophs were consistently identified as the most important predictor of the Cu-resistant (CuR) bacterial community. Phagotrophs positively contributed to the abundance of a Cu resistance gene (copA) through influencing the cumulative relative abundance of Cu-resistant and -sensitive ecological clusters. Microcosm experiments further confirmed the promotion effect of protist predation on bacterial Cu resistance. Our results indicate that the selection by protist predation can have a strong impact on the CuR bacterial community, which broadens our understanding of the ecological function of soil phagotrophic protists.
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Affiliation(s)
- Zhenguang Lv
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Regin Rønn
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Song Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shenghan Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Liao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
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44
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Warbrick I, Heke D, Breed M. Indigenous Knowledge and the Microbiome-Bridging the Disconnect between Colonized Places, Peoples, and the Unseen Influences That Shape Our Health and Well-Being. mSystems 2023; 8:e0087522. [PMID: 36695590 PMCID: PMC9948692 DOI: 10.1128/msystems.00875-22] [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] [Indexed: 01/26/2023] Open
Abstract
Indigenous Peoples have a rich and long-standing connection with the environments that they descend from-a connection that has informed a deep and multifaceted understanding of the relationship between human well-being and the environment. Through cultural narratives and practices, much of this knowledge has endured despite the ongoing effects that colonization has had on many Indigenous peoples across the world. These narratives and practices, based on observation, experimentation, and practical application over many generations, have the potential to make compelling contributions to our understanding of the environmental microbiome and its relationship to health. Furthermore, the inclusion of Indigenous perspectives regarding the microbiome opens pathways to those who rarely engage with the field and its learnings. Within the scientific community, Indigenous perspectives have not always been acknowledged as valid contributions and are often seen as myth or lacking rigor. Thus, this paper aims to explore an Indigenous perspective of the microbiome as an unseen influence on health and well-being by framing the importance of the natural environment, Indigenous knowledge and leadership, and future research directions that can contribute to this domain. Although the Indigenous perspective in this article reflects the experiences, worldviews, and knowledge of two New Zealand Māori authors, it is hoped that the concepts discussed can relate to Indigenous peoples, and non-Indigenous advocates, globally.
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Affiliation(s)
- Isaac Warbrick
- Taupua Waiora Centre for Māori Health Research–Auckland University of Technology, Auckland, New Zealand
| | - Deborah Heke
- Taupua Waiora Centre for Māori Health Research–Auckland University of Technology, Auckland, New Zealand
| | - Martin Breed
- College of Science and Engineering–Flinders University, Adelaide, Australia
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45
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Song P, Liu J, Huang P, Han Z, Wang D, Sun N. Diversity and structural analysis of rhizosphere soil microbial communities in wild and cultivated Rhizoma Atractylodis Macrocephalae and their effects on the accumulation of active components. PeerJ 2023; 11:e14841. [PMID: 36811005 PMCID: PMC9939024 DOI: 10.7717/peerj.14841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/11/2023] [Indexed: 02/18/2023] Open
Abstract
Rhizosphere microorganisms are the main factors affecting the formation of high quality medicinal materials and promoting the accumulation of secondary metabolites. However, the composition, diversity, and function of rhizosphere microbial communities in endangered wild and cultivated Rhizoma Atractylodis Macrocephalae (RAM) and their relationships with active component accumulation have remained unclear. In this study, high-throughput sequencing and correlation analysis were used to study the rhizosphere microbial community diversity (bacteria and fungi) of three RAM species and its correlation with the accumulation of polysaccharides, atractylone, and lactones (I, II, and III). A total of 24 phyla, 46 classes, and 110 genera were detected. The dominant taxa were Proteobacteria, Ascomycota, and Basidiomycota. The microbial communities in both wild and artificially cultivated soil samples were extremely species-rich, but there were some differences in their structure and the relative abundances of microorganism taxa. Meanwhile, the contents of effective components in wild RAM were significantly higher than those in cultivated RAM. Correlation analysis showed that 16 bacterial and 10 fungal genera were positively or negatively correlated with active ingredient accumulation. These results showed that rhizosphere microorganisms could play an important role in component accumulation and might lay a foundation for future research on endangered materials.
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Affiliation(s)
- Pingping Song
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Junling Liu
- Key Laboratory of Quality Research and Evaluation of Traditional Chinese Medicine, State Medical Products Administration, Hefei, China
| | - Peng Huang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China,Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, China
| | - Zhili Han
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China,Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, China
| | - Dianlei Wang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China,Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, China
| | - Nianxia Sun
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China,Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, China
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46
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Native plant gardens support more microbial diversity and higher relative abundance of potentially beneficial taxa compared to adjacent turf grass lawns. Urban Ecosyst 2023. [DOI: 10.1007/s11252-022-01325-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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47
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Du S, Feng J, Bi L, Hu HW, Hao X, Huang Q, Liu YR. Tracking soil resistance and virulence genes in rice-crayfish co-culture systems across China. ENVIRONMENT INTERNATIONAL 2023; 172:107789. [PMID: 36736026 DOI: 10.1016/j.envint.2023.107789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/03/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Rice-crayfish co-culture (RC) has been widely and rapidly promoted as a sustainable agricultural system in many countries. The accumulation of crayfish residues could enhance soil organic matters; however, impacts of this integrated farming model on the dissemination and pathogenicity of resistance and virulence genes remain poorly understood. Here, we characterized antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence factor genes (VFGs) using metagenomic methods in paired RC and rice monoculture (RM) systems across China. The RC model did not increase the abundance of soil ARGs, BRGs, MRGs, or VFGs in comparison to the RM model, but selectively enriched 35 subtypes of these potential resistance and virulence genes. Network analysis revealed that resistance and virulence genes had a higher number of connections with mobile genetic elements (MGEs) in the RC system than that in the RM system, suggesting a higher horizontal transfer potential of these genes. Moreover, the RC model had a higher abundance of human opportunistic pathogens such as Salmonella enterica, Vibrio cholerae, and Shigella dysenteriae which were potential hosts of VFGs such as phoP, fleS, and gspE, suggesting a potential threat to human health. We further unraveled that stochastic process was the main driver of the assembly of resistance and virulence genes in the RC system. The abundance of ARGs and VFGs were primarily associated with microbial community compositions, while the abundance of BRGs and MRGs were mainly associated with that of MGEs. Taken together, our results suggest that the RC model has potential to cause the dissemination and pathogenicity of resistance and virulence genes, which has important implications for the control of soil-borne biological risks and the strategic management of sustainable agriculture.
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Affiliation(s)
- Shuai Du
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiao Feng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Bi
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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48
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Abstract
The concept of one health highlights that human health is not isolated but connected to the health of animals, plants and environments. In this Review, we demonstrate that soils are a cornerstone of one health and serve as a source and reservoir of pathogens, beneficial microorganisms and the overall microbial diversity in a wide range of organisms and ecosystems. We list more than 40 soil microbiome functions that either directly or indirectly contribute to soil, plant, animal and human health. We identify microorganisms that are shared between different one health compartments and show that soil, plant and human microbiomes are perhaps more interconnected than previously thought. Our Review further evaluates soil microbial contributions to one health in the light of dysbiosis and global change and demonstrates that microbial diversity is generally positively associated with one health. Finally, we present future challenges in one health research and formulate recommendations for practice and evaluation.
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Affiliation(s)
- Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA.
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland. .,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
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49
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Fan K, Chu H, Eldridge DJ, Gaitan JJ, Liu YR, Sokoya B, Wang JT, Hu HW, He JZ, Sun W, Cui H, Alfaro FD, Abades S, Bastida F, Díaz-López M, Bamigboye AR, Berdugo M, Blanco-Pastor JL, Grebenc T, Duran J, Illán JG, Makhalanyane TP, Mukherjee A, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Verma JP, Rey A, Rodríguez A, Siebe C, Teixido AL, Trivedi P, Wang L, Wang J, Yang T, Zhou XQ, Zhou X, Zaady E, Tedersoo L, Delgado-Baquerizo M. Soil biodiversity supports the delivery of multiple ecosystem functions in urban greenspaces. Nat Ecol Evol 2023; 7:113-126. [PMID: 36631668 DOI: 10.1038/s41559-022-01935-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/03/2022] [Indexed: 01/13/2023]
Abstract
While the contribution of biodiversity to supporting multiple ecosystem functions is well established in natural ecosystems, the relationship of the above- and below-ground diversity with ecosystem multifunctionality remains virtually unknown in urban greenspaces. Here we conducted a standardized survey of urban greenspaces from 56 municipalities across six continents, aiming to investigate the relationships of plant and soil biodiversity (diversity of bacteria, fungi, protists and invertebrates, and metagenomics-based functional diversity) with 18 surrogates of ecosystem functions from nine ecosystem services. We found that soil biodiversity across biomes was significantly and positively correlated with multiple dimensions of ecosystem functions, and contributed to key ecosystem services such as microbially driven carbon pools, organic matter decomposition, plant productivity, nutrient cycling, water regulation, plant-soil mutualism, plant pathogen control and antibiotic resistance regulation. Plant diversity only indirectly influenced multifunctionality in urban greenspaces via changes in soil conditions that were associated with soil biodiversity. These findings were maintained after controlling for climate, spatial context, soil properties, vegetation and management practices. This study provides solid evidence that conserving soil biodiversity in urban greenspaces is key to supporting multiple dimensions of ecosystem functioning, which is critical for the sustainability of urban ecosystems and human wellbeing.
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Affiliation(s)
- Kunkun Fan
- 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
| | - 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.
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Juan J Gaitan
- National Institute of Agricultural Technology (INTA), Institute of Soil Science, Hurlingham, Argentina.,National University of Luján, Department of Technology, Luján, Argentina.,National Research Council of Argentina (CONICET), Buenos Aires, Argentina
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Blessing Sokoya
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
| | - Jun-Tao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Wei Sun
- Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Haiying Cui
- Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, Santiago, Chile
| | - Sebastian Abades
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, Santiago, Chile
| | | | | | - Adebola R Bamigboye
- Natural History Museum (Botany Unit), Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Miguel Berdugo
- Institut de Biologia Evolutiva (UPF-CSIC), Barcelona, Spain.,Institute of Integrative Biology, Department of Environment Systems Science, ETH Zurich, Univeritätstrasse, Zurich, Switzerland
| | | | - Tine Grebenc
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Jorge Duran
- Misión Biolóxica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain.,Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra, Portugal
| | - Javier G Illán
- Department of Entomology, Washington State University, Pullman, WA, USA
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Arpan Mukherjee
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Tina U Nahberger
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Gabriel F Peñaloza-Bojacá
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Brazil
| | - César Plaza
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jay Prakash Verma
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh, India.,Soil Microbiology Lab, Department of Soil Science, Federal University of Ceara, Fortaleza, Brazil
| | - Ana Rey
- Department of Biogeography and Global Change, National Museum of Natural History (MNCN), Spanish National Research Council (CSIC) C/ Serrano 115bis, Madrid, Spain
| | - Alexandra Rodríguez
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra, Portugal
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F., México
| | - Alberto L Teixido
- Departamento de Botância e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Boa Esperança, Cuiabá, Brazil
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Ling Wang
- Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Jianyong Wang
- Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Tianxue Yang
- Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Xin-Quan Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Xiaobing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Eli Zaady
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Negev, Israel
| | - Leho Tedersoo
- Department of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain. .,Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain.
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50
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Tedersoo L, Mikryukov V, Zizka A, Bahram M, Hagh‐Doust N, Anslan S, Prylutskyi O, Delgado‐Baquerizo M, Maestre FT, Pärn J, Öpik M, Moora M, Zobel M, Espenberg M, Mander Ü, Khalid AN, Corrales A, Agan A, Vasco‐Palacios A, Saitta A, Rinaldi AC, Verbeken A, Sulistyo BP, Tamgnoue B, Furneaux B, Ritter CD, Nyamukondiwa C, Sharp C, Marín C, Gohar D, Klavina D, Sharmah D, Dai DQ, Nouhra E, Biersma EM, Rähn E, Cameron E, De Crop E, Otsing E, Davydov EA, Albornoz F, Brearley FQ, Buegger F, Zahn G, Bonito G, Hiiesalu I, Barrio IC, Heilmann‐Clausen J, Ankuda J, Kupagme JY, Maciá‐Vicente JG, Fovo JD, Geml J, Alatalo JM, Alvarez‐Manjarrez J, Põldmaa K, Runnel K, Adamson K, Bråthen KA, Pritsch K, Tchan KI, Armolaitis K, Hyde KD, Newsham K, Panksep K, Lateef AA, Tiirmann L, Hansson L, Lamit LJ, Saba M, Tuomi M, Gryzenhout M, Bauters M, Piepenbring M, Wijayawardene N, Yorou NS, Kurina O, Mortimer PE, Meidl P, Kohout P, Nilsson RH, Puusepp R, Drenkhan R, Garibay‐Orijel R, Godoy R, Alkahtani S, Rahimlou S, Dudov SV, Põlme S, Ghosh S, Mundra S, Ahmed T, Netherway T, Henkel TW, Roslin T, Nteziryayo V, Fedosov VE, Onipchenko V, Yasanthika WAE, Lim YW, Soudzilovskaia NA, Antonelli A, Kõljalg U, Abarenkov K. Global patterns in endemicity and vulnerability of soil fungi. GLOBAL CHANGE BIOLOGY 2022; 28:6696-6710. [PMID: 36056462 PMCID: PMC9826061 DOI: 10.1111/gcb.16398] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/09/2022] [Indexed: 05/29/2023]
Abstract
Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | | | | | - Mohammad Bahram
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Sten Anslan
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Oleh Prylutskyi
- Department of Mycology and Plant Resistance, School of BiologyV.N. Karazin Kharkiv National UniversityKharkivUkraine
| | - Manuel Delgado‐Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, and Unidad Asociada CSIC‐UPO (BioFun)Universidad Pablo de OlavideSevillaSpain
| | - Fernando T. Maestre
- Departamento de Ecología, Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’Universidad de AlicanteAlicanteSpain
| | - Jaan Pärn
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Maarja Öpik
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Mari Moora
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Martin Zobel
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Mikk Espenberg
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Ülo Mander
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | | | - Adriana Corrales
- Centro de Investigaciones en Microbiología y Biotecnología‐UR (CIMBIUR)Universidad del RosarioBogotáColombia
| | - Ahto Agan
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Aída‐M. Vasco‐Palacios
- BioMicro, Escuela de MicrobiologíaUniversidad de Antioquia UdeAMedellinAntioquiaColombia
| | - Alessandro Saitta
- Department of Agricultural, Food and Forest SciencesUniversity of PalermoPalermoItaly
| | - Andrea C. Rinaldi
- Department of Biomedical SciencesUniversity of CagliariCagliariItaly
| | | | - Bobby P. Sulistyo
- Department of BiomedicineIndonesia International Institute for Life SciencesJakartaIndonesia
| | - Boris Tamgnoue
- Department of Crop ScienceUniversity of DschangDschangCameroon
| | - Brendan Furneaux
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
| | | | - Casper Nyamukondiwa
- Department of Biological Sciences and BiotechnologyBotswana International University of Science and TechnologyPalapyeBotswana
| | - Cathy Sharp
- Natural History Museum of ZimbabweBulawayoZimbabwe
| | - César Marín
- Centro de Investigación e Innovación para el Cambio Climático (CiiCC)Universidad SantoTomásSantiagoChile
| | - Daniyal Gohar
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Darta Klavina
- Latvian State Forest Research Insitute SilavaSalaspilsLatvia
| | - Dipon Sharmah
- Department of Botany, Jawaharlal Nehru Rajkeeya MahavidyalayaPondicherry UniversityPort BlairIndia
| | - Dong Qin Dai
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingChina
| | - Eduardo Nouhra
- Instituto Multidisciplinario de Biología Vegetal (CONICET)Universidad Nacional de CórdobaCordobaArgentina
| | | | - Elisabeth Rähn
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Erin K. Cameron
- Department of Environmental ScienceSaint Mary's UniversityHalifaxCanada
| | | | - Eveli Otsing
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | | | | | - Francis Q. Brearley
- Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
| | | | | | - Gregory Bonito
- Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Inga Hiiesalu
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Isabel C. Barrio
- Faculty of Natural and Environmental SciencesAgricultural University of IcelandHvanneyriIceland
| | | | - Jelena Ankuda
- Department of Silviculture and EcologyInstitute of Forestry of Lithuanian Research Centre for Agriculture and Forestry (LAMMC)GirionysLithuania
| | - John Y. Kupagme
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Jose G. Maciá‐Vicente
- Plant Ecology and Nature ConservationWageningen University & ResearchWageningenThe Netherlands
| | | | - József Geml
- ELKH‐EKKE Lendület Environmental Microbiome Research GroupEszterházy Károly Catholic UniversityEgerHungary
| | | | | | - Kadri Põldmaa
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Kadri Runnel
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Kalev Adamson
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Kari Anne Bråthen
- Department of Arctic and Marine BiologyThe Arctic University of NorwayTromsøNorway
| | | | - Kassim I. Tchan
- Research Unit Tropical Mycology and Plants‐Soil Fungi InteractionsUniversity of ParakouParakouBenin
| | - Kęstutis Armolaitis
- Department of Silviculture and EcologyInstitute of Forestry of Lithuanian Research Centre for Agriculture and Forestry (LAMMC)GirionysLithuania
| | - Kevin D. Hyde
- Center of Excellence in Fungal ResearchMae Fah Luang UniversityChiang RaiThailand
| | | | - Kristel Panksep
- Chair of Hydrobiology and FisheryEstonian University of Life SciencesTartuEstonia
| | | | - Liis Tiirmann
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Linda Hansson
- Gothenburg Centre for Sustainable DevelopmentGothenburgSweden
| | - Louis J. Lamit
- Department of BiologySyracuse UniversitySyracuseNew YorkUSA
- Department of Environmental and Forest BiologyState University of New York College of Environmental Science and ForestrySyracuseNew YorkUSA
| | - Malka Saba
- Department of Plant SciencesQuaid‐i‐Azam UniversityIslamabadPakistan
| | - Maria Tuomi
- Department of Arctic and Marine BiologyThe Arctic University of NorwayTromsøNorway
| | - Marieka Gryzenhout
- Department of GeneticsUniversity of the Free StateBloemfonteinSouth Africa
| | | | - Meike Piepenbring
- Mycology Working GroupGoethe University Frankfurt am MainFrankfurt am MainGermany
| | - Nalin Wijayawardene
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingChina
| | - Nourou S. Yorou
- Research Unit Tropical Mycology and Plants‐Soil Fungi InteractionsUniversity of ParakouParakouBenin
| | - Olavi Kurina
- Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartuEstonia
| | - Peter E. Mortimer
- Center For Mountain Futures, Kunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Peter Meidl
- Institut für BiologieFreie Universität BerlinBerlinGermany
| | - Petr Kohout
- Institute of MicrobiologyCzech Academy of SciencesPragueCzech Republic
| | - Rolf Henrik Nilsson
- Gothenburg Global Biodiversity CentreUniversity of GothenburgGothenburgSweden
| | - Rasmus Puusepp
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Rein Drenkhan
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | | | - Roberto Godoy
- Instituto Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | - Saad Alkahtani
- College of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Saleh Rahimlou
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Sergey V. Dudov
- Department of Ecology and Plant GeographyMoscow Lomonosov State UniversityMoscowRussia
| | - Sergei Põlme
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Soumya Ghosh
- Department of GeneticsUniversity of the Free StateBloemfonteinSouth Africa
| | - Sunil Mundra
- Department of Biology, College of ScienceUnited Arab Emirates UniversityAbu DhabiUAE
| | - Talaat Ahmed
- Environmental Science CenterQatar UniversityDohaQatar
| | - Tarquin Netherway
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Terry W. Henkel
- Department of Biological SciencesCalifornia State Polytechnic UniversityArcataCaliforniaUSA
| | - Tomas Roslin
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Vincent Nteziryayo
- Department of Food Science and TechnologyUniversity of BurundiBujumburaBurundi
| | - Vladimir E. Fedosov
- Department of Ecology and Plant GeographyMoscow Lomonosov State UniversityMoscowRussia
| | | | | | - Young Woon Lim
- School of Biological Sciences and Institute of MicrobiologySeoul National UniversitySeoulSouth Korea
| | | | | | - Urmas Kõljalg
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
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