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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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Kayiranga A, Isabwe A, Yao H, Shangguan H, Coulibaly JLK, Breed M, Sun X. Distribution patterns of soil bacteria, fungi, and protists emerge from distinct assembly processes across subcommunities. Ecol Evol 2024; 14:e11672. [PMID: 38988351 PMCID: PMC11236429 DOI: 10.1002/ece3.11672] [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: 03/06/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 07/12/2024] Open
Abstract
Environmental change exerts a profound effect on soil microbial domains-including bacteria, fungi, and protists-that each perform vital ecological processes. While these microbial domains are ubiquitous and extremely diverse, little is known about how they respond to environmental changes in urban soil ecosystems and what ecological processes shape them. Here we investigated the community assembly processes governing bacteria, fungi, and protists through the lens of four distinct subcommunities: abundant, conditionally rare, conditionally abundant, and rare taxa. We show that transient taxa, including the conditionally rare and conditionally rare or abundant taxa, were the predominant subcommunities. Deterministic processes (e.g., environmental filtering) had major roles in structuring all subcommunities of fungi, as well as conditionally rare and abundant protists. Stochastic processes had strong effects in structuring all subcommunities of bacteria (except rare taxa) and conditionally rare protists. Overall, our study underscores the importance of complementing the traditional taxonomy of microbial domains with the subcommunity approach when investigating microbial communities in urban soil ecosystems.
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Affiliation(s)
- Alexis Kayiranga
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Alain Isabwe
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
| | - Haifeng Yao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Huayuan Shangguan
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Justin Louis Kafana Coulibaly
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Martin Breed
- College of Science and Engineering Flinders University Bedford Park South Australia Australia
| | - Xin Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
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3
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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 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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4
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Zampolli J, De Giani A, Rossi M, Finazzi M, Di Gennaro P. Who inhabits the built environment? A microbiological point of view on the principal bacteria colonizing our urban areas. Front Microbiol 2024; 15:1380953. [PMID: 38863750 PMCID: PMC11165352 DOI: 10.3389/fmicb.2024.1380953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
Modern lifestyle greatly influences human well-being. Indeed, nowadays people are centered in the cities and this trend is growing with the ever-increasing population. The main habitat for modern humans is defined as the built environment (BE). The modulation of life quality in the BE is primarily mediated by a biodiversity of microbes. They derive from different sources, such as soil, water, air, pets, and humans. Humans are the main source and vector of bacterial diversity in the BE leaving a characteristic microbial fingerprint on the surfaces and spaces. This review, focusing on articles published from the early 2000s, delves into bacterial populations present in indoor and outdoor urban environments, exploring the characteristics of primary bacterial niches in the BE and their native habitats. It elucidates bacterial interconnections within this context and among themselves, shedding light on pathways for adaptation and survival across diverse environmental conditions. Given the limitations of culture-based methods, emphasis is placed on culture-independent approaches, particularly high-throughput techniques to elucidate the genetic and -omic features of BE bacteria. By elucidating these microbiota profiles, the review aims to contribute to understanding the implications for human health and the assessment of urban environmental quality in modern cities.
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Affiliation(s)
| | | | | | | | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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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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Sillo F, Neri L, Calvo A, Zampieri E, Petruzzelli G, Ferraris I, Delledonne M, Zaldei A, Gioli B, Baraldi R, Balestrini R. Correlation between microbial communities and volatile organic compounds in an urban soil provides clues on soil quality towards sustainability of city flowerbeds. Heliyon 2024; 10:e23594. [PMID: 38205296 PMCID: PMC10776942 DOI: 10.1016/j.heliyon.2023.e23594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024] Open
Abstract
Soil functionality is critical to the biosphere as it provides ecosystem services relevant for a healthy planet. The soil microbial composition is significantly impacted by anthropogenic activities, including urbanization. In this context, the study of soil microorganisms associated to urban green spaces has started to be crucial toward sustainable city development. Microbes living in the soil produce and degrade volatile organic compounds (VOCs). The VOC profiles may be used to distinguish between soils with various characteristics and management practices, reflecting variations in the activity of soil microbes that use a variety of metabolic pathways. Here, a combined approach based on DNA metabarcoding and GC-MS analysis was used to evaluate the soil quality from urban flowerbeds in Prato (Tuscany, Italy) in terms of microbial biodiversity and VOC emission profiles, with the final aim of evaluating the possible correlation between composition of microbial community and VOC patterns. Results showed that VOCs in the considered soil originated from anthropic and biological activity, and significant correlations between specific microbial taxa and VOCs were detected. Overall, the study demonstrated the feasibility of the use of microbe-VOC correlation as a proxy for soil quality assessment in urban soils.
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Affiliation(s)
- Fabiano Sillo
- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135 Torino, Italy
| | - Luisa Neri
- National Research Council, Institute of BioEconomy, Via P. Gobetti 101, 40129 Bologna and Via G. Caproni 8, 50145 Firenze, Italy
| | - Alice Calvo
- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135 Torino, Italy
| | - Elisa Zampieri
- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135 Torino, Italy
| | - Gianniantonio Petruzzelli
- National Research Council, Institute of Research on Terrestrial Ecosystems (IRET), Via Moruzzi 1, 56124 Pisa, Italy
| | - Irene Ferraris
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Alessandro Zaldei
- National Research Council, Institute of BioEconomy, Via P. Gobetti 101, 40129 Bologna and Via G. Caproni 8, 50145 Firenze, Italy
| | - Beniamino Gioli
- National Research Council, Institute of BioEconomy, Via P. Gobetti 101, 40129 Bologna and Via G. Caproni 8, 50145 Firenze, Italy
| | - Rita Baraldi
- National Research Council, Institute of BioEconomy, Via P. Gobetti 101, 40129 Bologna and Via G. Caproni 8, 50145 Firenze, Italy
| | - Raffaella Balestrini
- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135 Torino, Italy
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Adelana AO, Aiyelari EA, Are KS, Oluwatosin GA. Influence of urban land use types on ecosystem services in two rapidly urbanizing cities of southwestern Nigeria. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1279. [PMID: 37804466 DOI: 10.1007/s10661-023-11910-6] [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: 06/01/2023] [Accepted: 09/26/2023] [Indexed: 10/09/2023]
Abstract
Many ecological functions in cities are based on urban soils. In order to meet the needs of the expanding human population and the ensuing strain on natural resources, it is essential for soil-based ecosystems to function. Approximately 80% of the total urban land use in Akure and Okitipupa, Nigeria, are used for commercial, residential, and agricultural purposes. Thus, we investigated the potential of these three urban land use types (ULUTs) to offer a variety of ecosystem services in the two different cities. Soil properties that serve as proxy indicators for four ecosystem services were measured in the ULUTs: hydraulic conductivity (Kunsat) and available soil water for rainwater retention; soil organic carbon (SOC) stock for carbon storage; soil microbial respiration (SMR) for the capacity to support biological activity; and soil compaction (PR) and total nitrogen (TN) for promoting plant growth. The location and ULUT resulted in distinct ecosystem service provisioning. In comparison to Akure, Okitipupa soils had lower PR (1.0 vs 1.1 MPa) but higher Kunsat (36.9 vs 10.3 cm h-1), SOC stock (6.9 vs 5.7 Mg C ha-1), and SMR levels (35.2 vs 23.6 mg CO2-C g-1 soil). Commercial soils exhibited more compaction than residential and agricultural soils but less SOC stock and Kunsat, and TN in both locations. The properties of the urban soils showed that the soils could support a variety of ecosystem services. Different soil properties at the city level led to variations in the potential for ecosystem services in various locations, and these variations were observable in commercial, residential, and agricultural soils. Understanding urban soils would thus necessitate both cross-city comparative studies as well as within-city examinations of the potential for ecosystem services for various urban land use types.
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Affiliation(s)
- Ayodele O Adelana
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Moor Plantation, Ibadan, Nigeria.
| | | | - Kayode S Are
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Moor Plantation, Ibadan, Nigeria
| | - Gabriel A Oluwatosin
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Moor Plantation, Ibadan, Nigeria
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8
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Chaurasia M, Patel K, Rao KS. Impact of anthropogenic land uses on soil microbiological activity in a peri-urban landscape. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1233. [PMID: 37728781 DOI: 10.1007/s10661-023-11822-5] [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: 05/23/2023] [Accepted: 09/01/2023] [Indexed: 09/21/2023]
Abstract
Land use and land cover patterns impact soil properties and negatively affect soil microbial community and related processes. However, the information regarding the influence of urban land use on soil microbial composition and functioning is limited. Here, we investigated the impact of urban land use patterns on soil microbiological parameters by comparing five contrasting anthropogenic land use classes, i.e. agriculture, park, roadside plantation, street green, and bare land. Soil physicochemical properties, basal respiration (BR), microbial biomass carbon (MBC), and enzyme activities were estimated and correlated. The results revealed that soil physicochemical and microbiological properties greatly varied across the five land use classes. Among all the land use types, the roadside plantation had the highest nutrient content, i.e. soil organic carbon (SOC), total nitrogen (TN), and mineral nitrogen (MN) (1.33%, 0.13%, 84.0 mg kg-1, respectively), while the soil functional capacities measured in terms of BR, MBC, microbial quotient (QCO2), soil microbial activity (SMA), and dehydrogenase activity (DHA) (9.90 C µg g-1 h-1, 300 µg g-1, 0.045 µg h-1/ µg MBC, 9.0 µg ml-1, 1.30 TPF g-1 h-1, respectively) were highest in the park. Disturbed street greens were markedly nutrient depleted and apparently exhibited lower microbial activity. Variations in soil BR, MBC, and enzyme activity were revealed to be primarily influenced by soil moisture, available phosphorus, and SOC content. We concluded that the negative impacts of anthropogenic land use soil quality and microbiological functioning can be managed by integrating proper management approaches for various land use classes in urban systems.
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Affiliation(s)
| | - Kajal Patel
- Department of Botany, University of Delhi, New Delhi-110007, India
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9
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Ren Y, Shao Q, Ge W, Li X, Wang H, Dong C, Zhang Y, Deshmukh SK, Han Y. Assembly Processes and Biogeographical Characteristics of Soil Bacterial Sub-communities of Different Habitats in Urban Green Spaces. Curr Microbiol 2023; 80:309. [PMID: 37535152 DOI: 10.1007/s00284-023-03428-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 07/23/2023] [Indexed: 08/04/2023]
Abstract
The process of urbanization is one of the most important human-driven activities that reshape the natural distribution of soil microorganisms. However, it is still unclear about the effects of urbanization on the different taxonomic soil bacterial community dynamics. In this study, we collected soil samples from highly urbanized the regions of Yangtze River Delta, Beijing-Tianjin-Hebei in China, to explore the bio-geographic patterns, assembly processes, and symbiotic patterns of abundant, moderate, and rare bacterial communities. We found that the number of moderate and rare taxa species were lower than that of abundant taxa, but their α-diversity index was higher than abundant taxa. Proteobacteria, Acidobacteria, Actinobacteria, Bacterioidetes, and Chloroflexi were the dominant phylum across all three sub-communities. And the β-diversity value of rare taxa was significantly higher than those of moderate and abundant taxa. Abundant, moderate, and rare sub-communities showed a weak distance-decay relationship, and the moderate taxa had the highest turnover rate of microbial geography in the context of urbanization. Diffusion limitation was the dominant process of soil bacterial community assembly. The co-occurrence networks of abundant, moderate, and rare taxa were dominated by positive correlations. The network of moderate taxa had the highest modularity, followed by abundant taxa. The main functions of the abundant, moderate, and rare taxa were related to Chemoheterotrophy and N transformations. Redundancy analysis showed that the dispersal limitation, climate, and soil properties were the main factors dominating bio-geographic differences in soil bacterial community diversity. We conclude that human-dominated urbanization processes have generated more uncertain survival pressures on soil bacteria, which resulted in a stronger linkage but weak bio-geographic variation for soil bacteria. In the future urban planning process, we suggest that such maintenance of native vegetation and soil types should be considered to maintain the long-term stability of local microbial ecosystem functions.
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Affiliation(s)
- Yulian Ren
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Wei Ge
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xin Li
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Haiyan Wang
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Chunbo Dong
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yanwei Zhang
- School of Biological Sciences, Guizhou Education University, Guiyang, 550018, Guizhou, China
| | - Sunil Kumar Deshmukh
- TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003, India
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China.
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10
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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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11
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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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12
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Mejia MP, Rojas CA, Curd E, Renshaw MA, Edalati K, Shih B, Vincent N, Lin M, Nguyen PH, Wayne R, Jessup K, Parker SS. Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site. MICROBIAL ECOLOGY 2023; 85:998-1012. [PMID: 35802172 PMCID: PMC10156844 DOI: 10.1007/s00248-022-02061-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/21/2022] [Indexed: 05/04/2023]
Abstract
Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.
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Affiliation(s)
- Maura Palacios Mejia
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Connie A Rojas
- Ecology, Evolution, and Behavior Program, Michigan State University, Lansing, MI, USA
| | - Emily Curd
- Natural Science, Landmark College, Putney, VT, USA
| | - Mark A Renshaw
- Cherokee Federal, USGS Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - Kiumars Edalati
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Beverly Shih
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nitin Vincent
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Meixi Lin
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peggy H Nguyen
- Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert Wayne
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
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13
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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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14
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Scholier T, Lavrinienko A, Brila I, Tukalenko E, Hindström R, Vasylenko A, Cayol C, Ecke F, Singh NJ, Forsman JT, Tolvanen A, Matala J, Huitu O, Kallio ER, Koskela E, Mappes T, Watts PC. Urban forest soils harbour distinct and more diverse communities of bacteria and fungi compared to less disturbed forest soils. Mol Ecol 2023; 32:504-517. [PMID: 36318600 DOI: 10.1111/mec.16754] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 11/27/2022]
Abstract
Anthropogenic changes to land use drive concomitant changes in biodiversity, including that of the soil microbiota. However, it is not clear how increasing intensity of human disturbance is reflected in the soil microbial communities. To address this issue, we used amplicon sequencing to quantify the microbiota (bacteria and fungi) in the soil of forests (n = 312) experiencing four different land uses, national parks (set aside for nature conservation), managed (for forestry purposes), suburban (on the border of an urban area) and urban (fully within a town or city), which broadly represent a gradient of anthropogenic disturbance. Alpha diversity of bacteria and fungi increased with increasing levels of anthropogenic disturbance, and was thus highest in urban forest soils and lowest in the national parks. The forest soil microbial communities were structured according to the level of anthropogenic disturbance, with a clear urban signature evident in both bacteria and fungi. Despite notable differences in community composition, there was little change in the predicted functional traits of urban bacteria. By contrast, urban soils exhibited a marked loss of ectomycorrhizal fungi. Soil pH was positively correlated with the level of disturbance, and thus was the strongest predictor of variation in alpha and beta diversity of forest soil communities, indicating a role of soil alkalinity in structuring urban soil microbial communities. Hence, our study shows how the properties of urban forest soils promote an increase in microbial diversity and a change in forest soil microbiota composition.
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Affiliation(s)
- Tiffany Scholier
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Ilze Brila
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Ecology and Genetics Unit, University of Oulu, Oulu, Finland
| | - Eugene Tukalenko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Rasmus Hindström
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Ecology and Genetics Unit, University of Oulu, Oulu, Finland
| | - Andrii Vasylenko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Claire Cayol
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden.,The Pirbright Institute, Pirbright, UK
| | - Frauke Ecke
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden.,Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Navinder J Singh
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Jukka T Forsman
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Anne Tolvanen
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Juho Matala
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Otso Huitu
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Eva R Kallio
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Esa Koskela
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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15
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Adelana AO, Aiyelari EA, Oluwatosin GA, Are KS. Soil properties that differentiate urban land use types with different surface geology in Southwest Nigeria. Urban Ecosyst 2022. [DOI: 10.1007/s11252-022-01301-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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