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Yiallouris A, Pana ZD, Marangos G, Tzyrka I, Karanasios S, Georgiou I, Kontopyrgia K, Triantafyllou E, Seidel D, Cornely OA, Johnson EO, Panagiotou S, Filippou C. Fungal diversity in the soil Mycobiome: Implications for ONE health. One Health 2024; 18:100720. [PMID: 38699438 PMCID: PMC11064618 DOI: 10.1016/j.onehlt.2024.100720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Today, over 300 million individuals worldwide are afflicted by severe fungal infections, many of whom will perish. Fungi, as a result of their plastic genomes have the ability to adapt to new environments and extreme conditions as a consequence of globalization, including urbanization, agricultural intensification, and, notably, climate change. Soils and the impact of these anthropogenic environmental factors can be the source of pathogenic and non-pathogenic fungi and subsequent fungal threats to public health. This underscores the growing understanding that not only is fungal diversity in the soil mycobiome a critical component of a functioning ecosystem, but also that soil microbial communities can significantly contribute to plant, animal, and human health, as underscored by the One Health concept. Collectively, this stresses the importance of investigating the soil microbiome in order to gain a deeper understanding of soil fungal ecology and its interplay with the rhizosphere microbiome, which carries significant implications for human health, animal health and environmental health.
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Affiliation(s)
- Andreas Yiallouris
- School of Medicine, European University, Cyprus
- Medical innovation center (MEDIC), School of Medicine, European University, Cyprus
| | - Zoi D. Pana
- School of Medicine, European University, Cyprus
- Medical innovation center (MEDIC), School of Medicine, European University, Cyprus
| | | | | | | | | | | | | | - Danila Seidel
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Oliver A. Cornely
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center for Medical Mycology (ECMM), Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Elizabeth O. Johnson
- School of Medicine, European University, Cyprus
- Medical innovation center (MEDIC), School of Medicine, European University, Cyprus
| | - Stavros Panagiotou
- School of Medicine, European University, Cyprus
- Division of Medical Education, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester
| | - Charalampos Filippou
- School of Medicine, European University, Cyprus
- Medical innovation center (MEDIC), School of Medicine, European University, Cyprus
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zhao X, Cui H, Song H, Chen J, Wang J, Liu Z, Ali I, Yang Z, Hou X, Zhou X, Xiao S, Chen S. Contrasting responses of α- and β-multifunctionality to aboveground plant community in the Qinghai-Tibet Plateau. Sci Total Environ 2024; 917:170464. [PMID: 38290671 DOI: 10.1016/j.scitotenv.2024.170464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/01/2024]
Abstract
The aboveground plant communities are crucial in driving ecosystem functioning, particularly being the primary producers in terrestrial ecosystems. Numerous studies have investigated the impacts of aboveground plant communities on multiple ecosystem functions at α-scale. However, such critical effects have been unexplored at β-scale and the comparative assessment of the effects and underlying mechanisms of aboveground plant communities on α- and β-multifunctionality has been lacking. In this study, we examined the effects of aboveground plant communities on soil multifunctionality both at α- and β-scale in the alpine meadow of the Tibetan Plateau. Additionally, we quantified the direct effects of aboveground plant communities, as well as the indirect effects mediated by changes in biotic and abiotic factors, on soil multifunctionality at both scales. Our findings revealed that: 1) Aboveground plant communities had significantly positive effects on α-multifunctionality whereas, β-multifunctionality was not affected significantly. 2) Aboveground plant communities directly influence α- and β-multifunctionality in contrasting ways, with positive and negative effects, respectively. Apart from the direct effects of plant community, we found that soil water content and bacterial β-diversity serving as the primary predictors for the responses of α- and β-multifunctionality to the presence of aboveground plant communities, respectively. And β-soil biodiversity appeared to be a stronger predictor of multifunctionality relative to α-soil biodiversity. Our findings provide novel insights into the drivers of ecosystem multifunctionality at different scales, highlight the importance of maintaining biodiversity at multiple scales and offer valuable knowledge for the maintenance of ecosystem functioning and the restoration of alpine meadow ecosystems.
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Affiliation(s)
- Xia Zhao
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Hanwen Cui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Hongxian Song
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Jingwei Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Jiajia Wang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Ziyang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Izhar Ali
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Zi Yang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Xiao Hou
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Xianhui Zhou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Sa Xiao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Shuyan Chen
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China.
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Ren P, Sun A, Jiao X, Chen QL, Li F, He JZ, Hu HW. National-scale investigation reveals the dominant role of phyllosphere fungal pathogens in sorghum yield loss. Environ Int 2024; 185:108511. [PMID: 38382404 DOI: 10.1016/j.envint.2024.108511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Fungal plant pathogens threaten crop production and sustainable agricultural development. However, the environmental factors driving their diversity and nationwide biogeographic model remain elusive, impacting our capacity to predict their changes under future climate scenarios. Here, we analyzed potential fungal plant pathogens from 563 samples collected from 57 agricultural fields across China. Over 28.0% of fungal taxa in the phyllosphere were identified as potential plant pathogens, compared to 22.3% in the rhizosphere. Dominant fungal plant pathogen groups were Cladosporium (in the phyllosphere) and Fusarium (in the rhizosphere), with higher diversity observed in the phyllosphere than in rhizosphere soil. Deterministic processes played an important role in shaping the potential fungal plant pathogen community assembly in both habitats. Mean annual precipitation and temperature were the most important factor influencing phyllosphere fungal plant pathogen richness. Significantly negative relationships were found between fungal pathogen diversity and sorghum yield. Notably, compared to the rhizosphere, the phyllosphere fungal plant pathogen diversity played a more crucial role in sorghum yield. Together, our work provides novel insights into the factors governing the spatial patterns of fungal plant pathogens in the crop microbiome, and highlights the potential significance of aboveground phyllosphere fungal plant pathogens in crop productivity.
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Affiliation(s)
- Peixin Ren
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, 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
| | - Xiaoyan Jiao
- College of Resource and Environment, Shanxi Agricultural University, Taiyuan 030031, 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
| | - Fangfang Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Ji-Zheng He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Perron T, Legrand M, Janeau JL, Manizan A, Vierling C, Kouakou A, Brauman A, Gay F, Laclau JP, Mareschal L. Runoff and soil loss are drastically decreased in a rubber plantation combining the spreading of logging residues with a legume cover. Sci Total Environ 2024; 913:169335. [PMID: 38103613 DOI: 10.1016/j.scitotenv.2023.169335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/11/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Soil erosion on agricultural land is a major threat for food and raw materials production. It has become a major concern in rubber (Hevea brasiliensis) plantations introduced on sloping ground. Alternative agroecological crop management practices must be investigated. One aim of our study was to assess the ability of logging residues (i.e., trunks, branches, leaves and stumps of a clearcut plantation) and of legume cover (Pueraria phaseoloides) to mitigate N, P and K losses through runoff and soil detachment in a young rubber plantation. The other aim was to investigate the relationships of these nutrient losses with soil structure and soil macrofauna diversity. Runoff and soil loss were monitored for 3 years using 1-m2 plots under different practices as regards the management of logging residues and the use or not of a legume. The monitoring started when rubber trees were one-year-old. The planting row, where soil was bare, was the hotspot of soil erosion, with an average runoff of 832 mm y-1 and soil loss of 3.2 kg m-2 y-1. Sowing a legume in the inter-row reduced runoff and soil loss by 88 % and 98 % respectively, compared to bare soil. Spreading logging residues as well as growing a legume cover almost eliminated runoff and soil detachment (19 mm y-1 and 4 g m-2 y-1 respectively). Nutrient losses were negligible as long as the soil surface was covered by a legume crop, with or without logging residues. Total N loss from soil detachment ranged from 0.02 to 0.2 g m-2 y-1, for example. Spreading logging residues in the inter-rows significantly improved soil structure and soil macrofauna diversity compared to bare soil. Nutrient losses from runoff and soil detachment were negatively correlated with improved soil structure and soil macrofauna diversity. We recommend investigating alternative ways to manage planting rows.
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Affiliation(s)
- Thibaut Perron
- CIRAD, UMR ABSys, F-34398 Montpellier, France; ABSys, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, Montpellier, France; SAPH, Direction of Industrial Plantations (DPI), Cote d'Ivoire.
| | - Marianne Legrand
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France; CIRAD, UMR Eco&Sols, F-34398 Montpellier, France; INRAE, EMMAH, UMR 1114 INRAE-Avignon University, Domaine Saint Paul, F-84914 Avignon cedex 09, France
| | - Jean-Louis Janeau
- Institute of Ecology and Environmental Sciences (iEES-Paris), IRD, Sorbonne Université, CNRS, INRAE, Université Paris Diderot, Paris, France
| | - Antoine Manizan
- SOGB, Agricultural technique, auditing and Organisation Department (DTAO), SOCFIN, Côte d'Ivoire
| | - Cécile Vierling
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France; CIRAD, UMR Eco&Sols, F-34398 Montpellier, France; AgroParisTech, 22 place de l'Agronomie, 91123 Palaiseau Cedex, France
| | - Aymard Kouakou
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France; Nangui Abrogoua University, Ecology and Sustainable Development Laboratory, Abidjan, Côte d'Ivoire
| | - Alain Brauman
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Frédéric Gay
- CIRAD, UMR ABSys, F-34398 Montpellier, France; ABSys, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jean-Paul Laclau
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France; CIRAD, UMR Eco&Sols, F-34398 Montpellier, France
| | - Louis Mareschal
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France; CIRAD, UMR Eco&Sols, F-34398 Montpellier, France
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Zhou J, Su Y, Li X, Kuzyakov Y, Wang P, Gong J, Li X, Liu L, Zhang X, Ma C, Ma X, Huang T, Bai Y, Sun F. Arbuscular mycorrhizae mitigate negative impacts of soil biodiversity loss on grassland productivity. J Environ Manage 2024; 349:119509. [PMID: 37940487 DOI: 10.1016/j.jenvman.2023.119509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/10/2023]
Abstract
Grassland degradation decreases ecosystem productivity and diminishes soil biodiversity, leading to the loss of beneficial microorganisms. Arbuscular mycorrhizal fungi (AMF) play a critical role in ecosystem functioning, being a key link between plant and microbial communities, soil, and vegetation. Here, we evaluated the potential of increasing the productivity of degraded grassland by AMF inoculation. A gradient of soil biodiversity: complete sterilization, low, moderate, and high biodiversity was established using the dilution-to-extinction approach. Grassland microcosms under greenhouse conditions were inoculated with three AMF taxa in an increasing diversity: no AMF, single AMF taxa, and all three AMF taxa together. The loss of soil biodiversity decreased plant community productivity, primarily due to reduced biomass of legumes and non-N2-fixing forbs. AMF inoculation raised plant community productivity by 190%, mainly attributed to the greater biomass of legumes and non-N2-fixing forbs. This positive effect of AMF inoculation was particularly pronounced on soils with low biodiversity, where soil mutualists were absent. The biomass of grasses remained independent of AMF inoculation. This differential responsiveness to mycorrhiza was mainly due to the distinctive plant traits of each plant functional group. Inoculating with a single AMF was more beneficial for plant biomass production than inoculation with multiple AMF under lower levels of soil biodiversity, probably due to high functional redundancy among AMF taxa. In conclusion, AMF inoculation reduced the adverse impact of soil degradation and biodiversity loss on plant biomass and vegetation development, highlighting the key roles and importance of AMF for grassland restoration.
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Affiliation(s)
- Jiqiong Zhou
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China.
| | - Yingying Su
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China
| | - Xiangjun Li
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, 37077, Göttingen, Germany; Peoples Friendship University of Russia (RUDN University), 117198, Moscow, Russia
| | - Pengsen Wang
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China
| | - Jinchao Gong
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China
| | - Xuxu Li
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China
| | - Lin Liu
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China
| | - Xinquan Zhang
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China
| | - Congyu Ma
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China
| | - Xiao Ma
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China
| | - Ting Huang
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China
| | - Yanfu Bai
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China
| | - Feida Sun
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China
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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. Sci Total Environ 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] [What about the content of this article? (0)] [Affiliation(s)] [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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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. Sci Total Environ 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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Zhu L, Chen Y, Sun R, Zhang J, Hale L, Dumack K, Geisen S, Deng Y, Duan Y, Zhu B, Li Y, Liu W, Wang X, Griffiths BS, Bonkowski M, Zhou J, Sun B. Resource-dependent biodiversity and potential multi-trophic interactions determine belowground functional trait stability. Microbiome 2023; 11:95. [PMID: 37127665 PMCID: PMC10150482 DOI: 10.1186/s40168-023-01539-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND For achieving long-term sustainability of intensive agricultural practices, it is pivotal to understand belowground functional stability as belowground organisms play essential roles in soil biogeochemical cycling. It is commonly believed that resource availability is critical for controlling the soil biodiversity and belowground organism interactions that ultimately lead to the stabilization or collapse of terrestrial ecosystem functions, but evidence to support this belief is still limited. Here, we leveraged field experiments from the Chinese National Ecosystem Research Network (CERN) and two microcosm experiments mimicking high and low resource conditions to explore how resource availability mediates soil biodiversity and potential multi-trophic interactions to control functional trait stability. RESULTS We found that agricultural practice-induced higher resource availability increased potential cross-trophic interactions over 316% in fields, which in turn had a greater effect on functional trait stability, while low resource availability made the stability more dependent on the potential within trophic interactions and soil biodiversity. This large-scale pattern was confirmed by fine-scale microcosm systems, showing that microcosms with sufficient nutrient supply increase the proportion of potential cross-trophic interactions, which were positively associated with functional stability. Resource-driven belowground biodiversity and multi-trophic interactions ultimately feedback to the stability of plant biomass. CONCLUSIONS Our results indicated the importance of potential multi-trophic interactions in supporting belowground functional trait stability, especially when nutrients are sufficient, and also suggested the ecological benefits of fertilization programs in modern agricultural intensification. Video Abstract.
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Affiliation(s)
- Lingyue Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Nanjing, 210008, China.
| | - Ruibo Sun
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Nanjing, 210008, China.
| | - Lauren Hale
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- United States Department of Agriculture, Agricultural Research Service (ARS), Washington, DC, 20250, USA
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, 50674, Cologne, Germany
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6700AB, The Netherlands
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100081, China
| | - Yinghua Duan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bo Zhu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yan Li
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Wenzhao Liu
- Institute of Soil and Water Conservation, Chine, Academy of Sciences and Ministry of Water Resources , Yangling, 712100, China
| | - Xiaoyue Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Nanjing, 210008, China
| | - Bryan S Griffiths
- SRUC, Crop and Soil System Research Group, West Mains Road, Edinburgh, EH93JG, UK
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, 50674, Cologne, Germany
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Nanjing, 210008, China.
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10
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Barranger A, Klopp C, Le Bot B, Saramito G, Dupont L, Llopis S, Wiegand C, Binet F. Insights into the molecular mechanisms of pesticide tolerance in the Aporrectodea caliginosa earthworm. Environ Pollut 2023; 319:120945. [PMID: 36572272 DOI: 10.1016/j.envpol.2022.120945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/09/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Diffuse pollution of the environment by pesticides has become a major soil threat to non-target organisms, such as earthworms for which declines have been reported. However some endogeic species are still abundant and persist in intensively cultivated fields, suggesting they become tolerant to long-term anthropogenic pressure. We thus considered the working hypothesis that populations of Aporrectodea caliginosa earthworms from conventionally managed fields developed a tolerance to pesticides compared with those from organically managed fields. To investigate this hypothesis, we studied earthworm populations of the same genetic lineage from soils that were either lowly or highly contaminated by pesticides to detect any constitutive expression of differentially expressed molecular pathways between these populations. Earthworm populations were then experimentally exposed to a fungicide-epoxiconazole-in the laboratory to identify different molecular responses when newly exposed to a pesticide. State-of-the-art omics technology (RNA sequencing) and bioinformatics were used to characterize molecular mechanisms of tolerance in a non-targeted way. Additional physiological traits (respirometry, growth, bioaccumulation) were monitored to assess tolerance at higher levels of biological organization. In the present study, we generated the de novo assembly transcriptome of A. caliginosa consisting of 64,556 contigs with N50 = 2862 pb. In total, 43,569 Gene Ontology terms were identified for 21,593 annotated sequences under the three main ontologies (biological processes, cellular components and molecular functions). Overall, we revealed that two same lineage populations of A. caliginosa earthworms, inhabiting similar pedo-climatic environment, have distinct gene expression pathways after they long-lived in differently managed agricultural soils with a contrasted pesticide exposure history for more than 22 years. The main difference was observed regarding metabolism, with upregulated pathways linked to proteolytic activities and the mitochondrial respiratory chain in the highly exposed population. This study improves our understanding of the long-term impact of chronic exposure of soil engineers to pesticide residues.
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Affiliation(s)
- Audrey Barranger
- UMR CNRS ECOBIO 6553, Université de Rennes1, Campus de Beaulieu, 263 Avenue du Général Leclerc, 35042, Rennes, Cedex, France.
| | - Christophe Klopp
- UR INRAE 875 MIAT, GENOTOUL, 24 Chemin de Borde Rouge, 31326, Castanet-Tolosan, Cedex, France
| | - Barbara Le Bot
- Université de Rennes, EHESP, Inserm, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F 35000, Rennes, France
| | - Gaëlle Saramito
- Université de Rennes, EHESP, Inserm, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F 35000, Rennes, France
| | - Lise Dupont
- Université Paris Est Créteil (UPEC), Sorbonne Université, CNRS, INRAE, IRD, Institut d'Ecologie et des Sciences de l'Environnement de Paris, 94010, Créteil, Cedex, France
| | - Stéphanie Llopis
- UMR CNRS ECOBIO 6553, Université de Rennes1, Campus de Beaulieu, 263 Avenue du Général Leclerc, 35042, Rennes, Cedex, France
| | - Claudia Wiegand
- UMR CNRS ECOBIO 6553, Université de Rennes1, Campus de Beaulieu, 263 Avenue du Général Leclerc, 35042, Rennes, Cedex, France
| | - Françoise Binet
- UMR CNRS ECOBIO 6553, Université de Rennes1, Campus de Beaulieu, 263 Avenue du Général Leclerc, 35042, Rennes, Cedex, France
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11
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Yang Y, Chai Y, Xie H, Zhang L, Zhang Z, Yang X, Hao S, Gai J, Chen Y. Responses of soil microbial diversity, network complexity and multifunctionality to three land-use changes. Sci Total Environ 2023; 859:160255. [PMID: 36402341 DOI: 10.1016/j.scitotenv.2022.160255] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Land-use change is one of the greatest challenges for natural ecosystem services. Soil microbiomes are essential for modulating multiple ecosystem functions. However, little is known about the impact of land-use changes on soil microbial communities and their associated soil functions. In this study, 150 alpine soil samples representing conversion of forests to shrublands or grasslands, and of shrublands to grasslands were investigated for bacterial, fungal and protistan community diversity, co-occurrence network, as well as their relationships with soil multifunctionality via a sampling strategy of space-for-time substitution. The conversion of forest to grassland increased the diversity of fungi and bacteria, and altered the microbial community structures of bacteria, fungi and protists, resulting a greater impact on soil microbiome than other land-use conversions. Cross-trophic interaction analyses demonstrated this conversion increased microbial network complexity and robustness, whereas forest to shrubland had the opposite trend. The land-use induced changes in soil multifunctionality were related with microbial network modules, but were not always associated with variations of microbial diversity. Random forest modeling further suggested the significant role of microbial modules in explaining soil multifunctionality, together with environmental factors. These findings indicate divergent responses of belowground multitrophic organisms to land-use changes, and the potential role of microbial module in forecasting soil multifunctionality.
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Affiliation(s)
- Yi Yang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yabo Chai
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Hanjie Xie
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Lu Zhang
- State Key laboratory Urban & Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhiming Zhang
- School of Ecology and Environmental Sciences, Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming 650091, Yunnan, China
| | - Xue Yang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Shenglei Hao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Jingping Gai
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
| | - Yongliang Chen
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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12
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Mishra A, Singh L, Singh D. Unboxing the black box-one step forward to understand the soil microbiome: A systematic review. Microb Ecol 2023; 85:669-683. [PMID: 35112151 PMCID: PMC9957845 DOI: 10.1007/s00248-022-01962-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.
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Affiliation(s)
- Apurva Mishra
- Academy of Scientific and Innovative Research [AcSIR], Ghaziabad, 201002, India
- Environmental Biotechnology and Genomics Division, , CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Lal Singh
- Environmental Biotechnology and Genomics Division, , CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Dharmesh Singh
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Trogerstrasse 30, 81675, Munich, Bavaria, Germany.
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13
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Zverev A, Kimeklis A, Kichko A, Gladkov G, Andronov E, Abakumov E. Microbial features of mature and abandoned soils in refractory clay deposits. BMC Microbiol 2022; 22:237. [PMID: 36195831 PMCID: PMC9531468 DOI: 10.1186/s12866-022-02634-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 09/07/2022] [Indexed: 11/10/2022] Open
Abstract
Processes of soil restoration in anthropogenically disturbed soils is an urgent topic in modern ecology and nature management. Being mediator between mineral soil composition and plant vegetation, soil microbial community is important factor of soil restoration processes. Analysis of main soil nutrition components followed by 16S amplicon sequencing are sufficient methods for primary analysis of novel locations. Here is the primary analysis in a novel location in Northwest Europe (Russia). Main nutrition parameters (pH, P, Na and NH4+) and 16S rDNA Illumina amplicons were explored in abandoned soils from sandy pit quarry (2 sites) and refractory clay mining dumps (4 sites).Microbial communities of mature soils and dumps are variable and different in terms both nutritional and microbial components. pH, N and TOC are strong predictors for microbial composition. Dumps of refractory clays pQ_2 are non-developed soils, highly acidic and form specific microbial community. Differences between dumps and mature soils in both pre-quaternary and quaternary soils are connected with specific bacterial taxa. Those taxa are connected more with plant composition, not the soil properties themselves. The exact changes in microbial community are unique for different soils and areas.
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Affiliation(s)
- Aleksei Zverev
- Saint-Petersburg State University, Saint-Petersburg, Russia. .,All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia.
| | - Anastasiia Kimeklis
- Saint-Petersburg State University, Saint-Petersburg, Russia.,All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Arina Kichko
- Saint-Petersburg State University, Saint-Petersburg, Russia.,All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Grigory Gladkov
- Saint-Petersburg State University, Saint-Petersburg, Russia.,All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Evgeny Andronov
- All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Evgeny Abakumov
- Saint-Petersburg State University, Saint-Petersburg, Russia.,All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
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14
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Andújar C, Arribas P, López H, Arjona Y, Pérez-Delgado A, Oromí P, Vogler AP, Emerson BC. Community assembly and metaphylogeography of soil biodiversity: insights from haplotype-level community DNA metabarcoding within an oceanic island. Mol Ecol 2022; 31:4078-4094. [PMID: 35665980 PMCID: PMC9544582 DOI: 10.1111/mec.16560] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/04/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022]
Abstract
Most of our understanding of island diversity comes from the study of aboveground systems, while the patterns and processes of diversification and community assembly for belowground biotas remain poorly understood. Here, we take advantage of a relatively young and dynamic oceanic island to advance our understanding of ecoevolutionary processes driving community assembly within soil mesofauna. Using whole organism community DNA (wocDNA) metabarcoding and the recently developed metaMATE pipeline, we have generated spatially explicit and reliable haplotype‐level DNA sequence data for soil mesofaunal assemblages sampled across the four main habitats within the island of Tenerife. Community ecological and metaphylogeographic analyses have been performed at multiple levels of genetic similarity, from haplotypes to species and supraspecific groupings. Broadly consistent patterns of local‐scale species richness across different insular habitats have been found, whereas local insular richness is lower than in continental settings. Our results reveal an important role for niche conservatism as a driver of insular community assembly of soil mesofauna, with only limited evidence for habitat shifts promoting diversification. Furthermore, support is found for a fundamental role of habitat in the assembly of soil mesofauna, where habitat specialism is mainly due to colonization and the establishment of preadapted species. Hierarchical patterns of distance decay at the community level and metaphylogeographical analyses support a pattern of geographic structuring over limited spatial scales, from the level of haplotypes through to species and lineages, as expected for taxa with strong dispersal limitations. Our results demonstrate the potential for wocDNA metabarcoding to advance our understanding of biodiversity.
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Affiliation(s)
- Carmelo Andújar
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna Tenerife, Canary Islands, Spain
| | - Paula Arribas
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna Tenerife, Canary Islands, Spain
| | - Heriberto López
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna Tenerife, Canary Islands, Spain
| | - Yurena Arjona
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna Tenerife, Canary Islands, Spain
| | - Antonio Pérez-Delgado
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna Tenerife, Canary Islands, Spain.,School of Doctoral and Postgraduate Studies, University of La Laguna, La Laguna Tenerife, Canary Islands, Spain
| | - Pedro Oromí
- Department of Animal Biology, Edaphology and Geology, University of La Laguna, La Laguna Tenerife, Canary Islands, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, UK.,Department of Life Sciences, Imperial College London Silwood Park Campus, Ascot, UK
| | - Brent C Emerson
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna Tenerife, Canary Islands, Spain
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15
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Filgueiras CC, Kim Y, Wickings KG, El Borai F, Duncan LW, Willett DS. The Smart Soil Organism Detector: An instrument and machine learning pipeline for soil species identification. Biosens Bioelectron 2022; 221:114417. [PMID: 35690558 DOI: 10.1016/j.bios.2022.114417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/10/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
Understanding the diversity of soil organisms is complicated by both scale and substrate. Every footprint we leave in the soil covers hundreds to millions of organisms yet we cannot see them without extremely laborious extraction and microsopy endeavors. Studying them is also challenging. Keeping them alive so that we can understand their lifecycles and ecological roles ranges from difficult to impossible. Functional and taxonomic identification of soil organisms, while possible, is also challenging. Here we present the Smart Soil Organism Detector, an instrument and machine learning pipeline that combines high-resolution imaging, multi-spectral sensing, large-bore flow cytometry, and machine learning to extract, isolate, count, identify, and separate soil organisms in a high-throughput, high-resolution, non-destructive, and reproducible manner. This system is not only capable of separating alive nematodes, dead nematodes, and nematode cuticles from soil with 100% out-of-sample accuracy, but also capable of identifying nematode strains (sub-species) with 95.5% out-of-sample accuracy and 99.4% specificity. Soil micro-arthropods were identified to class with 96.1% out-of-sample accuracy. Broadly applicable across soil taxa, the Smart SOD system is a tool for understanding global soil biodiversity.
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Affiliation(s)
- Camila C Filgueiras
- Department of Biology, University of North Carolina Asheville, One University Heights, Asheville, 28804, NC, USA.
| | - Yongwoon Kim
- Union Biometrica, 84 October Hill Rd, Holliston, 01746, MA, USA
| | - Kyle G Wickings
- Department of Entolomogy, Cornell University, Cornell AgriTech, 15 Castle Creek Drive, Geneva, 14456, NY, USA
| | - Faheim El Borai
- Department of Entolomogy and Nematology, University of Florida, Gulf Coast Research and Education Center, 14625 CR 672, Wimauma, 33598, FL, USA
| | - Larry W Duncan
- Department of Entolomogy and Nematology, University of Florida, Citrus Research and Education Center, 700 Experiment Station Rd, Lake Alfred, 33850, FL, USA
| | - Denis S Willett
- North Carolina Institute for Climate Studies, North Carolina State University, 151 Patton Avenue, Asheville, 28801, NC, USA.
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16
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Perron T, Kouakou A, Simon C, Mareschal L, Frédéric G, Soumahoro M, Kouassi D, Rakotondrazafy N, Rapidel B, Laclau JP, Brauman A. Logging residues promote rapid restoration of soil health after clear-cutting of rubber plantations at two sites with contrasting soils in Africa. Sci Total Environ 2022; 816:151526. [PMID: 34752871 DOI: 10.1016/j.scitotenv.2021.151526] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Soil health is defined as the soil's capacity to deliver ecosystem functions within environmental constraints. On tree plantations, clear-cutting and land preparation between two crop cycles cause severe physical disturbances to the soil and seriously deplete soil organic carbon and biodiversity. Rubber, one of the main tropical perennial crops worldwide, has a plantation life cycle of 25 to 40 years, with successive replanting cycles on the same plot. The aim of this study was to assess the effects of clear-cutting disturbance on three soil functions (carbon transformation, nutrient cycling and structure maintenance) and their restoration after the planting of the new rubber crop, in two contrasting soil situations (Arenosol and Ferralsol) in Côte d'Ivoire. In this 18-month diachronic study, we intensively measured soil functions under different scenarios as regards the management of logging residues and the use or not of a legume cover crop. We investigated the relationship between soil macrofauna diversity and soil heath. At both sites, clear-cutting and land preparation disturbed carbon transformation and nutrient cycling significantly and, to a lesser extent, structure maintenance function. When logging residues were applied, carbon transformation and structure maintenance functions were fully restored within 12 to 18 months after disturbance. By contrast, no restoration of nutrient cycling was observed over the study period. A legume cover crop mainly improved the restoration of carbon transformation. We found a strong relationship (P ≤ 0.001; R2 = 0.62-0.66) between soil macrofauna diversity and soil health. Our overall results were very similar at the two sites, despite their contrasting soil conditions. Keeping logging residues in the plots and sowing a legume in the inter-row at replanting accelerated the restoration of soil functions after major disturbance caused by clear-cutting and land preparation. Our results confirm the necessity of taking soil macrofauna diversity into account in the management of tropical perennial crops.
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Affiliation(s)
- Thibaut Perron
- CIRAD, UMR ABSys, F-34398 Montpellier, France; ABSys, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, Montpellier, France; CIRAD, UMR Eco&Sols, F-34398 Montpellier, France; SAPH, Direction of Industrial Plantations (DPI), Côte d'Ivoire.
| | - Aymard Kouakou
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France; Nangui Abrogoua University, Ecology and Sustainable Development Laboratory, Abidjan, Côte d'Ivoire
| | - Charlotte Simon
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Louis Mareschal
- CIRAD, UMR Eco&Sols, F-34398 Montpellier, France; Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Gay Frédéric
- CIRAD, UMR ABSys, F-34398 Montpellier, France; ABSys, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Daouda Kouassi
- SOGB, Agricultural Technique, Auditing and Organisation Department (DTAO), SOCFIN, Côte d'Ivoire
| | - Nancy Rakotondrazafy
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Bruno Rapidel
- CIRAD, UMR ABSys, F-34398 Montpellier, France; ABSys, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jean-Paul Laclau
- CIRAD, UMR Eco&Sols, F-34398 Montpellier, France; Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Alain Brauman
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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17
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Ferreira CSS, Seifollahi-Aghmiuni S, Destouni G, Ghajarnia N, Kalantari Z. Soil degradation in the European Mediterranean region: Processes, status and consequences. Sci Total Environ 2022; 805:150106. [PMID: 34537691 DOI: 10.1016/j.scitotenv.2021.150106] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Soil, a non-renewable resource, sustains life on Earth by supporting around 95% of global food production and providing ecosystem services such as biomass production, filtration of contaminants and transfer of mass and energy between spheres. Unsustainable management practices and climate change are threatening the natural capital of soils, particularly in the Mediterranean region, where increasing population, rapid land-use changes, associated socio-economic activities and climate change are imposing high pressures on the region's shallow soils. Despite evidence of high soil susceptibility to degradation and desertification, the true extent of soil degradation in the region is unknown. This paper reviews and summarises the scientific literature and relevant official reports, with the aim to advance this knowledge by synthesizing, mapping, and identifying gaps regarding the status, causes, and consequences of soil degradation processes in the European Mediterranean region. This is needed as scientific underpinning of efforts to counteract soil degradation in the region. Three main degradation categories are then considered: physical (soil sealing, compaction, erosion), chemical (soil organic matter, contamination, salinisation), and biological. We find some degradation processes to be relatively well-documented (e.g. soil erosion), while others, such as loss of biodiversity, remain poorly addressed, with limited data availability. We suggest establishment of a continuous, harmonised soil monitoring system at national and regional scale in the Mediterranean region to provide comparable datasets and chart the spatial extent and temporal changes in soil degradation, and corresponding economic implications. This is critical to support decision-making and fulfilment of related sustainable development goals.
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Affiliation(s)
- Carla S S Ferreira
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, SE-106 91 Stockholm, Sweden; Navarino Environmental Observatory, Costa Navarino, Navarino Dunes Messinia 24001, Greece.
| | - Samaneh Seifollahi-Aghmiuni
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, SE-106 91 Stockholm, Sweden; Navarino Environmental Observatory, Costa Navarino, Navarino Dunes Messinia 24001, Greece
| | - Georgia Destouni
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, SE-106 91 Stockholm, Sweden; Navarino Environmental Observatory, Costa Navarino, Navarino Dunes Messinia 24001, Greece
| | - Navid Ghajarnia
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Zahra Kalantari
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, SE-106 91 Stockholm, Sweden; Navarino Environmental Observatory, Costa Navarino, Navarino Dunes Messinia 24001, Greece; Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
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18
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Arruda B, George PBL, Robin A, de L C Mescolotti D, Herrera WFB, Jones DL, Andreote FD. Manipulation of the soil microbiome regulates the colonization of plants by arbuscular mycorrhizal fungi. Mycorrhiza 2021; 31:545-558. [PMID: 34363527 DOI: 10.1007/s00572-021-01044-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are important symbionts of many plant species, facilitating the acquisition of soil nutrients by roots. We hypothesized that AMF root colonization is strongly influenced by the composition of the soil microbiome. Here, we evaluated mycorrhizal colonization of two plants, the grass Urochloa brizantha (Brachiaria) and the legume Crotalaria juncea (Crotalaria). These were cultivated in the same soil but hosting eight distinct microbiomes: natural soil (i); soil exposed to heat treatments for 1 h at 50 ºC (ii), 80 ºC (iii), or 100 ºC (iv); sterilized soil by autoclaving (AS) followed by re-inoculation of dilutions of the natural soil community at 10-1 (v), 10-3 (vi), and 10-6 (vii); and AS without re-inoculation (viii). Microbial diversity (bacteria and fungi) was assessed through 16S rDNA and ITS1 metabarcoding, respectively, and the soil acid phosphatase activity (APASE) was measured. Sequencing results showed the formation of distinct microbial communities according to the soil manipulations, which also correlated with the decline of APASE. Subsequently, seedlings of Brachiaria and Crotalaria were grown in those soils inoculated separately with three AMF (Acaulospora colombiana, Rhizophagus clarus, and Dentiscutata heterogama) which were compared to an AMF-free control treatment. Brachiaria showed higher colonization in natural soil when compared to the microbial community manipulations, regardless of the AMF species inoculated. In contrast, two mycorrhiza species were able to colonize Crotalaria under modified microbial communities at similar rates to natural soil. Furthermore, Brachiaria showed a possible inverse relationship between APASE and mycorrhization, but this trend was absent for Crotalaria. We conclude that mycorrhizal root colonization and soil acid phosphatase activity were associated with the structure of the soil microbiome, depending on the plant species evaluated.
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Affiliation(s)
- Bruna Arruda
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, Gwynedd, UK
| | - Paul B L George
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, Gwynedd, UK
- Département de Médecine Moléculaire, Université Laval, Québec, Canada
| | - Agnès Robin
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
- UMR Eco&Sols, CIRAD, Piracicaba, Brazil
- Eco&Sols, CIRAD, INRAE, IRD, Université Montpellier, Montpellier, France
| | - Denise de L C Mescolotti
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Davey L Jones
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, Gwynedd, UK
- SoilsWest, School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
| | - Fernando D Andreote
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil.
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19
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Doliwa A, Dunthorn M, Rassoshanska E, Mahé F, Bass D, Duarte Ritter C. Identifying Potential Hosts of Short-Branch Microsporidia. Microb Ecol 2021; 82:549-553. [PMID: 33420911 PMCID: PMC8384821 DOI: 10.1007/s00248-020-01657-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/03/2020] [Indexed: 05/17/2023]
Abstract
Microsporidia are obligate parasites that are closely related to Fungi. While the widely known "long-branch" Microsporidia infect mostly metazoans, the hosts of "short-branch" Microsporidia are only partially characterized or not known at all. Here, we used network analyses from Neotropical rainforest soil metabarcoding data, to infer co-occurrences between environmental lineages of short-branch microsporidians and their potential hosts. We found significant co-occurrences with several taxa, especially with Apicomplexa, Cercozoa, and Fungi, as well as some Metazoa. Our results are the first step to identify potential hosts of the environmental lineages of short-branch microsporidians, which can be targeted in future molecular and microscopic studies.
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Affiliation(s)
- Annemie Doliwa
- Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5, S05 R04 H83, 45141, Essen, Germany
| | - Micah Dunthorn
- Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5, S05 R04 H83, 45141, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, 45141, Essen, Germany
| | - Erika Rassoshanska
- Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5, S05 R04 H83, 45141, Essen, Germany
| | - Frédéric Mahé
- CIRAD, UMR BGPI, F-34398, Montpellier, France
- BGPI, Université de Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
| | - David Bass
- Centre for Environment, Aquaculture and Fisheries Science (Cefas), Barrack Road, Weymouth, Dorset, DT4 8UB, UK
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- Sustainable Aquaculture Futures, University of Exeter, Exeter, EX4 4QD, UK
| | - Camila Duarte Ritter
- Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5, S05 R04 H83, 45141, Essen, Germany.
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20
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Conde-Cid M, Arias-Estévez M, Núñez-Delgado A. How to study SARS-CoV-2 in soils? Environ Res 2021; 198:110464. [PMID: 33188764 PMCID: PMC7658612 DOI: 10.1016/j.envres.2020.110464] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/18/2020] [Accepted: 11/09/2020] [Indexed: 05/08/2023]
Abstract
Wastewater based epidemiology is increasingly being considered as a potentially useful tool for early warning about eventual new COVID-19 outbreaks. In addition, some authors are investigating on the detection and quantification of SARS-CoV-2 in sewage sludge. However, no paper has been published up to date indicating how this virus could be quantified in soil samples. In view of that, we review available data searching for methodological approaches that could guide on the quantification of SARS-CoV-2 (and even other pathogenic microorganisms) in soils.
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Affiliation(s)
- Manuel Conde-Cid
- Soil Science and Agricultural Chemistry, Faculty of Sciences, University of Vigo, 32004, Ourense, Spain
| | - Manuel Arias-Estévez
- Soil Science and Agricultural Chemistry, Faculty of Sciences, University of Vigo, 32004, Ourense, Spain
| | - Avelino Núñez-Delgado
- Dept. Soil Science and Agricultural Chemistry, Engineering Polytechnic School, University of Santiago de Compostela, Campus Univ, Lugo, Spain.
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21
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Ferreira DA, da Silva TF, Pylro VS, Salles JF, Andreote FD, Dini-Andreote F. Soil Microbial Diversity Affects the Plant-Root Colonization by Arbuscular Mycorrhizal Fungi. Microb Ecol 2021; 82:100-103. [PMID: 32200418 DOI: 10.1007/s00248-020-01502-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
Terrestrial plants establish symbiosis with arbuscular mycorrhizal fungi (AMF) to exchange water and nutrients. However, the extent to which soil biodiversity influences such association remains still unclear. Here, we manipulated the soil microbial diversity using a "dilution-to-extinction" approach in a controlled pot microcosm system and quantified the root length colonization of maize plants by the AMF Rhizophagus clarus. The experiment was performed by manipulating the soil microbiome within a native and foreign soil having distinct physicochemical properties. Overall, our data revealed significant positive correlations between the soil microbial diversity and AMF colonization. Most importantly, this finding opposes the diversity-invasibility hypothesis and highlights for a potential overall helper effect of the soil biodiversity on plant-AMF symbiosis.
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Affiliation(s)
- Dorotéia Alves Ferreira
- Department of Soil Science, 'Luiz de Queiroz' College of Agriculture, University of Sao Paulo, São Paulo, Brazil
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Thais Freitas da Silva
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Department of Microbiology, 'Paulo Goes' Microbiology Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Victor Satler Pylro
- Department of Biology, Federal University of Lavras, Lavras, Minas Gerais, Brazil
| | - Joana Falcão Salles
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Fernando Dini Andreote
- Department of Soil Science, 'Luiz de Queiroz' College of Agriculture, University of Sao Paulo, São Paulo, Brazil
| | - Francisco Dini-Andreote
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
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22
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Durán J, Rodríguez A, Heiðmarsson S, Lehmann JRK, Del Moral Á, Garrido-Benavent I, De Los Ríos A. Cryptogamic cover determines soil attributes and functioning in polar terrestrial ecosystems. Sci Total Environ 2021; 762:143169. [PMID: 33131854 DOI: 10.1016/j.scitotenv.2020.143169] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
We still lack studies that provide evidence for direct links between the development of soil surface cryptogamic communities and soil attributes and functioning. This is particularly true in areas free of potentially confounding factors such as different soil types, land uses, or anthropogenic disturbances. Despite the ecological importance of polar ecosystems and their sensitivity to climate change, we are far from understanding how their soils function and will respond to climate change-driven alterations in above- and belowground features. We used two complementary approaches (i.e. cover gradients in the forefront of retreating glaciers as well as long-time deglaciated areas with well-developed cryptogamic cover types) to evaluate the role of cryptogams driving multiple soil biotic and abiotic attributes and functioning rates in polar terrestrial ecosystems. Increases in cryptogamic cover were consistently related to increases in organic matter accumulation, soil fertility, and bacterial diversity, but also in enhanced soil functioning rates in both sampling areas. However, we also show that the ability to influence soil attributes varies among different polar cryptogamic covers, indicating that their differential ability to thrive under climate-change scenarios will largely determine the fate of polar soils in coming decades.
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Affiliation(s)
- Jorge Durán
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal.
| | - Alexandra Rodríguez
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Starri Heiðmarsson
- Icelandic Institute of Natural History, Akureyri Division, Borgir Nordurslod, 600 Akureyri, Iceland
| | - Jan R K Lehmann
- Institute of Landscape Ecology, University of Muenster, 48149 Muenster, Germany
| | - Álvaro Del Moral
- AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, STEM Faculty, The Open University, MK7 6AA Milton Keynes, United Kingdom; Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN), CSIC, E-28006 Madrid, Spain
| | - Isaac Garrido-Benavent
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN), CSIC, E-28006 Madrid, Spain
| | - Asunción De Los Ríos
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN), CSIC, E-28006 Madrid, Spain
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23
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Fournier B, Pereira Dos Santos S, Gustavsen JA, Imfeld G, Lamy F, Mitchell EAD, Mota M, Noll D, Planchamp C, Heger TJ. Impact of a synthetic fungicide (fosetyl-Al and propamocarb-hydrochloride) and a biopesticide (Clonostachys rosea) on soil bacterial, fungal, and protist communities. Sci Total Environ 2020; 738:139635. [PMID: 32534282 DOI: 10.1016/j.scitotenv.2020.139635] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 05/27/2023]
Abstract
The use of synthetic pesticides in agriculture is increasingly debated. However, few studies have compared the impact of synthetic pesticides and alternative biopesticides on non-target soil microorganisms playing a central role in soil functioning. We conducted a mesocosm experiment and used high-throughput amplicon sequencing to test the impact of a fungal biopesticide and a synthetic fungicide on the diversity, the taxonomic and functional compositions, and co-occurrence patterns of soil bacterial, fungal and protist communities. Neither the synthetic pesticide nor the biopesticide had a significant effect on microbial α-diversity. However, both types of pesticides decreased the complexity of the soil microbial network. The two pesticides had contrasting impacts on the composition of microbial communities and the identity of key taxa as revealed by microbial network analyses. The biopesticide impacted keystone taxa that structured the soil microbial network. The synthetic pesticide modified biotic interactions favouring taxa that are less efficient at degrading organic compounds. This suggests that the biopesticides and the synthetic pesticide have different impact on soil functioning. Altogether, our study shows that pest management products may have functionally significant impacts on the soil microbiome even if microbial α-diversity is unaffected. It also illustrates the potential of high-throughput sequencing analyses to improve the ecotoxicological risk assessment of pesticides on non-target soil microorganisms.
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Affiliation(s)
- Bertrand Fournier
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland; Institute of Environmental Science and Geography, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
| | - Sofia Pereira Dos Santos
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland.
| | | | - Gwenaël Imfeld
- Université de Strasbourg, Laboratory of Hydrology and Geochemistry of Strasbourg (LHyGeS), UMR 7517 CNRS/EOST, 1 Rue Blessig, 67084 Strasbourg Cedex, France.
| | - Frédéric Lamy
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland.
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile Argand 11, 2000 Neuchâtel, Switzerland; Jardin Botanique de Neuchâtel, Chemin du Pertuis-du-Sault 58, 2000 Neuchâtel, Switzerland.
| | - Matteo Mota
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland.
| | - Dorothea Noll
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland.
| | - Chantal Planchamp
- Soil and Biotechnology Division, Federal Office for the Environment (FOEN), 3003 Bern, Switzerland.
| | - Thierry J Heger
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland.
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24
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Lucas-Borja ME, Miralles I, Ortega R, Plaza-Álvarez PA, Gonzalez-Romero J, Sagra J, Soriano-Rodríguez M, Certini G, Moya D, Heras J. Immediate fire-induced changes in soil microbial community composition in an outdoor experimental controlled system. Sci Total Environ 2019; 696:134033. [PMID: 31470330 DOI: 10.1016/j.scitotenv.2019.134033] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/20/2019] [Accepted: 08/20/2019] [Indexed: 05/20/2023]
Abstract
Short-term fire-induced changes to the soil microbial community are usually closely associated to fire severity, which essentially consists in the fire-induced loss or decomposition of organic matter above ground and below ground. Many functional processes and soil properties, including plant recolonization and soil microorganism activity, depend on fire severity. Seven days after burning, we evaluated the impact of two fire severities (low and high) on basic soil properties and the microbial communities in an outdoor experimental controlled system composed of six forest soil monoliths. The magnitude of change in microbial community was far greater than the change in physical and chemical soil properties. Total N was the only selected soil property that significantly varied depending on fire severity. The severely burned soils experienced significant changes in overall microbial biomass composition and phylogenetic composition of bacterial communities in comparison with control plots. Immediately after the fire, in fact, phyla and genera such as Acidobacteria-Gp4 or Bacteroidetes-Ohtaekwangia were much more abundant in the control monoliths. On the other hand, Firmicutes or Proteobacteria (e.g. Firmicutes Paenibacillus, Proteobacteria Phenylobacterium) were relatively more abundant in the monoliths burned with high severity in comparison with the low severity burned ones. Overall, the effect of fire on soil microbial communities was greater in the high severity burned monoliths than in the low severity burned ones. We concluded that in Mediterranean forest ecosystems, fire significantly alters soil bacterial composition depending on its severity.
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Affiliation(s)
- M E Lucas-Borja
- Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha. Campus Universitario. 02071 Albacete, Spain.
| | - I Miralles
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAMBITAL), University of Almeria, E-04120, Almería, Spain
| | - R Ortega
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAMBITAL), University of Almeria, E-04120, Almería, Spain
| | - P A Plaza-Álvarez
- Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha. Campus Universitario. 02071 Albacete, Spain
| | - J Gonzalez-Romero
- Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha. Campus Universitario. 02071 Albacete, Spain
| | - J Sagra
- Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha. Campus Universitario. 02071 Albacete, Spain
| | - M Soriano-Rodríguez
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAMBITAL), University of Almeria, E-04120, Almería, Spain; Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research (GENYO), E-18016, Granada, Spain
| | - G Certini
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, P. le delle Cascine 28, 50144 Firenze, Italy
| | - D Moya
- Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha. Campus Universitario. 02071 Albacete, Spain
| | - J Heras
- Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha. Campus Universitario. 02071 Albacete, Spain
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25
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Sánchez-López KB, De Los Santos-Ramos FJ, Gómez-Acata ES, Luna-Guido M, Navarro-Noya YE, Fernández-Luqueño F, Dendooven L. TiO 2 nanoparticles affect the bacterial community structure and Eisenia fetida (Savigny, 1826) in an arable soil. PeerJ 2019; 7:e6939. [PMID: 31380145 PMCID: PMC6661143 DOI: 10.7717/peerj.6939] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/11/2019] [Indexed: 01/08/2023] Open
Abstract
The amount of nanoparticles (NP), such as TiO2, has increased substantially in the environment. It is still largely unknown, however, how NP might interact with earthworms and organic material and how this might affect the bacterial community structure and their functionality. Therefore, an arable soil was amended with TiO2 NP at 0, 150 or 300 mg kg−1 and subjected to different treatments. Treatments were soil amended with ten earthworms (Eisenia fetida (Savigny, 1826)) with fully developed clitellum and an average fresh mass of 0.5 to 500 g dry soil, 1.75 g tyndallized Quaker® oat seeds Avena sativa (L.) kg−1, or earthworms plus oat seeds, or left unamended. The bacterial community structure was monitored throughout the incubation period. The bacterial community in the unamended soil changed over time and application of oats, earthworm and a combination of both even further, with the largest change found in the latter. Application of NP to the unamended soil and the earthworm-amended soil altered the bacterial community, but combining it by adding oats negated that effect. It was found that the application of organic material, that is, oats, reduced the effect of the NP applied to soil. However, as the organic material applied was mineralized by the soil microorganisms, the effect of NP increased again over time.
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Affiliation(s)
- Katia Berenice Sánchez-López
- Nanoscience and Nanotechnology Program, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Francisco J De Los Santos-Ramos
- Department of Physiology, Biophysics and Neuroscience, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Elizabeth Selene Gómez-Acata
- Department of Biotechnology, Centro de investigación y de estudios avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Marco Luna-Guido
- Department of Biotechnology, Centro de investigación y de estudios avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Yendi E Navarro-Noya
- CONACYT Cathedra, Tlaxcala Center of the Behavior Biology, Autonomous University of Tlaxcala, Tlaxcala, Mexico
| | - Fabián Fernández-Luqueño
- Nanoscience and Nanotechnology Program, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Luc Dendooven
- Department of Biotechnology, Centro de investigación y de estudios avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
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Barbato D, Perini C, Mocali S, Bacaro G, Tordoni E, Maccherini S, Marchi M, Cantiani P, De Meo I, Bianchetto E, Landi S, Bruschini S, Bettini G, Gardin L, Salerni E. Teamwork makes the dream work: Disentangling cross-taxon congruence across soil biota in black pine plantations. Sci Total Environ 2019; 656:659-669. [PMID: 30529969 DOI: 10.1016/j.scitotenv.2018.11.320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
Soil plays a fundamental role in many ecological processes, throughout a complex network of above- and below-ground interactions. This has aroused increasing interest in the use of correlates for biodiversity assessment and has demonstrated their reliability with respect to proxies based on environmental data alone. Although co-variation of species richness and composition in forests has been discussed in the literature, only a few studies have explored these elements in forest plantations, which are generally thought to be poor in biodiversity, being aimed at timber production. Based on this premise our aims were 1) to test if cross-taxon congruence across different groups of organisms (bacteria, vascular plants, mushrooms, ectomycorrhizae, mycelium, carabids, microarthropods, nematodes) is consistent in artificial stands; 2) to evaluate the strength of relationships due to the existing environmental gradients as expressed by abiotic and biotic factors (soil, spatial-topographic, dendrometric variables). Correlations between groups were studied with Mantel and partial Mantel tests, while variance partition analysis was applied to assess the relative effect of environmental variables on the robustness of observed relationships. Significant cross-taxon congruence was observed across almost all taxonomic groups pairs. However, only bacteria/mycelium and mushrooms/mycelium correlations remained significant after removing the environmental effect, suggesting that a strong abiotic influence drives species composition. Considering variation partitioning, the results highlighted the importance of bacteria as a potential indicator: bacteria were the taxonomic group with the highest compositional variance explained by the predictors used; furthermore, they proved to be involved in the only cases where the variance attributed solely to the pure effect of biotic or abiotic predictors was significant. Remarkably, the co-dependent effect of all predictors always explained the highest portion of total variation in all dependent taxa, testifying the intricate and dynamic interplay of environmental factors and biotic interactions in explaining cross-taxon congruence in forest plantations.
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Affiliation(s)
- Debora Barbato
- Department of Life Sciences, University of Siena, Via Mattioli 4, 53100 Siena, Italy.
| | - Claudia Perini
- Department of Life Sciences, University of Siena, Via Mattioli 4, 53100 Siena, Italy.
| | - Stefano Mocali
- CREA - Research Centre for Agriculture and Environment, Via di Lanciola 12/A, 50125 Cascine del Riccio Firenze, Italy.
| | - Giovanni Bacaro
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 10, 34127 Trieste, Italy.
| | - Enrico Tordoni
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 10, 34127 Trieste, Italy.
| | - Simona Maccherini
- Department of Life Sciences, University of Siena, Via Mattioli 4, 53100 Siena, Italy.
| | - Maurizio Marchi
- CREA - Research Centre for Forestry and Wood, Viale S. Margherita 80, 52100 Arezzo, Italy.
| | - Paolo Cantiani
- CREA - Research Centre for Forestry and Wood, Viale S. Margherita 80, 52100 Arezzo, Italy.
| | - Isabella De Meo
- CREA - Research Centre for Agriculture and Environment, Via di Lanciola 12/A, 50125 Cascine del Riccio Firenze, Italy.
| | - Elisa Bianchetto
- CREA - Research Centre for Agriculture and Environment, Via di Lanciola 12/A, 50125 Cascine del Riccio Firenze, Italy.
| | - Silvia Landi
- CREA - Research Centre for Plant Protection and Certification, Via di Lanciola 12/A, 50125 Cascine del Riccio Firenze, Italy.
| | - Silvia Bruschini
- Compagnia delle Foreste Srl, Via Pietro Aretino 8, 52100 Arezzo, Italy.
| | | | - Lorenzo Gardin
- SOILDATA Srl Suolo territorio ambiente, Via Guerrazzi 2R, 50132 Firenze, Italy.
| | - Elena Salerni
- Department of Life Sciences, University of Siena, Via Mattioli 4, 53100 Siena, Italy.
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27
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Bacher MG, Fenton O, Bondi G, Creamer RE, Karmarkar M, Schmidt O. The impact of cattle dung pats on earthworm distribution in grazed pastures. BMC Ecol 2018; 18:59. [PMID: 30567522 PMCID: PMC6299995 DOI: 10.1186/s12898-018-0216-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/12/2018] [Indexed: 11/10/2022] Open
Abstract
Background Grazed grassland management regimes can have various effects on soil fauna. For example, effects on earthworms can be negative through compaction induced by grazing animals, or positive mediated by increases in sward productivity and cattle dung pats providing a food source. Knowledge gaps exist in relation to the behaviour of different earthworm species i.e. their movement towards and aggregation under dung pats, the legacy effects of pats and the spatial area of recruitment. The present study addressed these knowledge gaps in field experiments, over 2 years, using natural and simulated dung pats on two permanent, intensively grazed pastures in Ireland. Results Dung pats strongly affected spatial earthworm distribution, with up to four times more earthworms aggregating beneath pats, than in the control locations away from pats. In these earthworm communities comprising 11 species, temporally different aggregation and dispersal patterns were observed, including absence of individual species from control locations, but no clear successional responses. Epigeic species in general, but also certain species of the anecic and endogeic groups were aggregating under dung. Sampling after complete dung pat disappearance (27 weeks after application) suggested an absence of a dung pat legacy effect on earthworm communities. Based on species distributions, the maximum size of the recruitment area from which earthworms moved to pats was estimated to be 3.8 m2 per dung pat. Since actual grazing over 6 weeks would result in the deposition of about 300 dung pats per ha, it is estimated that a surface area of 1140 m2 or about 11% of the total grazing area can be influenced by dung pats in a given grazing period. Conclusions This study showed that the presence of dung pats in pastures creates temporary hot spots in spatial earthworm species distribution, which changes over time. The findings highlight the importance of considering dung pats, temporally and spatially, when sampling earthworms in grazed pastures. Published comparisons of grazed and cut grasslands probably reached incorrect conclusions by ignoring or deliberately avoiding dung pats. Furthermore, the observed intense aggregation of earthworms beneath dung pats suggests that earthworm functions need to be assessed separately at these hot spots. Electronic supplementary material The online version of this article (10.1186/s12898-018-0216-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M G Bacher
- Teagasc, Environment Research Centre, Wexford, Ireland. .,UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.
| | - O Fenton
- Teagasc, Environment Research Centre, Wexford, Ireland
| | - G Bondi
- Teagasc, Environment Research Centre, Wexford, Ireland
| | - R E Creamer
- Soil Biology Group, Wageningen University, Wageningen, The Netherlands
| | - M Karmarkar
- Teagasc, Environment Research Centre, Wexford, Ireland
| | - O Schmidt
- UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.,UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
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28
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Türke M, Lange M, Eisenhauer N. Gut shuttle service: endozoochory of dispersal-limited soil fauna by gastropods. Oecologia 2018; 186:655-64. [PMID: 29350285 DOI: 10.1007/s00442-018-4058-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/30/2017] [Indexed: 12/31/2022]
Abstract
Numerous important ecosystem functions and services depend on soil biodiversity. However, little is known about the mechanisms which maintain the vast belowground biodiversity and about the filters shaping soil community composition. Yet, biotic interactions like facilitation and dispersal by animals are assumed to play a crucial role, particularly as most soil animal taxa are strongly limited in their active dispersal abilities. Here, we report on a newfound interaction of potentially high ubiquity and importance in soil communities: the endozoochorous dispersal of soil fauna by gastropods. We focus on the dispersal-limited group of oribatid mites, one of the most diverse and abundant soil animal groups. In a field survey in a German riparian forest, 73% of 40 collected slugs (Arion vulgaris) egested a total of 135 oribatid mites, belonging to 35 species. Notably, 70% of the egested mites were alive and survived the gut passage through slugs. Similar results were found for Roman snails (Helix pomatia), indicating the generality of our findings across different gastropod taxa. Complementary laboratory experiments confirmed our field observations, revealing that oribatid mites are, indeed, ingested and egested alive by slugs, and that they are able to independently escape the faeces and colonise new habitats. Our results strongly indicate that gastropods may help soil organisms to disperse within habitats, to overcome dispersal barriers, and to reach short-lived resource patches. Gastropods might even disperse whole multi-trophic micro-ecosystems, a discovery that could have profound implications for our understanding of dispersal mechanisms and the distribution of soil biodiversity.
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29
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Franco ALC, Bartz MLC, Cherubin MR, Baretta D, Cerri CEP, Feigl BJ, Wall DH, Davies CA, Cerri CC. Loss of soil (macro)fauna due to the expansion of Brazilian sugarcane acreage. Sci Total Environ 2016; 563-564:160-168. [PMID: 27135579 DOI: 10.1016/j.scitotenv.2016.04.116] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/05/2016] [Accepted: 04/17/2016] [Indexed: 06/05/2023]
Abstract
Land use changes (LUC) from pasture to sugarcane (Saccharum spp.) crop are expected to add 6.4Mha of new sugarcane land by 2021 in the Brazilian Cerrado and Atlantic Forest biomes. We assessed the effects of these LUC on the abundance and community structure of animals that inhabit soils belowground through a field survey using chronosequences of land uses comprising native vegetation, pasture, and sugarcane along a 1000-km-long transect across these two major tropical biomes in Brazil. Macrofauna community composition differed among land uses. While most groups were associated with samples taken in native vegetation, high abundance of termites and earthworms appeared associated with pasture soils. Linear mixed effects analysis showed that LUC affected total abundance (X(2)(1)=6.79, p=0.03) and taxa richness (X(2)(1)=6.08, p=0.04) of soil macrofauna. Abundance increased from 411±70individualsm(-2) in native vegetation to 1111±202individualsm(-2) in pasture, but decreased sharply to 106±24individualsm(-2) in sugarcane soils. Diversity decreased 24% from native vegetation to pasture, and 39% from pasture to sugarcane. Thus, a reduction of ~90% in soil macrofauna abundance, besides a loss of ~40% in the diversity of macrofauna groups, can be expected when sugarcane crops replace pasture in Brazilian tropical soils. In general, higher abundances of major macrofauna groups (ants, coleopterans, earthworms, and termites) were associated with higher acidity and low contents of macronutrients and organic matter in soil. This study draws attention for a significant biodiversity loss belowground due to tropical LUC in sugarcane expansion areas. Given that many groups of soil macrofauna are recognized as key mediators of ecosystem processes such as soil aggregation, nutrients cycling and soil carbon storage, our results warrant further efforts to understand the impacts of altering belowground biodiversity and composition on soil functioning and agriculture performance across LUC in the tropics.
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Affiliation(s)
- André L C Franco
- Center for Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário 303, 13416-000, Piracicaba, SP, Brazil; School of Global Environmental Sustainability & Department of Biology, Colorado State University, 80523, Fort Collins, CO, USA.
| | - Marie L C Bartz
- Universidade Positivo, Rua Prof. Pedro de Souza 5300, 81280-330, Curitiba, PR, Brazil
| | - Maurício R Cherubin
- Center for Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário 303, 13416-000, Piracicaba, SP, Brazil
| | - Dilmar Baretta
- Santa Catarina State University, Rua Beloni Zanin 680E, 89815-630, Chapecó, SC, Brazil
| | - Carlos E P Cerri
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Av. Pádua Dias 11, 13418-900, Piracicaba, SP, Brazil
| | - Brigitte J Feigl
- Center for Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário 303, 13416-000, Piracicaba, SP, Brazil
| | - Diana H Wall
- School of Global Environmental Sustainability & Department of Biology, Colorado State University, 80523, Fort Collins, CO, USA
| | - Christian A Davies
- Shell Technology Centre Houston, 3333 Highway 6 South, Houston, TX 77082, USA
| | - Carlos C Cerri
- Center for Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário 303, 13416-000, Piracicaba, SP, Brazil
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Montiel-Rozas MDM, López-García Á, Kjøller R, Madejón E, Rosendahl S. Organic amendments increase phylogenetic diversity of arbuscular mycorrhizal fungi in acid soil contaminated by trace elements. Mycorrhiza 2016; 26:575-585. [PMID: 27072359 DOI: 10.1007/s00572-016-0694-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
In 1998, a toxic mine spill polluted a 55-km(2) area in a basin southward to Doñana National Park (Spain). Subsequent attempts to restore those trace element-contaminated soils have involved physical, chemical, or biological methodologies. In this study, the restoration approach included application of different types and doses of organic amendments: biosolid compost (BC) and leonardite (LEO). Twelve years after the last addition, molecular analyses of arbuscular mycorrhizal (AM) fungal communities associated with target plants (Lamarckia aurea and Chrysanthemum coronarium) as well as analyses of trace element concentrations both in soil and in plants were performed. The results showed an improved soil quality reflected by an increase in soil pH and a decrease in trace element availability as a result of the amendments and dosages. Additionally, the phylogenetic diversity of the AM fungal community increased, reaching the maximum diversity at the highest dose of BC. Trace element concentration was considered the predominant soil factor determining the AM fungal community composition. Thereby, the studied AM fungal community reflects a community adapted to different levels of contamination as a result of the amendments. The study highlights the long-term effect of the amendments in stabilizing the soil system.
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Affiliation(s)
- María Del Mar Montiel-Rozas
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC) Avda. Reina Mercedes, 10 41012, Sevilla, Spain.
| | - Álvaro López-García
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark
| | - Engracia Madejón
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC) Avda. Reina Mercedes, 10 41012, Sevilla, Spain
| | - Søren Rosendahl
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark
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31
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Gutiérrez C, Fernández C, Escuer M, Campos-Herrera R, Beltrán Rodríguez ME, Carbonell G, Rodríguez Martín JA. Effect of soil properties, heavy metals and emerging contaminants in the soil nematodes diversity. Environ Pollut 2016; 213:184-194. [PMID: 26895540 DOI: 10.1016/j.envpol.2016.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 02/02/2016] [Accepted: 02/04/2016] [Indexed: 05/12/2023]
Abstract
Among soil organisms, nematodes are seen as the most promising candidates for bioindications of soil health. We hypothesized that the soil nematode community structure would differ in three land use areas (agricultural, forest and industrial soils), be modulated by soil parameters (N, P, K, pH, SOM, CaCO3, granulometric fraction, etc.), and strongly affected by high levels of heavy metals (Cd, Pb, Zn, Cr, Ni, Cu, and Hg) and emerging contaminants (pharmaceuticals and personal care products, PPCPs). Although these pollutants did not significantly affect the total number of free-living nematodes, diversity and structure community indices vastly altered. Our data showed that whereas nematodes with r-strategy were tolerant, genera with k-strategy were negatively affected by the selected pollutants. These effects diminished in soils with high levels of heavy metals given their adaptation to the historical pollution in this area, but not to emerging pollutants like PPCPs.
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Affiliation(s)
- Carmen Gutiérrez
- Instituto de Ciencias Agrarias, ICA-CSIC, Serrano, 115bis, 28006 Madrid, Spain
| | - Carlos Fernández
- Depto. Medio Ambiente, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (I.N.I.A), Carretera de A Coruña 7.5 km, 28040, Madrid, Spain
| | - Miguel Escuer
- Instituto de Ciencias Agrarias, ICA-CSIC, Serrano, 115bis, 28006 Madrid, Spain
| | - Raquel Campos-Herrera
- Instituto de Ciencias Agrarias, ICA-CSIC, Serrano, 115bis, 28006 Madrid, Spain; Centro para os Recursos Biológicos e Alimentos Mediterrânicos (MeditBio), Campus Gambelas, Edf. 8, Universidade do Algarve, 8005-139, Faro, Portugal
| | - Mª Eulalia Beltrán Rodríguez
- Depto. Medio Ambiente, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (I.N.I.A), Carretera de A Coruña 7.5 km, 28040, Madrid, Spain
| | - Gregoria Carbonell
- Depto. Medio Ambiente, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (I.N.I.A), Carretera de A Coruña 7.5 km, 28040, Madrid, Spain
| | - Jose Antonio Rodríguez Martín
- Depto. Medio Ambiente, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (I.N.I.A), Carretera de A Coruña 7.5 km, 28040, Madrid, Spain.
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Orgiazzi A, Panagos P, Yigini Y, Dunbar MB, Gardi C, Montanarella L, Ballabio C. A knowledge-based approach to estimating the magnitude and spatial patterns of potential threats to soil biodiversity. Sci Total Environ 2016; 545-546:11-20. [PMID: 26745288 DOI: 10.1016/j.scitotenv.2015.12.092] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 12/16/2015] [Accepted: 12/20/2015] [Indexed: 05/28/2023]
Abstract
Because of the increasing pressures exerted on soil, below-ground life is under threat. Knowledge-based rankings of potential threats to different components of soil biodiversity were developed in order to assess the spatial distribution of threats on a European scale. A list of 13 potential threats to soil biodiversity was proposed to experts with different backgrounds in order to assess the potential for three major components of soil biodiversity: soil microorganisms, fauna, and biological functions. This approach allowed us to obtain knowledge-based rankings of threats. These classifications formed the basis for the development of indices through an additive aggregation model that, along with ad-hoc proxies for each pressure, allowed us to preliminarily assess the spatial patterns of potential threats. Intensive exploitation was identified as the highest pressure. In contrast, the use of genetically modified organisms in agriculture was considered as the threat with least potential. The potential impact of climate change showed the highest uncertainty. Fourteen out of the 27 considered countries have more than 40% of their soils with moderate-high to high potential risk for all three components of soil biodiversity. Arable soils are the most exposed to pressures. Soils within the boreal biogeographic region showed the lowest risk potential. The majority of soils at risk are outside the boundaries of protected areas. First maps of risks to three components of soil biodiversity based on the current scientific knowledge were developed. Despite the intrinsic limits of knowledge-based assessments, a remarkable potential risk to soil biodiversity was observed. Guidelines to preliminarily identify and circumscribe soils potentially at risk are provided. This approach may be used in future research to assess threat at both local and global scale and identify areas of possible risk and, subsequently, design appropriate strategies for monitoring and protection of soil biota.
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Affiliation(s)
- Alberto Orgiazzi
- European Commission, Joint Research Centre (JRC), Institute for Environment and Sustainability (IES), Land Resource Management Unit, Via E. Fermi, 2749-21027 Ispra, VA, Italy.
| | - Panos Panagos
- European Commission, Joint Research Centre (JRC), Institute for Environment and Sustainability (IES), Land Resource Management Unit, Via E. Fermi, 2749-21027 Ispra, VA, Italy
| | - Yusuf Yigini
- European Commission, Joint Research Centre (JRC), Institute for Environment and Sustainability (IES), Land Resource Management Unit, Via E. Fermi, 2749-21027 Ispra, VA, Italy
| | - Martha B Dunbar
- European Commission, Joint Research Centre (JRC), Institute for Environment and Sustainability (IES), Land Resource Management Unit, Via E. Fermi, 2749-21027 Ispra, VA, Italy
| | - Ciro Gardi
- European Commission, Joint Research Centre (JRC), Institute for Environment and Sustainability (IES), Land Resource Management Unit, Via E. Fermi, 2749-21027 Ispra, VA, Italy; European Food Safety Authority, Animal and Plant Health, Via Carlo Magno, 1A, 43126 Parma, Parma, Italy
| | - Luca Montanarella
- European Commission, Joint Research Centre (JRC), Institute for Environment and Sustainability (IES), Land Resource Management Unit, Via E. Fermi, 2749-21027 Ispra, VA, Italy
| | - Cristiano Ballabio
- European Commission, Joint Research Centre (JRC), Institute for Environment and Sustainability (IES), Land Resource Management Unit, Via E. Fermi, 2749-21027 Ispra, VA, Italy
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