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Zheng C, Song J, Shan M, Qiu M, Cui M, Huang C, Chen W, Wang J, Zhang L, Yu Y, Fang H. Key bacterial taxa with specific metabolisms and life history strategies sustain soil microbial network stability exposed to carbendazim and deoxynivalenol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176680. [PMID: 39366579 DOI: 10.1016/j.scitotenv.2024.176680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/23/2024] [Accepted: 09/30/2024] [Indexed: 10/06/2024]
Abstract
Co-contamination of carbendazim (CBD) and deoxynivalenol (DON) is common in agricultural soils, yet their ecological impact on soil microbiome remains poorly assessed. Here, we investigated the influence of CBD and DON on the structure, function, and co-occurrence networks of soil microbiome. The combined treatment of CBD and DON significantly exacerbated the negative impacts on soil microbial diversity, functional diversity, and microbial network stability compared to individual treatments. Specifically, Lysobacter, Gemmatimonas, Nitrospira, Massilia, and Bacillus were identified as indicator species for CBD and DON. Simultaneously, the abundance of genes involved in key ecological functions, such as nitrification (amoA) and organic phosphorus mineralization (phoAD), was significantly reduced. Notably, key bacterial taxa Nitrospira and Gemmatimonas, with K-life history strategy and capabilities for nitrification and organic nitrogen mineralization, played crucial roles in promoting positive interactions in networks. Furthermore, variance partitioning analysis (VPA) and structural equation modeling (SEM) demonstrated that the abundance and niche breadth of key bacterial taxa were the primary drivers of microbial network stability. In conclusion, our study provides new insights into how soil microbiomes and networks respond to pesticides and mycotoxins, aiding in a more comprehensive assessment of exposure risks.
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Affiliation(s)
- Conglai Zheng
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jiajin Song
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mei Shan
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mengting Qiu
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Minrong Cui
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chenyu Huang
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Weibin Chen
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jiao Wang
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Luqing Zhang
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yunlong Yu
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hua Fang
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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Parajuli A, Mäkelä I, Roslund MI, Ringqvist E, Manninen J, Sun Y, Nurminen N, Oikarinen S, Laitinen OH, Hyöty H, Flodström-Tullberg M, Sinkkonen A. Production, analysis, and safety assessment of a soil and plant-based natural material with microbiome- and immune-modulatory effects. Methods 2024; 231:94-102. [PMID: 39306218 DOI: 10.1016/j.ymeth.2024.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 09/15/2024] [Accepted: 09/16/2024] [Indexed: 09/27/2024] Open
Abstract
It has been suggested that reduced contact with microbiota from the natural environment contributes to the rising incidence of immune-mediated inflammatory disorders (IMIDs) in western, highly urbanized societies. In line with this, we have previously shown that exposure to environmental microbiota in the form of a blend comprising of soil and plant-based material (biodiversity blend; BDB) enhances the diversity of human commensal microbiota and promotes immunoregulation that may be associated with a reduced risk for IMIDs. To provide a framework for future preclinical studies and clinical trials, this study describes how the preparation of BDB was standardized, its microbial content analysed and safety assessments performed. Multiple batches of BDB were manufactured and microbial composition analysed using 16S rRNA gene sequencing. We observed a consistently high alpha diversity and relative abundance of bacteria normally found in soil and vegetation. We also found that inactivation of BDB by autoclaving effectively inactivates human and murine bacteria, viruses and parasites. Finally, we demonstrate that experimental mice prone to develop IMIDs (non-obese diabetic, NOD, mouse model) can be exposed to BDB without causing adverse effects on animal health and welfare. Our study provides insights into a potentially safe, sustainable, and cost-effective approach for simulating exposure to natural microbiota, which could have substantial impacts on health and socio-economic factors.
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Affiliation(s)
- Anirudra Parajuli
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, Stockholm, Sweden; Ecosystem and Environment Research Programme, Department of Ecological and Environmental Science, University of Helsinki, Helsinki, Finland
| | - Iida Mäkelä
- Horticulture Technologies, Natural Resources Institute Finland, Helsinki and Turku, Finland
| | - Marja I Roslund
- Horticulture Technologies, Natural Resources Institute Finland, Helsinki and Turku, Finland
| | - Emma Ringqvist
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Juulia Manninen
- Ecosystem and Environment Research Programme, Department of Ecological and Environmental Science, University of Helsinki, Helsinki, Finland
| | - Yan Sun
- Ecosystem and Environment Research Programme, Department of Ecological and Environmental Science, University of Helsinki, Helsinki, Finland
| | - Noora Nurminen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli H Laitinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Malin Flodström-Tullberg
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, Stockholm, Sweden.
| | - Aki Sinkkonen
- Horticulture Technologies, Natural Resources Institute Finland, Helsinki and Turku, Finland.
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Scholthof KBG. The Greening of One Health: Plants, Pathogens, and the Environment. ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:401-421. [PMID: 38857537 DOI: 10.1146/annurev-phyto-121423-042102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
One Health has an aspirational goal of ensuring the health of humans, animals, plants, and the environment through transdisciplinary, collaborative research. At its essence, One Health addresses the human clash with Nature by formulating strategies to repair and restore a (globally) perturbed ecosystem. A more nuanced evaluation of humankind's impact on the environment (Nature, Earth, Gaia) would fully intercalate plants, plant pathogens, and beneficial plant microbes into One Health. Here, several examples point out how plants and plant microbes are keystones of One Health. Meaningful cross-pollination between plant, animal, and human health practitioners can drive discovery and application of innovative tools to address the many complex problems within the One Health framework.
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Affiliation(s)
- Karen-Beth G Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA;
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Gao M, Sun J, Zheng Y, Lu T, Liu J. Daily dynamics of ground-dwelling invertebrate communities during and following an extreme high-temperature event in summer 2022, China. PLoS One 2024; 19:e0306823. [PMID: 39178186 PMCID: PMC11343418 DOI: 10.1371/journal.pone.0306823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 06/24/2024] [Indexed: 08/25/2024] Open
Abstract
The recent increase in the frequency of extreme weather events and declining soil biodiversity in global agricultural ecosystems make it crucial to assess the daily dynamics of soil communities in fields. To elucidate the daily dynamics of ground-dwelling invertebrate communities, their communities were monitored temporally using infrared camera traps in field farmland during and following an extremely high-temperature (EHT) event in summer 2022 in Ningbo City, China. Nine taxa and 1,147 individuals of the ground-dwelling invertebrate community were photographed in the 176,256 images. There were no significant differences in the taxonomic richness and abundance of the total ground-dwelling invertebrate communities during and following the EHT event. The abundance of ants was significantly decreased following the EHT event, whereas the abundance of other taxa was not. Significantly daily dynamics and obvious differences between each day in taxonomic richness, abundance of ground-dwelling invertebrate community, and abundance of each taxon were not observed during and following the EHT event. The results of this study showed that the daily dynamics of richness and abundance of the ground-dwelling invertebrate community and the abundance of each taxon were not significant during and following the EHT event. Overall, this study provides a useful monitoring method to observe the daily dynamics of ground-dwelling invertebrates in field farmlands and suggests that the daily dynamics of soil fauna communities should be further studied when assessing the effects of climate change on soil biodiversity.
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Affiliation(s)
- Meixiang Gao
- Department of Geography and Spatial Information Techniques, Ningbo University, Ningbo, China
- Ningbo Universities Collaborative Innovation Center for Land and Marine Spatial Utilization and Governance Research at Ningbo University, Ningbo, China
| | - Jiahuan Sun
- Department of Geography and Spatial Information Techniques, Ningbo University, Ningbo, China
- Ningbo Universities Collaborative Innovation Center for Land and Marine Spatial Utilization and Governance Research at Ningbo University, Ningbo, China
| | - Ye Zheng
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, China
| | - Tingyu Lu
- College of Geography and Environmental Sciences, Hainan Normal University, Haikou, China
| | - Jinwen Liu
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Changchun, China
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Rana ML, Hoque MN, Rahman MS, Pramanik PK, Islam MS, Punom SA, Ramasamy S, Schreinemachers P, Oliva R, Rahman MT. Soil bacteriome diversity and composition of rooftop and surface gardens in urban and peri-urban areas of Bangladesh. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:729. [PMID: 39001908 DOI: 10.1007/s10661-024-12850-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 06/22/2024] [Indexed: 07/15/2024]
Abstract
Soil microbiome science, rapidly evolving, predominantly focuses on field crop soils. However, understanding garden soil microbiomes is essential for enhancing food production sustainability in garden environments. This study aimed to unveil the bacteriome diversity and composition in rooftop garden soils (RGS) and surface garden soils (SGS) across urban (Dhaka North and Dhaka South City Corporations) and peri-urban (Gazipur City Corporation) areas of Dhaka Division, Bangladesh. We analyzed 11 samples, including six RGS and five SGS samples from 11 individual gardens using 16S rRNA (V3-V4 region) gene-based amplicon sequencing. A total of 977 operational taxonomic units (OTUs), including 270 and 707 in RGS and SGS samples, respectively, were identified. The observed OTUs were represented by 21 phyla, 45 classes, 84 orders, 173 families, and 293 genera of bacteria. Alpha diversity indices revealed significantly higher bacterial diversity in SGS samples (p = 0.01), while beta diversity analyses indicated distinct bacteriome compositions between RGS and SGS samples (p = 0.028, PERMANOVA). Despite substantial taxonomic variability between sample categories, there was also a considerable presence of shared bacterial taxa. At the phylum level, Bacilliota (61.14%), Pseudomonadota (23.42%), Actinobacteria (6.33%), and Bacteroidota (3.32%) were the predominant bacterial phyla (comprising > 94.0% of the total abundances) in both types of garden soil samples. Of the identified genera, Bacillus (69.73%) and Brevibacillus (18.81%) in RGS and Bacillus (19.22%), Methylophaga (19.21%), Acinetobacter (6.27%), Corynebacterium (5.06%), Burkholderia (4.78%), Paracoccus (3.98%) and Lysobacter (2.07%) in SGS were the major bacterial genera. Importantly, we detected that 52.90% of genera were shared between RGS and SGS soil samples. Our data reveal unique and shared bacteriomes with probiotic potential in soil samples from both rooftop and surface gardens. Further studies should explore the functional roles of shared bacterial taxa in garden soils and how urban environmental factors affect microbiome composition to optimize soil health and sustainable food production.
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Affiliation(s)
- Md Liton Rana
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Pritom Kumar Pramanik
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Saiful Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
- Department of Animal Sciences, University of California - Davis, Davis, 95616, USA
| | - Sadia Afrin Punom
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | | | | | | | - Md Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
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Hale B, Watts C, Conatser M, Brown E, Wijeratne AJ. Fine-scale characterization of the soybean rhizosphere microbiome via synthetic long reads and avidity sequencing. ENVIRONMENTAL MICROBIOME 2024; 19:46. [PMID: 38997772 PMCID: PMC11241880 DOI: 10.1186/s40793-024-00590-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND The rhizosphere microbiome displays structural and functional dynamism driven by plant, microbial, and environmental factors. While such plasticity is a well-evidenced determinant of host health, individual and community-level microbial activity within the rhizosphere remain poorly understood, due in part to the insufficient taxonomic resolution achieved through traditional marker gene amplicon sequencing. This limitation necessitates more advanced approaches (e.g., long-read sequencing) to derive ecological inferences with practical application. To this end, the present study coupled synthetic long-read technology with avidity sequencing to investigate eukaryotic and prokaryotic microbiome dynamics within the soybean (Glycine max) rhizosphere under field conditions. RESULTS Synthetic long-read sequencing permitted de novo reconstruction of the entire 18S-ITS1-ITS2 region of the eukaryotic rRNA operon as well as all nine hypervariable regions of the 16S rRNA gene. All full-length, mapped eukaryotic amplicon sequence variants displayed genus-level classification, and 44.77% achieved species-level classification. The resultant eukaryotic microbiome encompassed five kingdoms (19 genera) of protists in addition to fungi - a depth unattainable with conventional short-read methods. In the prokaryotic fraction, every full-length, mapped amplicon sequence variant was resolved at the species level, and 23.13% at the strain level. Thirteen species of Bradyrhizobium were thereby distinguished in the prokaryotic microbiome, with strain-level identification of the two Bradyrhizobium species most reported to nodulate soybean. Moreover, the applied methodology delineated structural and compositional dynamism in response to experimental parameters (i.e., growth stage, cultivar, and biostimulant application), unveiled a saprotroph-rich core microbiome, provided empirical evidence for host selection of mutualistic taxa, and identified key microbial co-occurrence network members likely associated with edaphic and agronomic properties. CONCLUSIONS This study is the first to combine synthetic long-read technology and avidity sequencing to profile both eukaryotic and prokaryotic fractions of a plant-associated microbiome. Findings herein provide an unparalleled taxonomic resolution of the soybean rhizosphere microbiota and represent significant biological and technological advancements in crop microbiome research.
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Affiliation(s)
- Brett Hale
- AgriGro Incorporated, Doniphan, MO, USA
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, USA
- College of Science and Mathematics, Arkansas State University, State University, AR, USA
| | - Caitlin Watts
- College of Agriculture, Arkansas State University, State University, AR, USA
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Matthew Conatser
- College of Agriculture, Arkansas State University, State University, AR, USA
| | - Edward Brown
- College of Agriculture, Arkansas State University, State University, AR, USA
| | - Asela J Wijeratne
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, USA.
- College of Science and Mathematics, Arkansas State University, State University, AR, USA.
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Tan T, Genova G, Heuvelink GBM, Lehmann J, Poggio L, Woolf D, You F. Importance of Terrain and Climate for Predicting Soil Organic Carbon Is Highly Variable across Local to Continental Scales. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11492-11503. [PMID: 38904357 DOI: 10.1021/acs.est.4c01172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Soil organic carbon (SOC) plays a vital role in global carbon cycling and sequestration, underpinning the need for a comprehensive understanding of its distribution and controls. This study explores the importance of various covariates on SOC spatial distribution at both local (up to 1.25 km) and continental (USA) scales using a deep learning approach. Our findings highlight the significant role of terrain attributes in predicting SOC concentration distribution with terrain, contributing approximately one-third of the overall prediction at the local scale. At the continental scale, climate is only 1.2 times more important than terrain in predicting SOC distribution, whereas at the local scale, the structural pattern of terrain is 14 and 2 times more important than climate and vegetation, respectively. We underscore that terrain attributes, while being integral to the SOC distribution at all scales, are stronger predictors at the local scale with explicit spatial arrangement information. While this observational study does not assess causal mechanisms, our analysis nonetheless presents a nuanced perspective about SOC spatial distribution, which suggests disparate predictors of SOC at local and continental scales. The insights gained from this study have implications for improved SOC mapping, decision support tools, and land management strategies, aiding in the development of effective carbon sequestration initiatives and enhancing climate mitigation efforts.
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Affiliation(s)
- Tianhong Tan
- Systems Engineering, Cornell University, Ithaca, New York 14853, United States
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Giulio Genova
- ISRIC─World Soil Information, Wageningen 6700 AJ, The Netherlands
| | | | - Johannes Lehmann
- School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Laura Poggio
- ISRIC─World Soil Information, Wageningen 6700 AJ, The Netherlands
| | - Dominic Woolf
- School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14853, United States
- Cornell Institute of Digital Agriculture, Cornell University, Ithaca, New York 14853, United States
| | - Fengqi You
- Systems Engineering, Cornell University, Ithaca, New York 14853, United States
- Cornell Institute of Digital Agriculture, Cornell University, Ithaca, New York 14853, United States
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Wang X, Yang Y, Nan Q, Guo JW, Tan Z, Shao X, Tian C. Barley farmland harbors a highly homogeneous soil bacterial community compared to wild ecosystems in the Qinghai-Xizang Plateau. Front Microbiol 2024; 15:1418161. [PMID: 38979541 PMCID: PMC11228161 DOI: 10.3389/fmicb.2024.1418161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/11/2024] [Indexed: 07/10/2024] Open
Abstract
Introduction Understanding patterns and processes of microbial biogeography in soils is important for monitoring ecological responses to human activities, particularly in ecologically vulnerable areas such as the Qinghai-Xizang Plateau. Highland barley is the staple food of local people and has mainly been cultivated along the Yarlung Zangbo River valley in Xizang. Methods Here we investigated soil bacterial communities from 33 sampling sites of highland barley farmland in this region and compared them to those from wild ecosystems including alpine tundra, meadow, forest, and swamp. Additionally, the effects of environmental factors on bacterial communities, as well as the relative importance of stochastic and deterministic processes in shaping the beta diversity of soil bacterial communities in alpine ecosystems were assessed. Results In contrast to soils of wild ecosystems, these farmland samples harbored a highly homogeneous bacterial community without significant correlations with geographic, elevation, and edaphic distances. Discriminant bacterial taxa identified for farmland samples belong to Acidobacteria, with Acidobacteria Gp4 as the dominant clade. Although Acidobacteria were the most abundant members in all ecosystems, characterized bacterial taxa of meadow and forest were members of other phyla such as Proteobacteria and Verrucomicrobia. pH and organic matter were major edaphic attributes shaping these observed patterns across ecosystems. Null model analyses revealed that the deterministic assembly was dominant in bacterial communities in highland barley farmland and tundra soils, whereas stochastic assembly also contributed a large fraction to the assembly of bacterial communities in forest, meadow and swamp soils. Discussion These findings provide an insight into the consequences of human activities and agricultural intensification on taxonomic homogenization of soil bacterial communities in the Qinghai-Xizang Plateau.
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Affiliation(s)
- Xiaolin Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yibin Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Qiong Nan
- Institute of Environmental Science and Technology, College of Environment and Resource Science, Zhejiang University, Hangzhou, China
| | - Jian-Wei Guo
- College of Agronomy and Life Sciences, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Zhiyuan Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Xiaoming Shao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Changfu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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Monaco P, Baldoni A, Naclerio G, Scippa GS, Bucci A. Impact of Plant-Microbe Interactions with a Focus on Poorly Investigated Urban Ecosystems-A Review. Microorganisms 2024; 12:1276. [PMID: 39065045 PMCID: PMC11279295 DOI: 10.3390/microorganisms12071276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
The urbanization process, which began with the Industrial Revolution, has undergone a considerable increase over the past few decades. Urbanization strongly affects ecological processes, often deleteriously, because it is associated with a decrease in green spaces (areas of land covered by vegetation), loss of natural habitats, increased rates of species extinction, a greater prevalence of invasive and exotic species, and anthropogenic pollutant accumulation. In urban environments, green spaces play a key role by providing many ecological benefits and contributing to human psychophysical well-being. It is known that interactions between plants and microorganisms that occur in the rhizosphere are of paramount importance for plant health, soil fertility, and the correct functioning of plant ecosystems. The growing diffusion of DNA sequencing technologies and "omics" analyses has provided increasing information about the composition, structure, and function of the rhizomicrobiota. However, despite the considerable amount of data on rhizosphere communities and their interactions with plants in natural/rural contexts, current knowledge on microbial communities associated with plant roots in urban soils is still very scarce. The present review discusses both plant-microbe dynamics and factors that drive the composition of the rhizomicrobiota in poorly investigated urban settings and the potential use of beneficial microbes as an innovative biological tool to face the challenges that anthropized environments and climate change impose. Unravelling urban biodiversity will contribute to green space management, preservation, and development and, ultimately, to public health and safety.
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Affiliation(s)
- Pamela Monaco
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (A.B.); (G.N.); (G.S.S.)
| | | | | | | | - Antonio Bucci
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (A.B.); (G.N.); (G.S.S.)
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10
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He K, Han R, Wang Z, Xiao Z, Hao Y, Dong Z, Xu Q, Li G. Soil source, not the degree of urbanization determines soil physicochemical properties and bacterial composition in Ningbo urban green spaces. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172550. [PMID: 38643872 DOI: 10.1016/j.scitotenv.2024.172550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/07/2024] [Accepted: 04/16/2024] [Indexed: 04/23/2024]
Abstract
Urban green spaces provide multiple ecosystem services and have great influences on human health. However, the compositions and properties of urban soil are not well understood yet. In this study, soil samples were collected from 45 parks in Ningbo to investigate the relationships among soil physicochemical properties, heavy metals and bacterial communities. The results showed that soil dissolved organic matter (DOM) was of high molecular weight, high aromaticity, and low degree of humification. The contents of heavy metals were all below the China's national standard safety limit (GB 3660-2018). The bioavailability of heavy metals highly correlated with soil pH, the content of DOC, the fluorescent component, the degree of humification and the source of DOM. The most abundant genera were Gemmatimonadaceae_uncultured, Xanthobacteraceae_uncultured, and Acidothermus in all samples, which were related to nitrogen cycle and bioavailability of heavy metals. Soil pH, bioavailability of Zn, Cd, and Pb (CaCl2 extracted) were the main edaphic factors influencing bacterial community composition. It should be noted that there was no significant impact of urbanization on soil physicochemical properties and bacterial composition, but they were determined by the source of soil in urban green spaces. However, with the passage of time, the effect of urbanization on urban green spaces cannot be ignored. Overall, this study provided new insight for understanding the linkage among soil physicochemical properties, heavy metals, and bacterial communities in urban green spaces.
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Affiliation(s)
- Kaiwen He
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruixia Han
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhe Wang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zufei Xiao
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yilong Hao
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuozhen Dong
- Agricultural Technology Management and Service Station of Haishu District in Ningbo, Ningbo 315012, China
| | - Qiao Xu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Qiao R, Xu M, Jiang J, Song Z, Wang M, Yang L, Guo H, Mao Z. Plant growth promotion and biocontrol properties of a synthetic community in the control of apple disease. BMC PLANT BIOLOGY 2024; 24:546. [PMID: 38872113 DOI: 10.1186/s12870-024-05253-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 06/05/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Apple Replant Disease (ARD) is common in major apple-growing regions worldwide, but the role of rhizosphere microbiota in conferring ARD resistance and promoting plant growth remains unclear. RESULTS In this study, a synthetic microbial community (SynCom) was developed to enhance apple plant growth and combat apple pathogens. Eight unique bacteria selected via microbial culture were used to construct the antagonistic synthetic community, which was then inoculated into apple seedlings in greenhouse experiments. Changes in the rhizomicroflora and the growth of aboveground plants were monitored. The eight strains, belonging to the genera Bacillus and Streptomyces, have the ability to antagonize pathogens such as Fusarium oxysporum, Rhizoctonia solani, Botryosphaeria ribis, and Physalospora piricola. Additionally, these eight strains can stably colonize in apple rhizosphere and some of them can produce siderophores, ACC deaminase, and IAA. Greenhouse experiments with Malus hupehensis Rehd indicated that SynCom promotes plant growth (5.23%) and increases the nutrient content of the soil, including soil organic matter (9.25%) and available K (1.99%), P (7.89%), and N (0.19%), and increases bacterial richness and the relative abundance of potentially beneficial bacteria. SynCom also increased the stability of the rhizosphere microbial community, the assembly of which was dominated by deterministic processes (|β NTI| > 2). CONCLUSIONS Our results provide insights into the contribution of the microbiome to pathogen inhibition and host growth. The formulation and manipulation of similar SynComs may be a beneficial strategy for promoting plant growth and controlling soil-borne disease.
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Affiliation(s)
- Rongye Qiao
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
| | - Mingzhen Xu
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
| | - Jihang Jiang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
| | - Zhen Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meibin Wang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
| | - Lei Yang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
| | - Hui Guo
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China.
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing, 100083, China.
| | - Zhiquan Mao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China.
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12
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Robinson JM, Liddicoat C, Muñoz-Rojas M, Breed MF. Restoring soil biodiversity. Curr Biol 2024; 34:R393-R398. [PMID: 38714171 DOI: 10.1016/j.cub.2024.02.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
Soil health is crucial for all terrestrial life, supporting, among other processes, food production, water purification and carbon sequestration. Soil biodiversity - the variety of life within soils - is key to these processes and thus key to soil restoration. Human activities that degrade ecosystems threaten soil biodiversity and associated ecosystem processes. Indeed, 75% of the world's soils are affected by degradation - a figure that could rise to 90% by 2050 if deforestation, overgrazing, urbanisation and other harmful practices persist. Restoring soil biodiversity is a prerequisite for planetary health, and it comes with many challenges and opportunities. Soil directly supports around 60% of all species on Earth, and land degradation poses a major problem for this biodiversity and the ecosystem services that sustain human populations. Indeed, 98% of human calories come from soil, and earthworms alone underpin 6.5% of the world's grain production. Moreover, the total carbon in terrestrial ecosystems is around 3,170 gigatons (1 gigaton (Gt) = 1 billion metric tons), of which approximately 80% (2,500 Gt) is found in soil. Therefore, restoring soil biodiversity is not just a human need but an ecological and Earth-system imperative. It is pivotal for maintaining ecosystem resilience, sustaining agricultural productivity and mitigating climate change impacts.
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Affiliation(s)
- Jake M Robinson
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia.
| | - Craig Liddicoat
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Miriam Muñoz-Rojas
- Departamento de Biologia Vegetal y Ecologia, Universidad de Sevilla, 41004 Sevilla, Spain; Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Sydney, NSW 2052, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
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13
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Lu T, Lei C, Gao M, Lv L, Zhang C, Qian H, Tang T. A risk entropy approach for linking pesticides and soil bacterial communities. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133970. [PMID: 38457974 DOI: 10.1016/j.jhazmat.2024.133970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Pesticides play a vital role in ensuring modern agricultural production, but also adversely affecting soil health. Microorganisms are the cornerstone of soil ecology, however, to date, there are few unified standards to measure the risk of soil pesticide residues to soil microbial community. To compensate for this gap, we collected soil samples from 55 orchards and monitored and risk-assessed 165 pesticides to microbial community in the soil. Results showed that a total of 137 pesticides were detected in all samples. Pesticide residues significantly influenced the microbial diversity and community structure in orchard soils, particularly fungicides and herbicides. The risk entropy of each pesticide was calculated in all samples and it was found that 60% of the samples had a "pesticide risk" (Risk quotient > 0.01), where the relative abundance significantly increased in 43 genera and significantly decreased in 111 genera (p < 0.05). Through multiple screens, we finally identified Bacillus and Sphingomonas as the most abundant sensitive genera under pesticide perturbation. The results showed that despite the complexity of the effects of pesticide residues on soils health, we could reveal them by identifying changes in soil bacterial, especially by the differences of microbial biomarkers abundance. The present study could provide new insights into the research strategy for pesticide pollution on soil microbial communities. ENVIRONMENTAL IMPLICATION: The risk of pesticide residues in soil needs to be quantified and standardized. We believe that microorganisms can be used as a marker to indicate soil pesticide residue risk. For this end, we investigated the residues of 165 pesticides in 55 orchard soil samples, calculated pesticide risk entropy and their effects on the soil microbial community. Through multiple analyzing and screening, we ultimately identified that, out of the 154 detected biomarkers, Bacillus and Sphingomonas were the most abundant sensitive genera under pesticide perturbation, which have the potential to be used as key biomarkers of soil microbiomes induced by pesticide perturbation.
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Affiliation(s)
- Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Mingyu Gao
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Lu Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory for Pesticide Residue Detection of Ministry of Agriculture and Rural Affairs, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Chunrong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory for Pesticide Residue Detection of Ministry of Agriculture and Rural Affairs, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory for Pesticide Residue Detection of Ministry of Agriculture and Rural Affairs, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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14
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Peng Z, Qian X, Liu Y, Li X, Gao H, An Y, Qi J, Jiang L, Zhang Y, Chen S, Pan H, Chen B, Liang C, van der Heijden MGA, Wei G, Jiao S. Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally. Nat Commun 2024; 15:3624. [PMID: 38684659 PMCID: PMC11058813 DOI: 10.1038/s41467-024-47348-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Agriculture contributes to a decline in local species diversity and to above- and below-ground biotic homogenization. Here, we conduct a continental survey using 1185 soil samples and compare microbial communities from natural ecosystems (forest, grassland, and wetland) with converted agricultural land. We combine our continental survey results with a global meta-analysis of available sequencing data that cover more than 2400 samples across six continents. Our combined results demonstrate that land conversion to agricultural land results in taxonomic and functional homogenization of soil bacteria, mainly driven by the increase in the geographic ranges of taxa in croplands. We find that 20% of phylotypes are decreased and 23% are increased by land conversion, with croplands enriched in Chloroflexi, Gemmatimonadota, Planctomycetota, Myxcoccota and Latescibacterota. Although there is no significant difference in functional composition between natural ecosystems and agricultural land, functional genes involved in nitrogen fixation, phosphorus mineralization and transportation are depleted in cropland. Our results provide a global insight into the consequences of land-use change on soil microbial taxonomic and functional diversity.
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Affiliation(s)
- Ziheng Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yu Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Xiaomeng Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Hang Gao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yining An
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Jiejun Qi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Lan Jiang
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yiran Zhang
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Shi Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Haibo Pan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Beibei Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Chunling Liang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China.
| | - Shuo Jiao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China.
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15
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Sun Y, Staley ZR, Woodbury B, Riethoven JJ, Li X. Composting reduces the risks of resistome in beef cattle manure at the transcriptional level. Appl Environ Microbiol 2024; 90:e0175223. [PMID: 38445903 PMCID: PMC11022583 DOI: 10.1128/aem.01752-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
Transcriptomic evidence is needed to determine whether composting is more effective than conventional stockpiling in mitigating the risk of resistome in livestock manure. The objective of this study is to compare composting and stockpiling for their effectiveness in reducing the risk of antibiotic resistance in beef cattle manure. Samples collected from the center and the surface of full-size manure stockpiling and composting piles were subject to metagenomic and metatranscriptomic analyses. While the distinctions in resistome between stockpiled and composted manure were not evident at the DNA level, the advantages of composting over stockpiling were evident at the transcriptomic level in terms of the abundance of antibiotic resistance genes (ARGs), the number of ARG subtypes, and the prevalence of high-risk ARGs (i.e., mobile ARGs associated with zoonotic pathogens). DNA and transcript contigs show that the pathogen hosts of high-risk ARGs included Escherichia coli O157:H7 and O25b:H4, Klebsiella pneumoniae, and Salmonella enterica. Although the average daily temperatures for the entire composting pile exceeded 55°C throughout the field study, more ARG and ARG transcripts were removed at the center of the composting pile than at the surface. This work demonstrates the advantage of composting over stockpiling in reducing ARG risk in active populations in beef cattle manure.IMPORTANCEProper treatment of manure before land application is essential to mitigate the spread of antibiotic resistance in the environment. Stockpiling and composting are two commonly used methods for manure treatment. However, the effectiveness of composting in reducing antibiotic resistance in manure has been debated. This work compared the ability of these two methods to reduce the risk of antibiotic resistance in beef cattle manure. Our results demonstrate that composting reduced more high-risk resistance genes at the transcriptomic level in cattle manure than conventional stockpiling. This finding not only underscores the effectiveness of composting in reducing antibiotic resistance in manure but also highlights the importance of employing RNA analyses alongside DNA analyses.
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Affiliation(s)
- Yuepeng Sun
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Zachery R. Staley
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Bryan Woodbury
- USDA-ARS U.S. Meat Animal Research Center, Clay Center, Clay Center, Nebraska, USA
| | - Jean-Jack Riethoven
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Xu Li
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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16
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Daunoras J, Kačergius A, Gudiukaitė R. Role of Soil Microbiota Enzymes in Soil Health and Activity Changes Depending on Climate Change and the Type of Soil Ecosystem. BIOLOGY 2024; 13:85. [PMID: 38392304 PMCID: PMC10886310 DOI: 10.3390/biology13020085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
The extracellular enzymes secreted by soil microorganisms play a pivotal role in the decomposition of organic matter and the global cycles of carbon (C), phosphorus (P), and nitrogen (N), also serving as indicators of soil health and fertility. Current research is extensively analyzing these microbial populations and enzyme activities in diverse soil ecosystems and climatic regions, such as forests, grasslands, tropics, arctic regions and deserts. Climate change, global warming, and intensive agriculture are altering soil enzyme activities. Yet, few reviews have thoroughly explored the key enzymes required for soil fertility and the effects of abiotic factors on their functionality. A comprehensive review is thus essential to better understand the role of soil microbial enzymes in C, P, and N cycles, and their response to climate changes, soil ecosystems, organic farming, and fertilization. Studies indicate that the soil temperature, moisture, water content, pH, substrate availability, and average annual temperature and precipitation significantly impact enzyme activities. Additionally, climate change has shown ambiguous effects on these activities, causing both reductions and enhancements in enzyme catalytic functions.
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Affiliation(s)
- Jokūbas Daunoras
- Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257 Vilnius, Lithuania
| | - Audrius Kačergius
- Lithuanian Research Centre for Agriculture and Forestry, Kedainiai Distr., LT-58344 Akademija, Lithuania
| | - Renata Gudiukaitė
- Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257 Vilnius, Lithuania
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17
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Zhai C, Han L, Xiong C, Ge A, Yue X, Li Y, Zhou Z, Feng J, Ru J, Song J, Jiang L, Yang Y, Zhang L, Wan S. Soil microbial diversity and network complexity drive the ecosystem multifunctionality of temperate grasslands under changing precipitation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167217. [PMID: 37751844 DOI: 10.1016/j.scitotenv.2023.167217] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]
Abstract
Soil microbiomes play a critical role in regulating ecosystem multifunctionality. However, whether and how soil protists and microbiome interactions affect ecosystem multifunctionality under climate change is unclear. Here, we transplanted 54 soil monoliths from three typical temperate grasslands (i.e., desert, typical, and meadow steppes) along a precipitation gradient in the Mongolian Plateau and examined their response to nighttime warming, decreased, and increased precipitation. Across the three steppes, nighttime warming only stimulated protistan diversity by 15.61 (absolute change, phylogenetic diversity) but had no effect on ecosystem multifunctionality. Decreased precipitation reduced bacterial (8.78) and fungal (22.28) diversity, but significantly enhanced soil microbiome network complexity by 1.40. Ecosystem multifunctionality was reduced by 0.23 under decreased precipitation, which could be largely attributed to the reduced soil moisture that negatively impacted bacterial and fungal communities. In contrast, increased precipitation had little impact on soil microbial communities. Overall, both bacterial and fungal diversity and network complexity play a fundamental role in maintaining ecosystem multifunctionality in response to drought stress. Protists alter ecosystem multifunctionality by indirectly affecting microbial network complexity. Therefore, not only microbial diversity but also their interactions (regulated by soil protists) should be considered in evaluating the responses of ecosystem multifunctionality, which has important implications for predicting changes in ecosystem functioning under future climate change scenarios.
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Affiliation(s)
- Changchun Zhai
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lili Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Anhui Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xiaojing Yue
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Ying Li
- School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Zhenxing Zhou
- School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Jiayin Feng
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Jingyi Ru
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Jian Song
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Limei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shiqiang Wan
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China.
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18
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Pino V, Fajardo M, McBratney A, Minasny B, Wilson N, Baldock C. Australian soil microbiome: A first sightseeing regional prediction driven by cycles of soil temperature and pedogenic variations. Mol Ecol 2023; 32:6243-6259. [PMID: 36862079 DOI: 10.1111/mec.16911] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/05/2023] [Accepted: 02/27/2023] [Indexed: 03/03/2023]
Abstract
Declines in soil multifunctionality (e.gsoil capacity to provide food and energy) are closely related to changes in the soil microbiome (e.g., diversity) Determining ecological drivers promoting such microbiome changes is critical knowledge for protecting soil functions. However, soil-microbe interactions are highly variable within environmental gradients and may not be consistent across studies. Here we propose that analysis of community dissimilarity (β-diversity) is a valuable tool for overviewing soil microbiome spatiotemporal changes. Indeed, β-diversity studies at larger scales (modelling and mapping) simplify complex multivariate interactions and refine our understanding of ecological drivers by also giving the possibility of expanding the environmental scenarios. This study represents the first spatial investigation of β-diversity in the soil microbiome of New South Wales (800,642 km2 ), Australia. We used metabarcoding soil data (16S rRNA and ITS genes) as exact sequence variants (ASVs) and UMAP (Uniform Manifold Approximation and Projection) as the distance metric. β-Diversity maps (1000-m resolution)-concordance correlations of 0.91-0.96 and 0.91-0.95 for bacteria and fungi, respectively-showed soil biome dissimilarities driven primarily by soil chemistry-pH and effective cation exchange capacity (ECEC)-and cycles of soil temperature-land surface temperature (LST-phase and LST-amplitude). Regionally, the spatial patterns of microbes parallel the distribution of soil classes (e.g., Vertosols) beyond spatial distances and rainfall, for example. Soil classes can be valuable discriminants for monitoring approaches, for example pedogenons and pedophenons. Ultimately, cultivated soils exhibited lower richness due to declines in rare microbes which might compromise soil functions over time.
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Affiliation(s)
- Vanessa Pino
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Mario Fajardo
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Alex McBratney
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Budiman Minasny
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Neil Wilson
- Metagenomic Laboratory, Metagen Pty, Ltd., Gatton, Queensland, Australia
| | - Chris Baldock
- Metagenomic Laboratory, Metagen Pty, Ltd., Gatton, Queensland, Australia
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19
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Siebert J, Sünnemann M, Hautier Y, Risch AC, Bakker JD, Biederman L, Blumenthal DM, Borer ET, Bugalho MN, Broadbent AAD, Caldeira MC, Cleland E, Davies KF, Eskelinen A, Hagenah N, Knops JMH, MacDougall AS, McCulley RL, Moore JL, Power SA, Price JN, Seabloom EW, Standish R, Stevens CJ, Zimmermann S, Eisenhauer N. Drivers of soil microbial and detritivore activity across global grasslands. Commun Biol 2023; 6:1220. [PMID: 38040868 PMCID: PMC10692199 DOI: 10.1038/s42003-023-05607-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023] Open
Abstract
Covering approximately 40% of land surfaces, grasslands provide critical ecosystem services that rely on soil organisms. However, the global determinants of soil biodiversity and functioning remain underexplored. In this study, we investigate the drivers of soil microbial and detritivore activity in grasslands across a wide range of climatic conditions on five continents. We apply standardized treatments of nutrient addition and herbivore reduction, allowing us to disentangle the regional and local drivers of soil organism activity. We use structural equation modeling to assess the direct and indirect effects of local and regional drivers on soil biological activities. Microbial and detritivore activities are positively correlated across global grasslands. These correlations are shaped more by global climatic factors than by local treatments, with annual precipitation and soil water content explaining the majority of the variation. Nutrient addition tends to reduce microbial activity by enhancing plant growth, while herbivore reduction typically increases microbial and detritivore activity through increased soil moisture. Our findings emphasize soil moisture as a key driver of soil biological activity, highlighting the potential impacts of climate change, altered grazing pressure, and eutrophication on nutrient cycling and decomposition within grassland ecosystems.
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Affiliation(s)
- Julia Siebert
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany
| | - Marie Sünnemann
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany.
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany.
| | - Yann Hautier
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Anita C Risch
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Community Ecology, Zuercherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Jonathan D Bakker
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Lori Biederman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50010, USA
| | - Dana M Blumenthal
- USDA-ARS Rangeland Resources & Systems Research Unit, Fort Collins, CO, 80526, USA
| | - Elizabeth T Borer
- Department of Ecology, Evolution, and Behavior; University of Minnesota, St. Paul, MN, 55108, USA
| | - Miguel N Bugalho
- Centre for Applied Ecology "Prof. Baeta Neves", School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Arthur A D Broadbent
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Maria C Caldeira
- Forest Research Centre, School of Agriculture, University of Lisbon, Lisbon, Portugal
| | - Elsa Cleland
- Ecology, Behavior and Evolution Section, University of California San Diego, 9500 Gilman Dr. #0116, La Jolla, California, 92093-0116, USA
| | - Kendi F Davies
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Anu Eskelinen
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany
- Ecology and Genetics Unit, University of Oulu, P.O. Box 8000, FI-90014 University of Oulu, Oulu, Finland
- Helmholtz Center for Environmental Research - UFZ, Department of Physiological Diversity, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Nicole Hagenah
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa
| | - Johannes M H Knops
- Health & Environmental Sciences Department, Xi'an Jiatong-Liverpool University, Suzhou, China
| | - Andrew S MacDougall
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Rebecca L McCulley
- Department of Plant & Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Joslin L Moore
- Arthur Rylah Institute for Environmental Research, 123 Brown Street, Heidelberg, VIC, 3084, Australia
- School of Biological Sciences, Monash University, 25 Rainforest Walk, Clayton, VIC, 3800, Australia
| | - Sally A Power
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Jodi N Price
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Albury, NSW, 2640, Australia
| | - Eric W Seabloom
- Department of Ecology, Evolution, and Behavior; University of Minnesota, St. Paul, MN, 55108, USA
| | - Rachel Standish
- Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Institute of Agriculture, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Carly J Stevens
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Stephan Zimmermann
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Forest Soils and Biogeochemistry, Zuercherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany
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20
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Lin C, Li WJ, Li LJ, Neilson R, An XL, Zhu YG. Movement of protistan trophic groups in soil-plant continuums. Environ Microbiol 2023; 25:2641-2652. [PMID: 37547979 DOI: 10.1111/1462-2920.16477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Protists, functionally divided into consumers, phototrophs, and parasites act as integral components and vital regulators of microbiomes in soil-plant continuums. However, the drivers of community structure, assembly mechanisms, co-occurrence patterns, and the associations with human pathogens and different protistan trophic groups remain unknown. Here, we characterized the phyllosphere and soil protistan communities associated with three vegetables under different fertilization treatments (none and organic fertilization) at five growth stages. In this study, consumers were the most diverse soil protist group, had the role of inter-kingdom connector, and were the primary biomarker for rhizosphere soils which were subjected to decreasing deterministic processes during plant growth. In contrast, phototrophs had the greatest niche breadth and formed soil protistan hubs, and were the primary biomarkers for both bulk soils and the phyllosphere. Parasites had minimal input to microbial co-occurrence networks. Organic fertilization increased the relative abundance (RA) of pathogenic protists and the number of pathogen-consumer connections in rhizosphere soils but decreased protistan richness and the number of internal protistan links. This study advances our understanding of the ecological roles and potential links between human pathogens and protistan trophic groups associated with soil-plant continuums, which is fundamental to the regulation of soil-plant microbiomes and maintenance of environmental and human health.
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Affiliation(s)
- Chenshuo Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Jing Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Juan Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, Scotland, UK
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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21
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Eisenhauer N, Ochoa-Hueso R, Huang Y, Barry KE, Gebler A, Guerra CA, Hines J, Jochum M, Andraczek K, Bucher SF, Buscot F, Ciobanu M, Chen H, Junker R, Lange M, Lehmann A, Rillig M, Römermann C, Ulrich J, Weigelt A, Schmidt A, Türke M. Ecosystem consequences of invertebrate decline. Curr Biol 2023; 33:4538-4547.e5. [PMID: 37757832 DOI: 10.1016/j.cub.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/21/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]
Abstract
Human activities cause substantial changes in biodiversity.1,2 Despite ongoing concern about the implications of invertebrate decline,3,4,5,6,7 few empirical studies have examined the ecosystem consequences of invertebrate biomass loss. Here, we test the responses of six ecosystem services informed by 30 above- and belowground ecosystem variables to three levels of aboveground (i.e., vegetation associated) invertebrate community biomass (100%, 36%, and 0% of ambient biomass) in experimental grassland mesocosms in a controlled Ecotron facility. In line with recent reports on invertebrate biomass loss over the last decade, our 36% biomass treatment also represented a decrease in invertebrate abundance (-70%) and richness (-44%). Moreover, we simulated the pronounced change in invertebrate biomass and turnover in community composition across the season. We found that the loss of invertebrate biomass decreases ecosystem multifunctionality, including two critical ecosystem services, aboveground pest control and belowground decomposition, while harvested plant biomass increases, likely because less energy was channeled up the food chain. Moreover, communities and ecosystem functions become decoupled with a lower biomass of invertebrates. Our study shows that invertebrate loss threatens the integrity of grasslands by decoupling ecosystem processes and decreasing ecosystem-service supply.
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Affiliation(s)
- Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany.
| | - Raúl Ochoa-Hueso
- Department of Biology, IVAGRO, University of Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Campus Del Rio San Pedro, 11510 Puerto Real, Cádiz, Spain; Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, the Netherlands
| | - Yuanyuan Huang
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
| | - Kathryn E Barry
- Ecology and Biodiversity; Department of Environmental Biology, Faculty of Science, Utrecht University Padualaan, 8 3584 CH Utrecht, the Netherlands
| | - Alban Gebler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
| | - Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
| | - Jes Hines
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
| | - Malte Jochum
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
| | - Karl Andraczek
- Systematic Botany and Functional Biodiversity, Leipzig University, Johannisallee 21, 04103 Leipzig, Germany
| | - Solveig Franziska Bucher
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Ecology and Evolution, Plant Biodiversity Group, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - Marcel Ciobanu
- Institute of Biological Research, Branch of the National Institute of Research and Development for Biological Sciences, 48 Republicii Street, 400015 Cluj-Napoca, Romania
| | - Hongmei Chen
- Systematic Botany and Functional Biodiversity, Leipzig University, Johannisallee 21, 04103 Leipzig, Germany; Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Robert Junker
- Evolutionary Ecology of Plants, Department of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Markus Lange
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Anika Lehmann
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research, Altensteinstr. 6, 14195 Berlin, Germany
| | - Matthias Rillig
- Institut für Biologie, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research, Altensteinstr. 6, 14195 Berlin, Germany
| | - Christine Römermann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Ecology and Evolution, Plant Biodiversity Group, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Josephine Ulrich
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Ecology and Evolution, Plant Biodiversity Group, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Alexandra Weigelt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Systematic Botany and Functional Biodiversity, Leipzig University, Johannisallee 21, 04103 Leipzig, Germany
| | - Anja Schmidt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany; Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - Manfred Türke
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany; Institute of Biological and Medical Imaging, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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22
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Qin Z, Zhao Z, Xia L, Yu G, Miao A, Yang Z. Vertical and seasonal dynamics of bacterial pathogenic communities at an aged organic contaminated site: Insights into microbial diversity, composition, interactions, and assembly processes. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132255. [PMID: 37703736 DOI: 10.1016/j.jhazmat.2023.132255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023]
Abstract
Under the background of the Coronavirus Disease 2019 (COVID-19) pandemic, research on pathogens deserves greater attention in the natural environment, especially in the widely distributed contaminated sites with complicated and severe organic pollution. In this study, the community composition and assembly of soil pathogens identified by the newly-developed 16S-based pipeline of multiple bacterial pathogen detection (MBPD) have been investigated on spatiotemporal scales in the selected organic polluted site. We demonstrated that the richness and diversity of the pathogenic communities were primarily controlled by soil depth, while the structure and composition of pathogenic communities varied pronouncedly with seasonal changes, which were driven by the alterations in both physiochemical parameters and organic contaminants over time. Network analysis revealed that the overwhelmingly positive interactions, identified multiple keystone species, and a well-organized modular structure maintained the stability and functionality of the pathogenic communities under environmental pressures. Additionally, the null-model analysis showed that deterministic processes dominated the pathogenic community assembly across soil profiles. In three seasons, stochasticity-dominated processes in spring and summer changed into determinism-dominated processes in winter. These findings extend our knowledge of the response of the bacterial pathogenic community to environmental disruptions brought on by organic contaminated sites.
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Affiliation(s)
- Zhirui Qin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Zhenhua Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Liling Xia
- Nanjing Vocational University of Industry Technology, Nanjing 210016, China
| | - Guangwen Yu
- China National Chemical Civil Engineering Co., Ltd, Nanjing 210031, China
| | - Aihua Miao
- China National Chemical Civil Engineering Co., Ltd, Nanjing 210031, China
| | - Zijun Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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23
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Chen L, Han H, Wang C, Warren A, Ning Y. Exploring Microeukaryote Community Characteristics and Niche Differentiation in Arid Farmland Soil at the Northeastern Edge of the Tibetan Plateau. Microorganisms 2023; 11:2510. [PMID: 37894168 PMCID: PMC10609477 DOI: 10.3390/microorganisms11102510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
The northeastern edge of the Tibetan Plateau exhibits diverse climate and landform variations, and has experienced substantial recent environmental changes, which may significantly impact local agricultural practices. Understanding the microeukaryote community structure within agricultural soils is crucial for finding out the biological responses to such changes and may guide future agricultural practices. In this study, we employed high-throughput amplicon sequencing to examine 29 agricultural soil samples from seven research areas around the northeastern edge of the Tibetan Plateau. The findings revealed that the predominant biological communities in these soils were characterized by a high abundance of Alveolata, Amoebozoa, and Rhizaria. Ascomycota displayed the highest relative abundance among fungal communities. Moreover, notable distinctions in microeukaryote community composition were observed among the study sites. Co-occurrence network analysis highlighted interactions between the biological communities. Furthermore, our results elucidated that deterministic and stochastic processes exerted diverse influences on the distribution of protozoan and fungal communities. This study provides valuable insight into the microeukaryote structure in the agricultural soils of the northeastern edge of the Tibetan Plateau, shedding light on the intricate relationships between environmental factors, microeukaryote communities, and agricultural productivity.
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Affiliation(s)
- Lingyun Chen
- College of Life Science, Northwest Normal University, Lanzhou 730070, China; (L.C.); (H.H.); (C.W.)
| | - Haifeng Han
- College of Life Science, Northwest Normal University, Lanzhou 730070, China; (L.C.); (H.H.); (C.W.)
| | - Chunhui Wang
- College of Life Science, Northwest Normal University, Lanzhou 730070, China; (L.C.); (H.H.); (C.W.)
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK;
| | - Yingzhi Ning
- College of Life Science, Northwest Normal University, Lanzhou 730070, China; (L.C.); (H.H.); (C.W.)
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24
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Luo X, Gong Y, Xu F, Wang S, Tao Y, Yang M. Soil horizons regulate bacterial community structure and functions in Dabie Mountain of the East China. Sci Rep 2023; 13:15866. [PMID: 37739984 PMCID: PMC10517015 DOI: 10.1038/s41598-023-42981-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
Soil bacterial communities regulate nutrient cycling and plant growth in forests. Although these bacterial communities vary with soil nutrients and plant traits, the variation and degree with soil horizons in different forest types remain unclear. Here, bacterial communities of 44 soil samples from organic horizon (O horizon) and mineral horizon (M horizon) of three forest types (Cunninghamia, broad-leaved and Pinus forests) in subtropical forests of Dabie Mountain, China were analyzed based on amplicon sequencing. We assessed the effects of soil horizons and forest types on bacterial communities. The results showed that the bacterial richness and diversity were significantly higher in the O horizon than in the M horizon. Furthermore, the bacterial community composition and functions were also remarkably different between the two soil horizons. Furthermore, forest types could affect bacterial community composition but not for diversity and functions. Moreover, soil organic matter, including the total organic carbon, available phosphorus, total organic nitrogen, available potassium, ammonium nitrogen, and pH were main drivers for bacterial community composition. The results propose robust evidence that soil horizons strongly driven bacterial community composition and diversity, and suggest that microhabitat of soil bacterial communities is important to maintain the stability of forest ecosystem.
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Affiliation(s)
- Xia Luo
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China.
| | - Yinping Gong
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
| | - Feiyan Xu
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
| | - Shuai Wang
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
| | - Yingying Tao
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
| | - Mengmeng Yang
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
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25
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Li P, Gu S, Zhu Y, Xu T, Yang Y, Wang Z, Deng X, Wang B, Li W, Mei W, Hu Q. Soil microbiota plays a key regulatory role in the outbreak of tobacco root rot. Front Microbiol 2023; 14:1214167. [PMID: 37779693 PMCID: PMC10540700 DOI: 10.3389/fmicb.2023.1214167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Root rot caused by the fungal pathogen Fusarium sp. poses significant challenges to tobacco cultivation in China, leading to major economic setbacks. The interplay between this pathogen and the wider soil microbial community remains poorly understood. Methods High-throughput sequencing technology was utilized to evaluate soil prokaryotic, fungal, and protistan communities. We compared microbial communities in infected soils to those in healthy soils from the same field. Additionally, the influence of pH on the microbial communities was assessed. Results Infected soils displayed elevated levels of soil nutrients but diminished observed richness across prokaryotic, fungal, and protistan groups. The pathogenic fungi Fusarium solani f sp. eumartii's abundance was notably increased in infected soils. Infection with F. solani significantly altered the soil's microbial community structure and interactions, manifested as a decrease in network scale and the number of keystone species. An evaluation of prokaryotes' role in F. solani's invasion revealed an increased number of connecting nodes in infected soils. Additionally, relationships between predatory protists and fungi were augmented, whereas predation on F. solani declined. Discussion The study underscores the significance of comprehending the interactions among soil microorganisms and brings to light the susceptibility of soil microbial communities to pathogen invasion. It offers insights into the multifaceted relationships and potential vulnerabilities within the soil ecosystem in the context of Fusarium sp. invasion.
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Affiliation(s)
- Pengfei Li
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Songsong Gu
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yanmei Zhu
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Tianyang Xu
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Yishuai Yang
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhengqiang Wang
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, Hunan, China
| | - Xiangdong Deng
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, Hunan, China
| | - Bin Wang
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Wei Li
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Wenqiang Mei
- Wenshan Tobacco Company of Yunnan Province, Wenshan, Yunnan, China
| | - Qiulong Hu
- College of Horticulture and Landscape Architecture, Hunan Agricultural University, Changsha, Hunan, China
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26
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Mattoo R, Mallikarjuna S. Soil microbiome influences human health in the context of climate change. Future Microbiol 2023; 18:845-859. [PMID: 37668469 DOI: 10.2217/fmb-2023-0098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023] Open
Abstract
Soil microbiomes continue to evolve and shape the human microbiota according to external anthropogenic and climate change effects. Ancient microbes are being exposed as a result of glacier melting, soil erosion and poor agricultural practices. Soil microbes subtly regulate greenhouse gas emissions and undergo profound alterations due to poor soil maintenance. This review highlights how the soil microbiome influences human digestion processes, mineral and vitamin production, mental health and mood stimulation. Although much about microbial functions remains unknown, increasing evidence suggests that beneficial soil microbes are vital for enhancing human tolerance to diseases and pathogens. Further research is essential to delineate the specific role of the soil microbiome in promoting human health, especially in light of the increasing anthropogenic pressures and changing climatic conditions.
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Affiliation(s)
- Rohini Mattoo
- Divecha Center for Climate Change, Indian Institute of Science, Bangalore, 560038, India
| | - Suman Mallikarjuna
- Divecha Center for Climate Change, Indian Institute of Science, Bangalore, 560038, India
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27
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Kim I, Chhetri G, So Y, Park S, Jung Y, Woo H, Seo T. Characterization and Antioxidant Activity of Exopolysaccharides Produced by Lysobacter soyae sp. nov Isolated from the Root of Glycine max L. Microorganisms 2023; 11:1900. [PMID: 37630460 PMCID: PMC10456730 DOI: 10.3390/microorganisms11081900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Microbial exopolysaccharides (EPSs) have attracted attention from several fields due to their high industrial applicability. In the present study, rhizosphere strain CJ11T was isolated from the root of Glycine max L. in Goyang-si, Republic of Korea, and a novel exopolysaccharide was purified from the Lysobacter sp. CJ11T fermentation broth. The exopolysaccharide's average molecular weight was 0.93 × 105 Da. Its monosaccharide composition included 72.2% mannose, 17.2% glucose, 7.8% galactose, and 2.8% arabinose. Fourier-transform infrared spectroscopy identified the exopolysaccharide carbohydrate polymer functional groups, and the structural properties were investigated using nuclear magnetic resonance. In addition, a microstructure of lyophilized EPS was determined by scanning electron microscopy. Using thermogravimetric analysis, the degradation of the exopolysaccharide produced by strain CJ11T was determined to be 210 °C. The exopolysaccharide at a concentration of 4 mg/mL exhibited 2,2-diphenyl-1-picrylhydrazyl free-radical-scavenging activity of 73.47%. Phylogenetic analysis based on the 16S rRNA gene sequencing results revealed that strain CJ11T was a novel isolate for which the name Lysobacter soyae sp. nov is proposed.
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Affiliation(s)
| | | | | | | | | | | | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea; (I.K.); (G.C.); (Y.S.); (S.P.); (Y.J.); (H.W.)
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28
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Eisenhauer N, Angst G, Asato AEB, Beugnon R, Bönisch E, Cesarz S, Dietrich P, Jurburg SD, Madaj AM, Reuben RC, Ristok C, Sünnemann M, Yi H, Guerra CA, Hines J. The heterogeneity-diversity-system performance nexus. Natl Sci Rev 2023; 10:nwad109. [PMID: 37575691 PMCID: PMC10423029 DOI: 10.1093/nsr/nwad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 03/24/2023] [Accepted: 04/16/2023] [Indexed: 08/15/2023] Open
Abstract
Ever-growing human population and nutritional demands, supply chain disruptions, and advancing climate change have led to the realization that changes in diversity and system performance are intimately linked. Moreover, diversity and system performance depend on heterogeneity. Mitigating changes in system performance and promoting sustainable living conditions requires transformative decisions. Here, we introduce the heterogeneity-diversity-system performance (HDP) nexus as the conceptual basis upon which to formulate transformative decisions. We suggest that managing the heterogeneity of systems will best allow diversity to provide multiple benefits to people. Based on ecological theory, we pose that the HDP nexus is broadly applicable across systems, disciplines, and sectors, and should thus be considered in future decision making as a way to have a more sustainable global future.
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Affiliation(s)
- Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
| | - Gerrit Angst
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
- Institute of Soil Biology and Biogeochemistry, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 37005, České Budějovice, Czech Republic
| | - Ana E B Asato
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
| | - Rémy Beugnon
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Leipzig Institute for Meteorology, Universität Leipzig, Stephanstraße 3, Leipzig 04103, Germany
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919, route de Mende, F-34293 Montpellier, Cedex 5, France
| | - Elisabeth Bönisch
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
| | - Peter Dietrich
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
| | - Stephanie D Jurburg
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig 04318, Germany
| | - Anna-Maria Madaj
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
| | - Rine C Reuben
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
| | - Christian Ristok
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
| | - Marie Sünnemann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
| | - Huimin Yi
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
| | - Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
| | - Jes Hines
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Puschstr. 4, Leipzig 04103Germany
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Yang R, Yang Z, Yang S, Chen LL, Xin J, Xu L, Zhang X, Zhai B, Wang Z, Zheng W, Li Z. Nitrogen inhibitors improve soil ecosystem multifunctionality by enhancing soil quality and alleviating microbial nitrogen limitation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163238. [PMID: 37011677 DOI: 10.1016/j.scitotenv.2023.163238] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 05/27/2023]
Abstract
Soil quality (SQI) is a comprehensive indicator reflecting the agricultural productivity of soil, and soil ecosystem multifunctionality (performing multiple functions simultaneously; EMF) can reflect complex biogeochemical processes. However, the effects of enhanced efficiency nitrogen fertilizers (EENFs; urease inhibitors (NBPT), nitrification inhibitors (DCD), and coated controlled-release urea (RCN)) application on the SQI and soil EMF and their relationships are still unclear. Therefore, we conducted a field experiment to study the effects of different EENFs on the SQI, enzyme stoichiometry and soil EMF in semiarid areas of Northwest China (Gansu, Ningxia, Shaanxi, Shanxi). Across the four study sites, DCD and NBPT increased SQI by 7.61-16.80 % and 2.61 %-23.20 % compared to mineral fertilizer, respectively. N fertilizer application (N200 and EENFs) alleviated microbial N limitation, and EENFs alleviated microbial N and C limitations to a greater extent in Gansu and Shanxi. Moreover, nitrogen inhibitors (Nis; DCD and NBPT) improved the soil EMF to a greater extent than N200 and RCN, DCD increased by 205.82-340.00 % and 145.00-215.47 % in Gansu and Shanxi, respectively; NBPT increased by 332.75-778.59 % and 364.44-929.62 % in Ningxia and Shanxi, respectively. A random forest model showed that the microbial biomass carbon (MBC), microbial biomass nitrogen (MBN) and soil water content (SWC) of the SQI factors were the main driving forces of soil EMF. Moreover, SQI improvement could alleviate microbial C and N limitations and promote the improvement of soil EMF. It is worth noting that soil EMF was mainly affected by microbial N limitation rather than C limitation. Overall, NIs application is an effective way to improve the SQI and soil EMF in the semiarid region of Northwest China.
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Affiliation(s)
- Ruizhe Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Ze Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Shilong Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Lan-Lan Chen
- College of Resources and Environmental Sciences, Gansu Agricultural University/Gansu Provincial Key Laboratory of Arid-land Crop Science, Lanzhou 730070, PR China
| | - Jia Xin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Changshu National Agro-Ecosystem Observation and Research Station, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Lingying Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Changshu National Agro-Ecosystem Observation and Research Station, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xuechen Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Bingnian Zhai
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Zhaohui Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Wei Zheng
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China.
| | - Ziyan Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China.
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30
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Roy J, Reichel R, Brüggemann N, Rillig MC. Functional, not Taxonomic, Composition of Soil Fungi Reestablishes to Pre-mining Initial State After 52 Years of Recultivation. MICROBIAL ECOLOGY 2023; 86:213-223. [PMID: 35821127 PMCID: PMC10293406 DOI: 10.1007/s00248-022-02058-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Open-cast mining leads to the loss of naturally developed soils and their ecosystem functions and services. Soil restoration after mining aims to restore the agricultural productivity in which the functions of the fungal community play a crucial role. Whether fungi reach a comparable functional state as in the soil before mining within half a century of recultivation is still unanswered. Here, we characterised the soil fungal community using ITS amplicon Illumina sequencing across a 52-year chronosequence of agricultural recultivation after open-cast mining in northern Europe. Both taxonomic and functional community composition showed profound shifts over time, which could be attributed to the changes in nutrient status, especially phosphorus availability. However, taxonomic composition did not reach the pre-mining state, whereas functional composition did. Importantly, we identified a positive development of arbuscular mycorrhizal root fungal symbionts after the initial three years of alfalfa cultivation, followed by a decline after conversion to conventional farming, with arbuscular mycorrhizal fungi being replaced by soil saprobes. We conclude that appropriate agricultural management can steer the fungal community to its functional pre-mining state despite stochasticity in the reestablishment of soil fungal communities. Nonetheless, conventional agricultural management results in the loss of plant symbionts, favouring non-symbiotic fungi.
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Affiliation(s)
- Julien Roy
- Institut Für Biologie, Ökologie Der Pflanzen, Freie Universität Berlin, 14195, Berlin, Germany.
- Brandenburg Institute of Advanced Biodiversity Research, 14195, Berlin, Germany.
| | - Rüdiger Reichel
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Agrosphere (IBG-3), 52425, Jülich, Germany
| | - Nicolas Brüggemann
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Agrosphere (IBG-3), 52425, Jülich, Germany
| | - Matthias C Rillig
- Institut Für Biologie, Ökologie Der Pflanzen, Freie Universität Berlin, 14195, Berlin, Germany
- Brandenburg Institute of Advanced Biodiversity Research, 14195, Berlin, Germany
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31
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Meng J, Li W, Diao C, Li Z, Zhao J, Haider G, Zhang H, Xu J, Hu M, Shan S, Chen H. Microplastics drive microbial assembly, their interactions, and metagenomic functions in two soils with distinct pH and heavy metal availability. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131973. [PMID: 37406526 DOI: 10.1016/j.jhazmat.2023.131973] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/01/2023] [Accepted: 06/28/2023] [Indexed: 07/07/2023]
Abstract
Microplastics (MPs) have emerged as widely existing global environmental concerns in terrestrial ecosystems. However, the mechanisms that how MPs are affecting soil microbes and their metagenomic functioning is currently uncertain. Herein, we investigated the response mechanisms of bacterial and fungal communities as well as the metagenomic functions to the addition of MPs in two soils with distinct pH and heavy metals. In this study, the acidic soil (Xintong) and the neutral soil (Huanshan) contaminated by heavy metals were incubated with Polyvinyl Chloride (PVC) MPs at ratios of 2.5% and 5% on 60 and 120 days. We aimed to evaluate the responding, assembly, and interactions of the metagenomic taxonomy and function. Results showed that only in the acidic soil, PVC MPs significantly increased soil pH and decreased CaCl2-extractable heavy metals, and also reduced bacterial alpha diversity and interaction networks. The relative proportions of Proteobacteria and Bacteroidota in bacteria, and Mortierellomycota in fungi, were increased, but Chloroflexi and Acidobacteriota in bacteria, Ascomycota and Basidiomycota in fungi, were significantly decreased by PVC MPs. Metagenomic functions related to C cycling were repressed but the nutrient cycles were enriched with PVC MPs. In conclusion, our study suggests that the addition of PVC MPs could shift soil microbial community and metagenomic functioning, as well as increasing soil pH and reduced heavy metal availability.
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Affiliation(s)
- Jun Meng
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environment and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Wenjin Li
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environment and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Chengmei Diao
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environment and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Zhangtao Li
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environment and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
| | - Ghulam Haider
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Haibo Zhang
- Zhejiang Province Key Laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Jun Xu
- Agricultural Technology Extension Center of Fuyang District, Hangzhou, Zhejiang 311400, China
| | - Minjun Hu
- Agricultural Technology Extension Center of Fuyang District, Hangzhou, Zhejiang 311400, China
| | - Shengdao Shan
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environment and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
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32
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Ye C, Wang S, Wang Y, Zhou T, Li R. Impacts of human pressure and climate on biodiversity-multifunctionality relationships on the Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2023; 14:1106035. [PMID: 37332689 PMCID: PMC10270690 DOI: 10.3389/fpls.2023.1106035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/28/2023] [Indexed: 06/20/2023]
Abstract
Many studies have investigated the effects of environmental context on biodiversity or multifunctionality in alpine regions, but it is uncertain how human pressure and climate may affect their relationships. Here, we combined the comparative map profile method with multivariate datasets to assess the spatial pattern of ecosystem multifunctionality and further identify the effects of human pressure and climate on the spatial distribution of biodiversity-multifunctionality relationships in alpine ecosystems of the Qinghai-Tibetan Plateau (QTP). Our results indicate that at least 93% of the areas in the study region show a positive correlation between biodiversity and ecosystem multifunctionality across the QTP. Biodiversity-multifunctionality relationships with increasing human pressure show a decreasing trend in the forest, alpine meadow, and alpine steppe ecosystems, while an opposite pattern was found in the alpine desert steppe ecosystem. More importantly, aridity significantly strengthened the synergistic relationship between biodiversity and ecosystem multifunctionality in forest and alpine meadow ecosystems. Taken together, our results provide insights into the importance of protecting and maintaining biodiversity and ecosystem multifunctionality in response to climate change and human pressure in the alpine region.
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Affiliation(s)
- Chongchong Ye
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Shuai Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Yi Wang
- School of Life Sciences and State Key Lab of Biological Control, Sun Yat-sen University, Guangzhou, China
| | - Tiancai Zhou
- Synthesis Research Centre of Chinese Ecosystem Research Network, Key Laboratory of Ecosystem Network Observation and Modelling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Ruowei Li
- College of Grassland, Resource and Environment, Inner Mongolia Agricultural University, Hohhot, China
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33
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Timmusk S, Pall T, Raz S, Fetsiukh A, Nevo E. The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology. Front Microbiol 2023; 14:1141862. [PMID: 37275175 PMCID: PMC10235605 DOI: 10.3389/fmicb.2023.1141862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/28/2023] [Indexed: 06/07/2023] Open
Abstract
Global climate change poses challenges to land use worldwide, and we need to reconsider agricultural practices. While it is generally accepted that biodiversity can be used as a biomarker for healthy agroecosystems, we must specify what specifically composes a healthy microbiome. Therefore, understanding how holobionts function in native, harsh, and wild habitats and how rhizobacteria mediate plant and ecosystem biodiversity in the systems enables us to identify key factors for plant fitness. A systems approach to engineering microbial communities by connecting host phenotype adaptive traits would help us understand the increased fitness of holobionts supported by genetic diversity. Identification of genetic loci controlling the interaction of beneficial microbiomes will allow the integration of genomic design into crop breeding programs. Bacteria beneficial to plants have traditionally been conceived as "promoting and regulating plant growth". The future perspective for agroecosystems should be that microbiomes, via multiple cascades, define plant phenotypes and provide genetic variability for agroecosystems.
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Affiliation(s)
- Salme Timmusk
- Department of Forest Mycology and Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Taavi Pall
- Estonian Health Care Board Department of Gene Technology, Tallinn, Estonia
| | - Shmuel Raz
- Department of Information Systems, University of Haifa, Haifa, Israel
| | - Anastasiia Fetsiukh
- Department of Forest Mycology and Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, Israel
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34
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Umair M, Hu X, Cheng Q, Ali S, Ni J. Distribution patterns of fern species richness along elevations the Tibetan Plateau in China: regional differences and effects of climate change variables. FRONTIERS IN PLANT SCIENCE 2023; 14:1178603. [PMID: 37229119 PMCID: PMC10203567 DOI: 10.3389/fpls.2023.1178603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 05/27/2023]
Abstract
Because of its distinct geological history, frigid temperature, and rich biodiversity, the Tibetan Plateau gives an excellent opportunity to assess the effect of climate change on determining species richness. The distribution patterns of fern species richness and their underlying processes have long been a matter of debate in ecology research, with various hypotheses suggested over the years. Here, we explore richness patterns of fern species in Xizang on the southern and western Tibetan Plateau along an elevational gradient (100-5300 m a.s.l.) and evaluate climatic factors causing the spatial decrease and increase of fern species richness. We used regression and correlation analyses to relate the species richness with elevation and climatic variables. Throughout our research, we identified 441 fern species from 97 genera and 30 families. The Dryopteridaceae family (S = 97) has the highest number of species. All energy-temperature and moisture variables except drought index (DI) had a significant correlation with elevation. The altitude has a unimodal relationship with fern species, and the species richness is the largest at an altitude of 2500 m. The horizontal richness pattern of fern species on the Tibetan Plateau also showed that areas of extremely high species richness are mainly distributed in Zayü and Mêdog County, with an average elevation of 2800 m and 2500 m, respectively. The richness of fern species has a log-linear relationship with moisture-related factors such as moisture index (MI), mean annual precipitation (MAP), and drought index (DI). Because the peak corresponds spatially with the MI index, the unimodal patterns confirm the significance of moisture on fern distributions. Our results showed that mid-altitudes have the highest species richness (high MI), but high elevations have lower richness due to high solar radiation, and low elevations have lower richness due to high temperatures and low precipitation. Twenty-two of the total species are classified as nearly threatened, vulnerable or critically endangered, and varied in elevation from 800 m to 4200 m. Such relationships between the distribution and richness of fern species and climates on the Tibetan Plateau can provide data support for future predictions of the impacts of climate change scenarios on fern species, the ecological protection of representative fern species, and references for the planning and construction of nature reserves in the future.
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Affiliation(s)
| | | | | | | | - Jian Ni
- *Correspondence: Muhammad Umair, ; Jian Ni,
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35
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Agache I, Laculiceanu A, Spanu D, Grigorescu D. The Concept of One Health for Allergic Diseases and Asthma. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2023; 15:290-302. [PMID: 37188486 DOI: 10.4168/aair.2023.15.3.290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/05/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023]
Abstract
The worldwide prevalence of allergic disease is rising as a result of complex gene-environment interactions that shape the immune system and host response. Climate change and loss of biodiversity are existential threats to humans, animals, plants, and ecosystems. While there is significant progress in the development of targeted therapeutic options to treat allergies and asthma, these approaches are inadequate to meet the challenges faced by climate change. The exposomic approach is needed with the recognition of the bidirectional effect between human beings and the environment. All stakeholders need to work together toward mitigating the effects of climate change and promoting a One Health concept in order to decrease the burden of asthma and allergy and to improve immune health. Healthcare professionals should strive to incorporate One Health counseling, environmental health precepts, and advocacy into their practice.
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Affiliation(s)
- Ioana Agache
- Faculty of Medicine, Transylvania University, Brasov, Romania.
| | | | - Daniela Spanu
- Faculty of Medicine, Transylvania University, Brasov, Romania
| | - Dan Grigorescu
- Faculty of Medicine, Transylvania University, Brasov, Romania
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36
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Leal Filho W, Nagy GJ, Setti AFF, Sharifi A, Donkor FK, Batista K, Djekic I. Handling the impacts of climate change on soil biodiversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161671. [PMID: 36657677 DOI: 10.1016/j.scitotenv.2023.161671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
Land as a whole, and soil, in particular, plays a critical function in the climate system. The various types of land use, especially agriculture and forestry, account for nearly a quarter of the greenhouse gas emissions. On the other hand, the world's soil is under pressure from many factors, including climate change and land use change. Increases in temperature, prolonged drought and floods put pressure on the soil. In order to contribute to a better understanding of these interactions, we conducted a review combining a narrative-focused approach, selecting examples worldwide, and a bibliometric analysis (VosViewer software). This review reports on a study that analyses how climate change and land use change may negatively influence soil biodiversity and related services. It also outlines some of the actions needed to increase the resilience of soil biodiversity in the context of a changing climate. Some key findings are: 1) Well-managed soils are critical for resilient production systems. 2) Integrated agricultural production systems have gained prominence as climate-resilient production systems. 3) Agricultural zoning may be a valuable tool in integrated systems to minimise the effects of climate change. However, it is vital to continuously monitor environmental variations so producers can be more prepared for climate change and extreme events. Finally, adequate water management is essential for soil functioning under climate change aggravating water scarcity. An intersectoral approach between critical sectors facilitates comprehensive water management.
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Affiliation(s)
- Walter Leal Filho
- Department of Natural Sciences, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, UK; European School of Sustainability Science and Research, Hamburg University of Applied Sciences, Germany.
| | - Gustavo J Nagy
- Instituto de Ecología y Ciencias Ambientales (IECA), Universidad de la República (UdelaR), Montevideo 11400, Uruguay.
| | - Andréia Faraoni Freitas Setti
- Department of Biology & CESAM Centre for Environmental and Marine Studies, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Ayyoob Sharifi
- Graduate School of Humanities and Social Sciences and Network for Education and Research on Peace and Sustainability, Hiroshima University, Higashi, Hiroshima 739-8530, Japan.
| | - Felix Kwabena Donkor
- College of Agriculture & Environmental Sciences (CAES), University of South Africa (UNISA), 28 Pioneer Ave, Florida Park, Roodepoort 1709, South Africa
| | - Karina Batista
- Instituto de Zootecnia, Agência Paulista de Tecnologia dos Agronegócios, Secretaria de Agricultura e Abastecimento do Estado de São Paulo, 56 Heitor Penteado St. Centro, Zip Code: 13.460-000 Nova Odessa, SP, Brazil
| | - Ilija Djekic
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, Zemun, 11080 Belgrade, Serbia.
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37
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Louisson Z, Hermans SM, Buckley HL, Case BS, Taylor M, Curran-Cournane F, Lear G. Land use modification causes slow, but predictable, change in soil microbial community composition and functional potential. ENVIRONMENTAL MICROBIOME 2023; 18:30. [PMID: 37024971 PMCID: PMC10080853 DOI: 10.1186/s40793-023-00485-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/19/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Bacterial communities are critical to ecosystem functioning and sensitive to their surrounding physiochemical environment. However, the impact of land use change on microbial communities remains understudied. We used 16S rRNA gene amplicon sequencing and shotgun metagenomics to assess soil microbial communities' taxonomic and functional responses to land use change. We compared data from long-term grassland, exotic forest and horticulture reference sites to data from sites that transitioned from (i) Grassland to exotic forest or horticulture and from (ii) Exotic forest to grassland. RESULTS Community taxonomic and functional profiles of the transitional sites significantly differed from those within reference sites representing both their historic and current land uses (P < 0.001). The bacterial communities in sites that transitioned more recently were compositionally more similar to those representing their historic land uses. In contrast, the composition of communities from sites exposed to older conversion events had shifted towards the compositions at reference sites representing their current land use. CONCLUSIONS Our study indicates that microbial communities respond in a somewhat predictable way after a land use conversion event by shifting from communities reflecting their former land use towards those reflecting their current land use. Our findings help us to better understand the legacy effects of land use change on soil microbial communities and implications for their role in soil health and ecosystem functioning. Understanding the responsiveness of microbial communities to environmental disturbances will aid us in incorporating biotic variables into soil health monitoring techniques in the future.
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Affiliation(s)
- Z. Louisson
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010 New Zealand
| | - S. M. Hermans
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland, 1010 New Zealand
| | - H. L. Buckley
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland, 1010 New Zealand
| | - B. S. Case
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland, 1010 New Zealand
| | - M. Taylor
- Waikato Regional Council, 160 Ward St, Hamilton, 3204 New Zealand
| | - F. Curran-Cournane
- Joint Evidence Data and Insights, Ministry for the Environment, 45 Queens Street, Auckland, 1010 New Zealand
| | - G. Lear
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010 New Zealand
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Graham EB, Knelman JE. Implications of Soil Microbial Community Assembly for Ecosystem Restoration: Patterns, Process, and Potential. MICROBIAL ECOLOGY 2023; 85:809-819. [PMID: 36735065 DOI: 10.1007/s00248-022-02155-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/02/2022] [Indexed: 05/04/2023]
Abstract
While it is now widely accepted that microorganisms provide essential functions in restoration ecology, the nature of relationships between microbial community assembly and ecosystem recovery remains unclear. There has been a longstanding challenge to decipher whether microorganisms facilitate or simply follow ecosystem recovery, and evidence for each is mixed at best. We propose that understanding microbial community assembly processes is critical to understanding the role of microorganisms during ecosystem restoration and thus optimizing management strategies. We examine how the connection between environment, community structure, and function is fundamentally underpinned by the processes governing community assembly of these microbial communities. We review important factors to consider in evaluating microbial community structure in the context of ecosystem recovery as revealed in studies of microbial succession: (1) variation in community assembly processes, (2) linkages to ecosystem function, and (3) measurable microbial community attributes. We seek to empower restoration ecology with microbial assembly and successional understandings that can generate actionable insights and vital contexts for ecosystem restoration efforts.
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Affiliation(s)
- Emily B Graham
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
- School of Biological Sciences, Washington State University, Richland, WA, USA.
| | - Joseph E Knelman
- Institute for Arctic and Alpine Research, University of Colorado, Boulder, CO, USA
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39
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Bonato Asato AE, Wirth C, Eisenhauer N, Hines J. On the phenology of soil organisms: Current knowledge and future steps. Ecol Evol 2023; 13:e10022. [PMID: 37113518 PMCID: PMC10126832 DOI: 10.1002/ece3.10022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Phenology is the study of timing of periodic activities in biological life cycles. It describes an inherent component of ecosystem dynamics, and shifts in biological activity have been increasingly recognized as an indicator of global change. Although phenology is mainly studied above the ground, major ecosystem processes, such as decomposition, mineralization, and nutrient cycling, are soil-dependent. Therefore, the phenology of soil organisms is a crucial, but understudied, aspect of terrestrial ecosystem functioning. We performed a systematic review of 96 studies, which reported 228 phenological observations, to evaluate the current knowledge of soil microbial and animal phenology. Despite the increasing number of soil phenology reports, most research is still concentrated in a few countries (centered in the Northern Hemisphere) and taxa (microbiota), with significant gaps in the most diverse regions of the globe (i.e., tropics) and important taxa (e.g., ants, termites, and earthworms). Moreover, biotic predictors (e.g., biodiversity and species interactions) have rarely been considered as possible drivers of soil organisms' phenology. We present recommendations for future soil phenology research based on an evaluation of the reported geographical, taxonomic, and methodologic trends that bias current soil phenology research. First, we highlight papers that depict good soil phenology practice, either regarding the research foci, methodological approaches, or results reporting. Then, we discuss the gaps, challenges, and opportunities for future research. Overall, we advocate that focusing both on highly diverse ecosystems and key soil organisms, while testing for the direct and indirect effects of biodiversity loss and climatic stressors, could increase our knowledge of soil functioning and enhance the accuracy of predictions depicting the effects of global change on terrestrial ecosystem functioning as a whole.
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Affiliation(s)
- Ana E Bonato Asato
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
- Institute of Biology Leipzig University Leipzig Germany
| | - Christian Wirth
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
- Institute of Biology Leipzig University Leipzig Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
- Institute of Biology Leipzig University Leipzig Germany
| | - Jes Hines
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
- Institute of Biology Leipzig University Leipzig Germany
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40
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Gong X, Shi S, Li X, Chen X, Sun J, Hu F, Liu M, Delgado-Baquerizo M. Fauna-microbe diversity coupling lost in agricultural soils: Implications from the bacteria hidden in earthworm gut. FUNDAMENTAL RESEARCH 2023. [DOI: 10.1016/j.fmre.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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41
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Miyamoto H, Shigeta K, Suda W, Ichihashi Y, Nihei N, Matsuura M, Tsuboi A, Tominaga N, Aono M, Sato M, Taguchi S, Nakaguma T, Tsuji N, Ishii C, Matsushita T, Shindo C, Ito T, Kato T, Kurotani A, Shima H, Moriya S, Wada S, Horiuchi S, Satoh T, Mori K, Nishiuchi T, Miyamoto H, Kodama H, Hattori M, Ohno H, Kikuchi J, Hirai MY. An agroecological structure model of compost-soil-plant interactions for sustainable organic farming. ISME COMMUNICATIONS 2023; 3:28. [PMID: 37002405 PMCID: PMC10066230 DOI: 10.1038/s43705-023-00233-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023]
Abstract
Compost is used worldwide as a soil conditioner for crops, but its functions have still been explored. Here, the omics profiles of carrots were investigated, as a root vegetable plant model, in a field amended with compost fermented with thermophilic Bacillaceae for growth and quality indices. Exposure to compost significantly increased the productivity, antioxidant activity, color, and taste of the carrot root and altered the soil bacterial composition with the levels of characteristic metabolites of the leaf, root, and soil. Based on the data, structural equation modeling (SEM) estimated that amino acids, antioxidant activity, flavonoids and/or carotenoids in plants were optimally linked by exposure to compost. The SEM of the soil estimated that the genus Paenibacillus and nitrogen compounds were optimally involved during exposure. These estimates did not show a contradiction between the whole genomic analysis of compost-derived Paenibacillus isolates and the bioactivity data, inferring the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by the compost itself. These observations have provided information on the qualitative indicators of compost in complex soil-plant interactions and offer a new perspective for chemically independent sustainable agriculture through the efficient use of natural nitrogen.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan.
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan.
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan.
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan.
| | | | - Wataru Suda
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Naoto Nihei
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Fukushima, 960-1296, Japan
| | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Arisa Tsuboi
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | | | | | - Muneo Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Shunya Taguchi
- Center for Frontier Medical Engineering, Chiba University, Chiba, Chiba, 263-8522, Japan
| | - Teruno Nakaguma
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Naoko Tsuji
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Chitose Ishii
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Teruo Matsushita
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Chie Shindo
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Toshiaki Ito
- Keiyo Gas Energy Solution Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Tamotsu Kato
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Hideaki Shima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Shigeharu Moriya
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Satoshi Wada
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Sankichi Horiuchi
- Division of Gastroenterology and Hepatology, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa, Chiba, 277-8567, Japan
| | - Takashi Satoh
- Division of Hematology, Kitasato University School of Allied Health Sciences, Sagamihara, Kanagawa, 252-0373, Japan
| | - Kenichi Mori
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Takumi Nishiuchi
- Division of Integrated Omics research, Bioscience Core Facility, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
| | - Hisashi Miyamoto
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Miroku Co., Ltd., Kitsuki, Oita, 873-0021, Japan
| | - Hiroaki Kodama
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
| | - Masahira Hattori
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
- School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
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42
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Biogas Residues Improved Microbial Diversity and Disease Suppression Function under Extent Indigenous Soil Microbial Biomass. Life (Basel) 2023; 13:life13030774. [PMID: 36983929 PMCID: PMC10055779 DOI: 10.3390/life13030774] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/23/2023] [Accepted: 03/03/2023] [Indexed: 03/16/2023] Open
Abstract
Indigenous soil microbial biomass (ISMB) plays a key role in maintaining essential functions and biodiversity of soil health. One of the critical unknowns is how the indigenous microorganisms respond to different fertilizers which is directly related to agricultural production. Therefore, we used Mi-Seq sequencing and network analyses to compare the response of ISMB to biogas residue and chemical fertilizers. The results showed that crop production was profoundly influenced by levels of ISMB present and is further dependent on the strategy of fertilizer application. Higher ISMB primarily manifests through retention of richer microbial abundance, a balanced community structure, and tightened co-occurrence within a certain proportion of Nitrospirae, Rhizophlyctidaceae, and Gemmatimonadetes. Compared to chemical fertilizer, biogas residue resulted in higher production with more strongly linked nodes such as Actinobacteria, Chloroflexi and Gemmatimonadetes. Under the same level of ISMB, the microbial diversity was richer and co-occurrence was tighter when biogas residues were applied compared with chemical fertilizer. In addition, the higher level of ISMB with biogas residue applied had a lower abundance of potential fungal pathogens in both bulk and rhizosphere soil compared with chemical fertilizer. This study provides critical data to understand the influence of ISMB and biogas residue on soil ecological system.
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43
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Shao Y, Wang Z, Liu T, Kardol P, Ma C, Hu Y, Cui Y, Zhao C, Zhang W, Guo D, Fu S. Drivers of nematode diversity in forest soils across climatic zones. Proc Biol Sci 2023; 290:20230107. [PMID: 36855871 PMCID: PMC9975660 DOI: 10.1098/rspb.2023.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/30/2023] [Indexed: 03/02/2023] Open
Abstract
Nematodes are the most abundant multi-cellular animals in soil, influencing key processes and functions in terrestrial ecosystems. Yet, little is known about the drivers of nematode abundance and diversity in forest soils across climatic zones. This is despite forests covering approximately 30% of the Earth's land surface, providing many crucial ecosystem services but strongly varying in climatic conditions and associated ecosystem properties across biogeographic zones. Here, we collected nematode samples from 13 forests across a latitudinal gradient. We divided this gradient into temperate, warm-temperate and tropical climatic zones and found that, across the gradient, nematode abundance and diversity were mainly influenced by soil organic carbon content. However, mean annual temperature and total soil phosphorus content in temperate zones, soil pH in warm-temperate zones, and mean annual precipitation in tropical zones were more important in driving nematode alpha-diversity, biomass and abundance. Additionally, nematode beta-diversity was higher in temperate than in warm-temperate and tropical zones. Together, our findings demonstrate that the drivers of nematode diversity in forested ecosystems are affected by the spatial scale and climatic conditions considered. This implies that high resolution studies are needed to accurately predict how soil functions respond if climate conditions move beyond the coping range of soil organisms.
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Affiliation(s)
- Yuanhu Shao
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Ministry of Education, College of Geography and Environmental Science, Henan University, Kaifeng, Henan 475004, People's Republic of China
| | - Zuyan Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Tao Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, People's Republic of China
| | - Paul Kardol
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Science, 756 51 Uppsala, Sweden
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 907 51 Umeå, Sweden
| | - Chengen Ma
- Center of Forest Ecosystem Studies and Qianyanzhou Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Yonghong Hu
- Key Laboratory of Digital Earth Science, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100094, People's Republic of China
| | - Yang Cui
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Ministry of Education, College of Geography and Environmental Science, Henan University, Kaifeng, Henan 475004, People's Republic of China
| | - Cancan Zhao
- International Joint Research Laboratory for Global Change Ecology, School of Life Sciences, Henan University, Kaifeng, Henan 475004, People's Republic of China
| | - Weixin Zhang
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Ministry of Education, College of Geography and Environmental Science, Henan University, Kaifeng, Henan 475004, People's Republic of China
| | - Dali Guo
- Center of Forest Ecosystem Studies and Qianyanzhou Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Shenglei Fu
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Ministry of Education, College of Geography and Environmental Science, Henan University, Kaifeng, Henan 475004, People's Republic of China
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Wang J, Shi X, Lucas-Borja ME, Guo Q, Mao J, Tan Y, Zhang G. Soil nematode abundances drive agroecosystem multifunctionality under short-term elevated CO 2 and O 3. GLOBAL CHANGE BIOLOGY 2023; 29:1618-1627. [PMID: 36458513 DOI: 10.1111/gcb.16546] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/23/2022] [Indexed: 05/28/2023]
Abstract
The response of soil biotas to climate change has the potential to regulate multiple ecosystem functions. However, it is still challenging to accurately predict how multiple climate change factors will affect multiple ecosystem functions. Here, we assessed the short-term responses of agroecosystem multifunctionality to a factorial combination of elevated CO2 (+200 ppm) and O3 (+40 ppb) and identified the key soil biotas (i.e., bacteria, fungi, protists, and nematodes) concerning the changes in the multiple ecosystem functions for two rice varieties (Japonica, Nanjing 5055 vs. Wuyujing 3). We provided strong evidence that combined treatment rather than individual treatments of short-term elevated CO2 and O3 significantly increased the agroecosystem multifunctionality index by 32.3% in the Wuyujing 3 variety, but not in the Nanjing 5055 variety. Soil biotas exhibited an important role in regulating multifunctionality under short-term elevated CO2 and O3 , with soil nematode abundances better explaining the changes in ecosystem multifunctionality than soil biota diversity. Furthermore, the higher trophic groups of nematodes, omnivores-predators served as the principal predictor of agroecosystem multifunctionality. These results provide unprecedented new evidence that short-term elevated CO2 and O3 can potentially affect agroecosystem multifunctionality through soil nematode abundances, especially omnivores-predators. Our study demonstrates that high trophic groups were specifically beneficial for regulating multiple ecosystem functions and highlights the importance of soil nematode communities for the maintenance of agroecosystem functions and health under climate change in the future.
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Affiliation(s)
- Jianqing Wang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Xiuzhen Shi
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Manuel Esteban Lucas-Borja
- Higher Technical School of Agricultural and Forestry Engineering, Castilla-La Mancha University, Albacete, Spain
| | - Qiling Guo
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Jiaoyan Mao
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Yunyan Tan
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Guoyou Zhang
- Key Laboratory of Agrometeorology of Jiangsu Province, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
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Rónavári A, Balázs M, Szilágyi Á, Molnár C, Kotormán M, Ilisz I, Kiricsi M, Kónya Z. Multi-round recycling of green waste for the production of iron nanoparticles: synthesis, characterization, and prospects in remediation. NANOSCALE RESEARCH LETTERS 2023; 18:8. [PMID: 36757485 PMCID: PMC9911567 DOI: 10.1186/s11671-023-03784-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/30/2023] [Indexed: 02/10/2023]
Abstract
Due to the widespread applications of metal nanoparticles (NPs), green synthesis strategies have recently advanced, e.g., methods that utilize extracts made from different plant wastes. A particularly innovative approach to reducing large amounts of available household/agricultural green wastes is their application in nanoparticle generation. Regarding this, the aim of our work was to examine the possibility of upgrading green nanoparticle syntheses from an innovative economic and environmental point of view, namely by investigating the multiple recyclabilities of green tea (GT), coffee arabica (CA), and Virginia creeper (Parthenocissus quinquefolia) (VC) waste residues for iron nanoparticle (FeNPs) synthesis. The plant extracts obtained by each extraction round were analyzed individually to determine the amount of main components anticipated to be involved in NPs synthesis. The synthesized FeNPs were characterized by X-ray powder diffraction and transmission electron microscopy. The activity of the generated FeNPs in degrading chlorinated volatile organic compounds (VOC) and thus their future applicability for remediation purposes were also assessed. We have found that VC and especially GT residues could be reutilized in multiple extraction rounds; however, only the first extract of CA was suitable for FeNPs' generation. All of the obtained FeNPs could degrade VOC with efficiencies GT1-Fe 91.0%, GT2-Fe 83.2%, GT3-Fe 68.5%; CA1-Fe 76.2%; VC1-Fe 88.2%, VC2-Fe 79.7%, respectively, where the number (as in GT3) marked the extraction round. These results indicate that the adequately selected green waste material can be reutilized in multiple rounds for nanoparticle synthesis, thus offering a clean, sustainable, straightforward alternative to chemical methods.
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Affiliation(s)
- Andrea Rónavári
- grid.9008.10000 0001 1016 9625Department of Applied and Environmental Chemistry, University of Szeged, Szeged, Hungary
| | - Margit Balázs
- Division for Biotechnology, Bay Zoltan Nonprofit Ltd. for Applied Research, Szeged, Hungary
| | - Árpád Szilágyi
- grid.9008.10000 0001 1016 9625Department of Biochemistry and Molecular Biology, University of Szeged, Közép fasor 52, Szeged, 6726 Hungary
| | - Csaba Molnár
- grid.516087.dKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Márta Kotormán
- grid.9008.10000 0001 1016 9625Department of Biochemistry and Molecular Biology, University of Szeged, Közép fasor 52, Szeged, 6726 Hungary
| | - István Ilisz
- grid.9008.10000 0001 1016 9625Institute of Pharmaceutical Analysis, University of Szeged, Szeged, Hungary
| | - Mónika Kiricsi
- Department of Biochemistry and Molecular Biology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.
| | - Zoltán Kónya
- grid.9008.10000 0001 1016 9625Department of Applied and Environmental Chemistry, University of Szeged, Szeged, Hungary ,ELKH-SZTE Reaction Kinetics and Surface Chemistry Research Group, Szeged, Hungary
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Zhao S, Zhang J, Feng SJ. The era of low-permeability sites remediation and corresponding technologies: A review. CHEMOSPHERE 2023; 313:137264. [PMID: 36400189 DOI: 10.1016/j.chemosphere.2022.137264] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Rational utilization of soil resources and remediation of contaminated soils are imperative due to the rapidly growing demand for clean soils. Currently, many in-situ remediation technologies are less suitable at low-permeability sites due to the limitations of soil permeability. This work defines a low-permeability site as a site with hydraulic conductivity less than 10-4 cm/s, and summarizes the migration characteristics of representative contaminants at low-permeability sites, and discusses the principles and practical applications of different technologies suitable for the remediation of low-permeability sites, including electrokinetic remediation technology, polymer flushing technology, fracturing technology, and in-situ thermal remediation technology. Enhanced and combined remediation technologies are further described because one remediation technology cannot remediate all contaminants. The prospects for the application of remediation technologies to low-permeability sites are also proposed. This work highlights the necessity of low-permeability sites remediation and the urgent need for new remediation technologies, with the hope to inspire future research on low-permeability sites.
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Affiliation(s)
- Shan Zhao
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai, 201306, China; College of Civil Engineering, Tongji University, Shanghai, 200092, China
| | - Jian Zhang
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai, 201306, China
| | - Shi-Jin Feng
- College of Civil Engineering, Tongji University, Shanghai, 200092, China.
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Su C, Wang J, Chen Z, Meng J, Yin G, Zhou Y, Wang T. Sources and health risks of heavy metals in soils and vegetables from intensive human intervention areas in South China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159389. [PMID: 36243077 DOI: 10.1016/j.scitotenv.2022.159389] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/30/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Heavy metal pollution greatly harms the soil environment and poses threats to food safety and human health. This study aimed to quantify and analyze the sources of heavy metals and assess the health risks associated with the human intake of contaminated vegetables in South China. Heavy metals (Cd, As, Hg, Cu, Ni, Pb, Zn, and Cr) in soil and vegetables (leaf vegetables, legume vegetables, and cucurbits) were investigated and evaluated for contamination. By combining the correlation analysis (CA), positive matrix factorization (PMF), and GeoDetector model, source apportionments were comprehensively identified. Results showed that Cd was the predominant element in soils throughout the study area. Industrial (28.36 %, 20.24 %, 31.50 %), agricultural (27.19 %, 46.50 %, 27.30 %), besides traffic, atmospheric deposition and natural sources were identified as the dominant sources of heavy metals in GD01, GD02, and GD03, respectively. The human health risk assessment showed that the total non-cancer risk of heavy metals (i.e., Cr, Ni, As, Cd, and Pb) ingested through vegetables was 2.3E+00 for children and 9.67E-01 for adults, and the total cancer risk for children was 2.54E-02 and 1.07E-02 for adults, both of which exceeded acceptable levels. It is worth noting that children are more susceptible to health risks due to the consumption of contaminated vegetables than adults.
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Affiliation(s)
- Chuanghong Su
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China
| | - Jianwen Wang
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China
| | - Zhenwei Chen
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China
| | - Jing Meng
- Key Laboratory of Environment Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Guangcai Yin
- Guangdong Industrial Contaminated Site Remediation Technology and Equipment, Engineering Research Center, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yunqiao Zhou
- Key Laboratory of Environment Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Tieyu Wang
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China.
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Miyamoto H, Kikuchi J. An evaluation of homeostatic plasticity for ecosystems using an analytical data science approach. Comput Struct Biotechnol J 2023; 21:869-878. [PMID: 36698969 PMCID: PMC9860287 DOI: 10.1016/j.csbj.2023.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/05/2023] Open
Abstract
The natural world is constantly changing, and planetary boundaries are issuing severe warnings about biodiversity and cycles of carbon, nitrogen, and phosphorus. In other views, social problems such as global warming and food shortages are spreading to various fields. These seemingly unrelated issues are closely related, but it can be said that understanding them in an integrated manner is still a step away. However, progress in analytical technologies has been recognized in various fields and, from a microscopic perspective, with the development of instruments including next-generation sequencers (NGS), nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC/MS), and liquid chromatography-mass spectrometry (LC/MS), various forms of molecular information such as genome data, microflora structure, metabolome, proteome, and lipidome can be obtained. The development of new technology has made it possible to obtain molecular information in a variety of forms. From a macroscopic perspective, the development of environmental analytical instruments and environmental measurement facilities such as satellites, drones, observation ships, and semiconductor censors has increased the data availability for various environmental factors. Based on these background, the role of computational science is to provide a mechanism for integrating and understanding these seemingly disparate data sets. This review describes machine learning and the need for structural equations and statistical causal inference of these data to solve these problems. In addition to introducing actual examples of how these technologies can be utilized, we will discuss how to use these technologies to implement environmentally friendly technologies in society.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa 230-0045, Japan
- Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co. Ltd., Chiba, Chiba 260-0034, Japan
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Jun Kikuchi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
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Abstract
The concept of one health highlights that human health is not isolated but connected to the health of animals, plants and environments. In this Review, we demonstrate that soils are a cornerstone of one health and serve as a source and reservoir of pathogens, beneficial microorganisms and the overall microbial diversity in a wide range of organisms and ecosystems. We list more than 40 soil microbiome functions that either directly or indirectly contribute to soil, plant, animal and human health. We identify microorganisms that are shared between different one health compartments and show that soil, plant and human microbiomes are perhaps more interconnected than previously thought. Our Review further evaluates soil microbial contributions to one health in the light of dysbiosis and global change and demonstrates that microbial diversity is generally positively associated with one health. Finally, we present future challenges in one health research and formulate recommendations for practice and evaluation.
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Affiliation(s)
- Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA.
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland. .,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
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Wang J, Shi X. Soil biodiversity in natural forests potentially exhibits higher resistance than planted forests under global warming. FRONTIERS IN PLANT SCIENCE 2023; 14:1135549. [PMID: 37188321 PMCID: PMC10177395 DOI: 10.3389/fpls.2023.1135549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 03/28/2023] [Indexed: 05/17/2023]
Affiliation(s)
- Jianqing Wang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Institute of Geography, Fujian Normal University, Fuzhou, China
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Xiuzhen Shi
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Institute of Geography, Fujian Normal University, Fuzhou, China
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
- *Correspondence: Xiuzhen Shi,
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