1
|
Xie ST, Zhu D, Song YQ, Zhu YG, Ding LJ. Unveiling potential roles of earthworms in mitigating the presence of virulence factor genes in terrestrial ecosystems. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135133. [PMID: 38986408 DOI: 10.1016/j.jhazmat.2024.135133] [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: 03/28/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Earthworms can redistribute soil microbiota, and thus might affect the profile of virulence factor genes (VFGs) which are carried by pathogens in soils. Nevertheless, the knowledge of VFG profile in the earthworm guts and its interaction with earthworm gut microbiome is still lacking. Herein, we characterized earthworm gut and soil microbiome and VFG profiles in natural and agricultural ecosystems at a national scale using metagenomics. VFG profiles in the earthworm guts significantly differed from those in the surrounding soils, which was mainly driven by variations of bacterial communities. Furthermore, the total abundance of different types of VFGs in the earthworm guts was about 20-fold lower than that in the soils due to the dramatic decline (also by approximately 20-fold) of VFG-carrying bacterial pathogens in the earthworm guts. Additionally, five VFGs related to nutritional/metabolic factors and stress survival were identified as keystones merely in the microbe-VFG network in the earthworm guts, implying their pivotal roles in facilitating pathogen colonization in earthworm gut microhabitats. These findings suggest the potential roles of earthworms in reducing risks related to the presence of VFGs in soils, providing novel insights into earthworm-based bioremediation of VFG contamination in terrestrial ecosystems.
Collapse
Affiliation(s)
- Shu-Ting Xie
- 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, 19A Yuquan Road, Beijing 100049, China
| | - Dong Zhu
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; 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
| | - Ya-Qiong Song
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Sino-Danish College of University of Chinese Academy of Sciences, Beijing 101400, China; Sino-Danish Centre for Education and Research, Beijing 100049, China; Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Yong-Guan Zhu
- 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, 19A Yuquan Road, Beijing 100049, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Jimei District, Xiamen 361021, China
| | - Long-Jun Ding
- 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, 19A Yuquan Road, Beijing 100049, China.
| |
Collapse
|
2
|
Fang K, Kou YP, Tang N, Liu J, Zhang XY, He HL, Xia RX, Zhao WQ, Li DD, Liu Q. Differential responses of soil bacteria, fungi and protists to root exudates and temperature. Microbiol Res 2024; 286:127829. [PMID: 39018940 DOI: 10.1016/j.micres.2024.127829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 06/30/2024] [Indexed: 07/19/2024]
Abstract
The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.
Collapse
Affiliation(s)
- Kai Fang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; College of Agriculture and Biological Sciences, Dali University, Dali 671003, China
| | - Yong-Ping Kou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China.
| | - Na Tang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Jia Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Xiao-Ying Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - He-Liang He
- College of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644007, China
| | - Rui-Xue Xia
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Wen-Qiang Zhao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Dan-Dan Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Qing Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China.
| |
Collapse
|
3
|
Carreira C, Lønborg C, Acharya B, Aryal L, Buivydaite Z, Borim Corrêa F, Chen T, Lorenzen Elberg C, Emerson JB, Hillary L, Khadka RB, Langlois V, Mason-Jones K, Netherway T, Sutela S, Trubl G, Wa Kang'eri A, Wang R, White RA, Winding A, Zhao T, Sapkota R. Integrating viruses into soil food web biogeochemistry. Nat Microbiol 2024:10.1038/s41564-024-01767-x. [PMID: 39095499 DOI: 10.1038/s41564-024-01767-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/19/2024] [Indexed: 08/04/2024]
Abstract
The soil microbiome is recognized as an essential component of healthy soils. Viruses are also diverse and abundant in soils, but their roles in soil systems remain unclear. Here we argue for the consideration of viruses in soil microbial food webs and describe the impact of viruses on soil biogeochemistry. The soil food web is an intricate series of trophic levels that span from autotrophic microorganisms to plants and animals. Each soil system encompasses contrasting and dynamic physicochemical conditions, with labyrinthine habitats composed of particles. Conditions are prone to shifts in space and time, and this variability can obstruct or facilitate interactions of microorganisms and viruses. Because viruses can infect all domains of life, they must be considered as key regulators of soil food web dynamics and biogeochemical cycling. We highlight future research avenues that will enable a more robust understanding of the roles of viruses in soil function and health.
Collapse
Affiliation(s)
- Cátia Carreira
- Department of Environmental Science, Aarhus University, Roskilde, Denmark.
- Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal.
| | | | - Basistha Acharya
- Directorate of Agricultural Research, Nepal Agricultural Research Council, Khajura, Nepal
| | - Laxman Aryal
- Nepal Agricultural Research Council, National Wheat Research Program, Bhairahawa, Nepal
| | - Zivile Buivydaite
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Felipe Borim Corrêa
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Tingting Chen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
- Department of Ecology, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | | | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
| | - Luke Hillary
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
| | - Ram B Khadka
- National Plant Pathology Research Center, Nepal Agricultural Research Council, Lalitpur, Nepal
| | - Valérie Langlois
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec City, Québec, Canada
| | - Kyle Mason-Jones
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Suvi Sutela
- Natural Resources Institute Finland, Helsinki, Finland
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | | | - Ruiqi Wang
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, the Netherlands
| | - Richard Allen White
- Computational Intelligence to Predict Health and Environmental Risks, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
- North Carolina Research Campus, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Anne Winding
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Tianci Zhao
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Rumakanta Sapkota
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| |
Collapse
|
4
|
Toyber I, Kumar R, Jami E. Rumen protozoa are a hub for diverse hydrogenotrophic functions. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13298. [PMID: 38961629 PMCID: PMC11222294 DOI: 10.1111/1758-2229.13298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/08/2024] [Indexed: 07/05/2024]
Abstract
Ciliate protozoa are an integral part of the rumen microbial community involved in a variety of metabolic processes. These processes are thought to be in part the outcome of interactions with their associated prokaryotic community. For example, methane production is enhanced through interspecies hydrogen transfer between protozoa and archaea. We hypothesize that ciliate protozoa are host to a stable prokaryotic community dictated by specific functions they carry. Here, we modify the microbial community by varying the forage-to-concentrate ratios and show that, despite major changes in the prokaryotic community, several taxa remain stably associated with ciliate protozoa. By quantifying genes belonging to various known reduction pathways in the rumen, we find that the bacterial community associated with protozoa is enriched in genes belonging to hydrogen utilization pathways and that these genes correspond to the same taxonomic affiliations seen enriched in protozoa. Our results show that ciliate protozoa in the rumen may serve as a hub for various hydrogenotrophic functions and a better understanding of the processes driven by different protozoa may unveil the potential role of ciliates in shaping rumen metabolism.
Collapse
Affiliation(s)
- Ido Toyber
- Department of Ruminant Science, Institute of Animal SciencesAgricultural Research Organization, Volcani CenterRishon LeZionIsrael
- Department of Animal Sciencethe Hebrew University of JerusalemRehovotIsrael
| | - Raghawendra Kumar
- Department of Ruminant Science, Institute of Animal SciencesAgricultural Research Organization, Volcani CenterRishon LeZionIsrael
| | - Elie Jami
- Department of Ruminant Science, Institute of Animal SciencesAgricultural Research Organization, Volcani CenterRishon LeZionIsrael
| |
Collapse
|
5
|
Sun S, Liu C, Zhang Y, Yue Y, Sun S, Bai Y, Zhang P, Ravanbakhsh M, Dini-Andreote F, Li R, Zhang Z, Jousset A, Shen Q, A Kowalchuk G, Xiong W. Divergent impacts of fertilization regimes on below-ground prokaryotic and eukaryotic communities in the Tibetan Plateau. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 364:121379. [PMID: 38870787 DOI: 10.1016/j.jenvman.2024.121379] [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: 12/17/2023] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 06/15/2024]
Abstract
Chemical nutrient amendment by human activities can lead to environmental impacts contributing to global biodiversity loss. However, the comprehensive understanding of how below- and above-ground biodiversity shifts under fertilization regimes in natural ecosystems remains elusive. Here, we conducted a seven-year field experiment (2011-2017) and examined the effects of different fertilization on plant biodiversity and soil belowground (prokaryotic and eukaryotic) communities in the alpine meadow of the Tibetan Plateau, based on data collected in 2017. Our results indicate that nitrogen addition promoted total plant biomass but reduced the plant species richness. Conversely, phosphorus enrichment did not promote plant biomass and exhibited an unimodal pattern with plant richness. In the belowground realm, distinct responses of soil prokaryotic and eukaryotic communities were observed under fertilizer application. Specifically, soil prokaryotic diversity decreased with nitrogen enrichment, correlating with shifts in soil pH. Similarly, soil eukaryotic diversity decreased with increased phosphorous inputs, aligning with the equilibrium between soil available and total phosphorus. We also established connections between these soil organism communities with above-ground plant richness and biomass. Overall, our study contributes to a better understanding of the sustainable impacts of human-induced nutrient enrichment on the natural environment. Future research should delve deeper into the long-term effects of fertilization on soil health and ecosystem functioning, aiming to achieve a balance between agricultural productivity and environmental conservation.
Collapse
Affiliation(s)
- Shuo Sun
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Chen Liu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yun Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yang Yue
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Shiqi Sun
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yang Bai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu Province, People's Republic of China
| | - Pengfei Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu Province, People's Republic of China; Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA.
| | - Mohammadhossein Ravanbakhsh
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Rong Li
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Zhenhua Zhang
- Key Laboratory of Biodiversity and Biosafety, Nanjing Institute of Environmental Sciences, Nanjing, People's Republic of China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands
| | - Wu Xiong
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| |
Collapse
|
6
|
Hu Y, Zhang H, Sun X, Zhang B, Wang Y, Rafiq A, Jia H, Liang C, An S. Impact of grassland degradation on soil multifunctionality: Linking to protozoan network complexity and stability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172724. [PMID: 38663601 DOI: 10.1016/j.scitotenv.2024.172724] [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: 02/08/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
Soil protozoa, as predators of microbial communities, profoundly influence multifunctionality of soils. Understanding the relationship between soil protozoa and soil multifunctionality (SMF) is crucial to unraveling the driving mechanisms of SMF. However, this relationship remains unclear, particularly in grassland ecosystems that are experiencing degradation. By employing 18S rRNA gene sequencing and network analysis, we examined the diversity, composition, and network patterns of the soil protozoan community along a well-characterized gradient of grassland degradation at four alpine sites, including two alpine meadows (Cuona and Jiuzhi) and two alpine steppes (Shuanghu and Gonghe) on the Qinghai-Tibetan Plateau. Our findings showed that grassland degradation decreased SMF for 1-2 times in all four sites but increased soil protozoan diversity (Shannon index) for 13.82-298.01 % in alpine steppes. Grassland degradation-induced changes in soil protozoan composition, particularly to the Intramacronucleata with a large body size, were consistently observed across all four sites. The enhancing network complexity (average degree), stability (robustness), and cooperative relationships (positive correlation) are the responses of protozoa to grassland degradation. Further analyses revealed that the increased network complexity and stability led to a decrease in SMF by affecting microbial biomass. Overall, protozoa increase their diversity and strengthen their cooperative relationships to resist grassland degradation, and emphasize the critical role of protozoan network complexity and stability in regulating SMF. Therefore, not only protozoan diversity and composition but also their interactions should be considered in evaluating SMF responses to grassland degradation, which has important implications for predicting changes in soil function under future scenarios of anthropogenic change.
Collapse
Affiliation(s)
- Yang Hu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China; College of Resources and Environment, Xinjiang Agricultural University, Urumqi 830052, China
| | - Haolin Zhang
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Xinya Sun
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Bicheng Zhang
- Institute of Soil and Water Conservation, CAS & MWR, Yangling, Shannxi 712100, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Yubin Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Anum Rafiq
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Hongtao Jia
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi 830052, China
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China.
| |
Collapse
|
7
|
Berlinches de Gea A, Geisen S, Grootjans F, Wilschut RA, Schwelm A. Species-specific predation determines the feeding impacts of six soil protist species on bacterial and eukaryotic prey. Eur J Protistol 2024; 94:126090. [PMID: 38795654 DOI: 10.1016/j.ejop.2024.126090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/28/2024]
Abstract
Predatory protists play a central role in nutrient cycling and are involved in other ecosystem functions by predating the microbiome. While most soil predatory protist species arguably are bacterivorous, some protist species can prey on eukaryotes. However, studies about soil protist feeding mainly focused on bacteria as prey and rarely tested both bacteria and eukaryotes as potential prey. In this study, we aimed to decipher soil predator-prey interactions of three amoebozoan and three heterolobosean soil protists and potential bacterial (Escherichia coli; 0.5-1.5 µm), fungal (Saccharomyces cerevisiae; 5-7 µm) and protist (Plasmodiophora brassicae; 3-5 µm) prey, either as individual prey or in all their combinations. We related protist performance (relative abundance) and prey consumption (qPCR) to the protist phylogenetic group and volume. We showed that for the six soil protist predators, the most suitable prey was E. coli, but some species also grew on P. brassicae or S. cerevisiae. While protist relative abundances and growth rates depended on prey type in a protist species-specific manner, phylogenetic groups and volume affected prey consumption. Yet we conclude that protist feeding patterns are mainly species-specific and that some known bacterivores might be more generalist than expected, even preying on eukaryotic plant pathogens such as P. brassicae.
Collapse
Affiliation(s)
- Alejandro Berlinches de Gea
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands.
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Franka Grootjans
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Rutger A Wilschut
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Arne Schwelm
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands; TEAGASC - The Agriculture and Food Development Authority Department of Crops, Environment & Land Use, Wexford, Ireland.
| |
Collapse
|
8
|
Li YM, Wang YM, Qiu GW, Yu HJ, Liu FM, Wang GL, Duan Y. Conservation tillage facilitates the accumulation of soil organic carbon fractions by affecting the microbial community in an eolian sandy soil. Front Microbiol 2024; 15:1394179. [PMID: 38881670 PMCID: PMC11176501 DOI: 10.3389/fmicb.2024.1394179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/13/2024] [Indexed: 06/18/2024] Open
Abstract
Conservation tillage (CT) is an important agronomic measure that facilitates soil organic carbon (SOC) accumulation by reducing soil disturbance and plant residue mulching, thus increasing crop yields, improving soil fertility and achieving C neutrality. However, our understanding of the microbial mechanism underlying SOC fraction accumulation under different tillage practices is still lacking. Here, a 6-year in situ field experiment was carried out to explore the effects of CT and traditional tillage (CK) practices on SOC fractions in an eolian sandy soil. Compared with CK, CT increased the particulate OC (POC) content in the 0-30 cm soil layer and the mineral-associated OC (MAOC) content in the 0-20 cm soil layer. Moreover, tillage type and soil depth had significant influences on the bacterial, fungal and protistan community compositions and structures. The co-occurrence network was divided into 4 ecological modules, and module 1 exhibited significant correlations with the POC and MOC contents. After determining their topological roles, we identified the keystone taxa in the network. The results indicated that the most common bacterial taxa may result in SOC loss due to low C use efficiency, while specific fungal (Cephalotrichum) and protistan (Cercozoa) species could facilitate SOC fraction accumulation by promoting macroaggregate formation and predation. Therefore, the increase in keystone fungi and protists, as well as the reduction in bacteria, drove module 1 community function, which in turn promoted SOC sequestration under CT. These results strengthen our understanding of microbial functions in the accrual of SOC fractions, which contributes to the development of conservation agriculture on the Northeast China Plain.
Collapse
Affiliation(s)
- Yu-Mei Li
- Heilongjiang Black Soil Conservation and Utilization Research Institute, Harbin, China
| | - Yu-Ming Wang
- The Centre for Ion Beam Bioengineering Green Agriculture, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Science Island Branch, Graduate School of USTC, Hefei, China
| | - Guang-Wei Qiu
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Hong-Jiu Yu
- Heilongjiang Black Soil Conservation and Utilization Research Institute, Harbin, China
| | - Feng-Man Liu
- Heilongjiang Black Soil Conservation and Utilization Research Institute, Harbin, China
| | - Gen-Lin Wang
- Heilongjiang Black Soil Conservation and Utilization Research Institute, Harbin, China
| | - Yan Duan
- The Centre for Ion Beam Bioengineering Green Agriculture, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| |
Collapse
|
9
|
Tan J, Wei N, Turcotte MM. Trophic interactions in microbiomes influence plant host population size and ecosystem function. Proc Biol Sci 2024; 291:20240612. [PMID: 38772419 DOI: 10.1098/rspb.2024.0612] [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: 03/14/2024] [Accepted: 04/08/2024] [Indexed: 05/23/2024] Open
Abstract
Plant microbiomes that comprise diverse microorganisms, including prokaryotes, eukaryotes and viruses, are the key determinants of plant population dynamics and ecosystem function. Despite their importance, little is known about how species interactions (especially trophic interactions) between microbes from different domains modify the importance of microbiomes for plant hosts and ecosystems. Using the common duckweed Lemna minor, we experimentally examined the effects of predation (by bacterivorous protists) and parasitism (by bacteriophages) within microbiomes on plant population size and ecosystem phosphorus removal. Our results revealed that the addition of predators increased plant population size and phosphorus removal, whereas the addition of parasites showed the opposite pattern. The structural equation modelling further pointed out that predation and parasitism affected plant population size and ecosystem function via distinct mechanisms that were both mediated by microbiomes. Our results highlight the importance of understanding microbial trophic interactions for predicting the outcomes and ecosystem impacts of plant-microbiome symbiosis.
Collapse
Affiliation(s)
- Jiaqi Tan
- Department of Biological Sciences, Louisianan State University, Baton Rouge, LA 70803, USA
| | - Na Wei
- The Holden Arboretum, Kirtland, OH 44094, USA
| | - Martin M Turcotte
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| |
Collapse
|
10
|
Micciulla JL, Shor LM, Gage DJ. Enhanced transport of bacteria along root systems by protists can impact plant health. Appl Environ Microbiol 2024; 90:e0201123. [PMID: 38534145 PMCID: PMC11022564 DOI: 10.1128/aem.02011-23] [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: 11/08/2023] [Accepted: 01/25/2024] [Indexed: 03/28/2024] Open
Abstract
Soil protists have been shown to contribute to the structure and function of the rhizosphere in a variety of ways. Protists are key contributors to nutrient cycling through the microbial loop, where biomass is digested by protists and otherwise stored nutrients are returned to the environment. Protists have also been shown to feed on plant pathogenic bacteria and alter root microbiomes in ways that may benefit plants. Recently, a mechanism involving bacterial transport, facilitated by protists, has been hypothesized to contribute to the spatial distribution of bacteria in the rhizosphere. Here, we observe the differential abilities of three soil protists: a ciliate (Colpoda sp.), a flagellate (Cercomonas sp.), and a naked amoeba (Acanthamoeba castellanii) to transport nitrogen-fixing Sinorhizobium meliloti to infectible root tips. Co-inoculation of protists plus S. meliloti resulted in the movement of bacteria, as measured by the presence of nitrogen-fixing nodules, up to 15 cm farther down the root systems when compared to plants inoculated with S. meliloti alone. Co-inoculation of the ciliate, Colpoda sp., with S. meliloti, resulted in shoot weights that were similar to plants that grew in nitrogen-replete potting mix. Colpoda sp.-feeding style and motility likely contributed to their success at transporting bacteria through the rhizosphere. We observed that the addition of protists alone without the co-inoculum of S. meliloti resulted in plants with larger shoot weights than control plants. Follow-up experiments showed that protists plus their associated microbiomes were aiding in plant health, likely through means of nutrient cycling.IMPORTANCEProtists represent a significant portion of the rhizosphere microbiome and have been shown to contribute to plant health, yet they are understudied compared to their bacterial and fungal counterparts. This study elucidates their role in the rhizosphere community and suggests a mechanism by which protists can be used to move bacteria along plant roots. We found that the co-inoculation of protists with nitrogen-fixing beneficial bacteria, Sinorhizobium meliloti, resulted in nodules farther down the roots when compared to plants inoculated with S. meliloti alone, and shoot weights similar to plants that received nitrogen fertilizer. These data illustrate the ability of protists to transport viable bacteria to uninhabited regions of the root system.
Collapse
Affiliation(s)
- Jamie L. Micciulla
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Leslie M. Shor
- Center for Environmental Sciences & Engineering, University of Connecticut, Storrs, Connecticut, USA
| | - Daniel J. Gage
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut, USA
| |
Collapse
|
11
|
Ma L, Zhou G, Zhang J, Jia Z, Zou H, Chen L, Zhang C, Ma D, Han C, Duan Y. Long-term conservation tillage enhances microbial carbon use efficiency by altering multitrophic interactions in soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170018. [PMID: 38224879 DOI: 10.1016/j.scitotenv.2024.170018] [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: 03/15/2023] [Revised: 12/03/2023] [Accepted: 01/06/2024] [Indexed: 01/17/2024]
Abstract
Microbial carbon (C) use efficiency (CUE) plays a key role in soil C storage. The predation of protists on bacteria and fungi has potential impacts on the global C cycle. However, under conservation tillage conditions, the effects of multitrophic interactions on soil microbial CUE are still unclear. Here, we investigate the multitrophic network (especially the keystone ecological cluster) and its regulation of soil microbial CUE and soil organic C (SOC) under different long-term (15-year) tillage practices. We found that conservation tillage (CT) significantly enhanced microbial CUE, turnover, and SOC (P < 0.05) compared to traditional tillage (control, CK). At the same time, tillage practice and soil depth had significant effects on the structure of fungal and protistan communities. Furthermore, the soil biodiversity of the keystone cluster was positively correlated with the microbial physiological traits (CUE, microbial growth rate (MGR), microbial respiration rate (Rs), microbial turnover) and SOC (P < 0.05). Protistan richness played the strongest role in directly shaping the keystone cluster. Compared with CK, CT generally enhanced the correlation between microbial communities and microbial physiological characteristics and SOC. Overall, our results illustrate that the top-down control (the organisms at higher trophic levels affect the organisms at lower trophic levels) of protists in the soil micro-food web plays an important role in improving microbial CUE under conservation tillage. Our findings provide a theoretical basis for promoting the application of protists in targeted microbial engineering and contribute to the promotion of conservation agriculture and the improvement of soil C sequestration potential.
Collapse
Affiliation(s)
- Ling Ma
- College of Land and Environment, Shenyang Agricultural University, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Arable Land Conservation in Northeast China, Ministry of Agriculture and Rural Affairs, Shenyang 110866, China
| | - Guixiang Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Zhongjun Jia
- Chinese Academy of Sciences, Northeast Institute of Geography and Agroecology, Changchun 130102, China
| | - Hongtao Zou
- College of Land and Environment, Shenyang Agricultural University, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Arable Land Conservation in Northeast China, Ministry of Agriculture and Rural Affairs, Shenyang 110866, China
| | - Lin Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Congzhi Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Donghao Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Changdong Han
- College of Land and Environment, Shenyang Agricultural University, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Arable Land Conservation in Northeast China, Ministry of Agriculture and Rural Affairs, Shenyang 110866, China
| | - Yan Duan
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| |
Collapse
|
12
|
Law SR, Mathes F, Paten AM, Alexandre PA, Regmi R, Reid C, Safarchi A, Shaktivesh S, Wang Y, Wilson A, Rice SA, Gupta VVSR. Life at the borderlands: microbiomes of interfaces critical to One Health. FEMS Microbiol Rev 2024; 48:fuae008. [PMID: 38425054 PMCID: PMC10977922 DOI: 10.1093/femsre/fuae008] [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: 07/26/2023] [Revised: 02/12/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.
Collapse
Affiliation(s)
- Simon R Law
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Falko Mathes
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Floreat, WA 6014, Australia
| | - Amy M Paten
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Canberra, ACT 2601, Australia
| | - Pamela A Alexandre
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, St Lucia, Qld 4072, Australia
| | - Roshan Regmi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
| | - Cameron Reid
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Urrbrae, SA 5064, Australia
| | - Azadeh Safarchi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Westmead, NSW 2145, Australia
| | - Shaktivesh Shaktivesh
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Data 61, Clayton, Vic 3168, Australia
| | - Yanan Wang
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Adelaide SA 5000, Australia
| | - Annaleise Wilson
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Geelong, Vic 3220, Australia
| | - Scott A Rice
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture, and Food, Westmead, NSW 2145, Australia
| | - Vadakattu V S R Gupta
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
| |
Collapse
|
13
|
Kilner CL, Carrell AA, Wieczynski DJ, Votzke S, DeWitt K, Yammine A, Shaw J, Pelletier DA, Weston DJ, Gibert JP. Temperature and CO 2 interactively drive shifts in the compositional and functional structure of peatland protist communities. GLOBAL CHANGE BIOLOGY 2024; 30:e17203. [PMID: 38433341 DOI: 10.1111/gcb.17203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 03/05/2024]
Abstract
Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long-term whole-ecosystem warming experiment at a boreal peatland to answer how temperature and CO2 jointly influence communities of abundant, diverse, yet poorly understood, non-fungi microbial Eukaryotes (protists). These microbes influence ecosystem function directly through photosynthesis and respiration, and indirectly, through predation on decomposers (bacteria and fungi). Using a combination of high-throughput fluid imaging and 18S amplicon sequencing, we report large climate-induced, community-wide shifts in the community functional composition of these microbes (size, shape, and metabolism) that could alter overall function in peatlands. Importantly, we demonstrate a taxonomic convergence but a functional divergence in response to warming and elevated CO2 with most environmental responses being contingent on organismal size: warming effects on functional composition are reversed by elevated CO2 and amplified in larger microbes but not smaller ones. These findings show how the interactive effects of warming and rising CO2 levels could alter the structure and function of peatland microbial food webs-a fragile ecosystem that stores upwards of 25% of all terrestrial carbon and is increasingly threatened by human exploitation.
Collapse
Affiliation(s)
- Christopher L Kilner
- Department of Biology, Duke University, Durham, North Carolina, USA
- Bird Conservancy of the Rockies, Fort Collins, Colorado, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Samantha Votzke
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Katrina DeWitt
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Andrea Yammine
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Jonathan Shaw
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jean P Gibert
- Department of Biology, Duke University, Durham, North Carolina, USA
| |
Collapse
|
14
|
Shi X, Eisenhauer N, Peñuelas J, Fu Y, Wang J, Chen Y, Liu S, He L, Lucas-Borja ME, Wang L, Huang Z. Trophic interactions in soil micro-food webs drive ecosystem multifunctionality along tree species richness. GLOBAL CHANGE BIOLOGY 2024; 30:e17234. [PMID: 38469998 DOI: 10.1111/gcb.17234] [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: 12/07/2023] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
Rapid biodiversity losses under global climate change threaten forest ecosystem functions. However, our understanding of the patterns and drivers of multiple ecosystem functions across biodiversity gradients remains equivocal. To address this important knowledge gap, we measured simultaneous responses of multiple ecosystem functions (nutrient cycling, soil carbon stocks, organic matter decomposition, plant productivity) to a tree species richness gradient of 1, 4, 8, 16, and 32 species in a young subtropical forest. We found that tree species richness had negligible effects on nutrient cycling, organic matter decomposition, and plant productivity, but soil carbon stocks and ecosystem multifunctionality significantly increased with tree species richness. Linear mixed-effect models showed that soil organisms, particularly arbuscular mycorrhizal fungi (AMF) and soil nematodes, elicited the greatest relative effects on ecosystem multifunctionality. Structural equation models revealed indirect effects of tree species richness on ecosystem multifunctionality mediated by trophic interactions in soil micro-food webs. Specifically, we found a significant negative effect of gram-positive bacteria on soil nematode abundance (a top-down effect), and a significant positive effect of AMF biomass on soil nematode abundance (a bottom-up effect). Overall, our study emphasizes the significance of a multitrophic perspective in elucidating biodiversity-multifunctionality relationships and highlights the conservation of functioning soil micro-food webs to maintain multiple ecosystem functions.
Collapse
Affiliation(s)
- Xiuzhen Shi
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Institute of Geography, Fujian Normal University, Fuzhou, China
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Nico Eisenhauer
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Josep Peñuelas
- CREAF, Centre de Recerca Ecològicai Aplicacions Forestals, Cerdanyola del Vallès, Bellaterra, Catalonia, Spain
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, Catalonia, Spain
| | - Yanrong Fu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Institute of Geography, Fujian Normal University, Fuzhou, China
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Jianqing Wang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Institute of Geography, Fujian Normal University, Fuzhou, China
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Yuxin Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & Ecology, Xiamen University, Xiamen, China
| | - Shengen Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lulu He
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Institute of Geography, Fujian Normal University, Fuzhou, China
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, 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
| | - Liyan Wang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Institute of Geography, Fujian Normal University, Fuzhou, China
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Zhiqun Huang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Institute of Geography, Fujian Normal University, Fuzhou, China
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| |
Collapse
|
15
|
Zhou L, Höfte M, Hennessy RC. Does regulation hold the key to optimizing lipopeptide production in Pseudomonas for biotechnology? Front Bioeng Biotechnol 2024; 12:1363183. [PMID: 38476965 PMCID: PMC10928948 DOI: 10.3389/fbioe.2024.1363183] [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: 12/29/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Lipopeptides (LPs) produced by Pseudomonas spp. are specialized metabolites with diverse structures and functions, including powerful biosurfactant and antimicrobial properties. Despite their enormous potential in environmental and industrial biotechnology, low yield and high production cost limit their practical use. While genome mining and functional genomics have identified a multitude of LP biosynthetic gene clusters, the regulatory mechanisms underlying their biosynthesis remain poorly understood. We propose that regulation holds the key to unlocking LP production in Pseudomonas for biotechnology. In this review, we summarize the structure and function of Pseudomonas-derived LPs and describe the molecular basis for their biosynthesis and regulation. We examine the global and specific regulator-driven mechanisms controlling LP synthesis including the influence of environmental signals. Understanding LP regulation is key to modulating production of these valuable compounds, both quantitatively and qualitatively, for industrial and environmental biotechnology.
Collapse
Affiliation(s)
- Lu Zhou
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Rosanna C. Hennessy
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
16
|
Wang M, Ge AH, Ma X, Wang X, Xie Q, Wang L, Song X, Jiang M, Yang W, Murray JD, Wang Y, Liu H, Cao X, Wang E. Dynamic root microbiome sustains soybean productivity under unbalanced fertilization. Nat Commun 2024; 15:1668. [PMID: 38395981 PMCID: PMC10891064 DOI: 10.1038/s41467-024-45925-5] [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: 05/25/2023] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Root-associated microbiomes contribute to plant growth and health, and are dynamically affected by plant development and changes in the soil environment. However, how different fertilizer regimes affect quantitative changes in microbial assembly to effect plant growth remains obscure. Here, we explore the temporal dynamics of the root-associated bacteria of soybean using quantitative microbiome profiling (QMP) to examine its response to unbalanced fertilizer treatments (i.e., lacking either N, P or K) and its role in sustaining plant growth after four decades of unbalanced fertilization. We show that the root-associated bacteria exhibit strong succession during plant development, and bacterial loads largely increase at later stages, particularly for Bacteroidetes. Unbalanced fertilization has a significant effect on the assembly of the soybean rhizosphere bacteria, and in the absence of N fertilizer the bacterial community diverges from that of fertilized plants, while lacking P fertilizer impedes the total load and turnover of rhizosphere bacteria. Importantly, a SynCom derived from the low-nitrogen-enriched cluster is capable of stimulating plant growth, corresponding with the stabilized soybean productivity in the absence of N fertilizer. These findings provide new insights in the quantitative dynamics of the root-associated microbiome and highlight a key ecological cluster with prospects for sustainable agricultural management.
Collapse
Affiliation(s)
- Mingxing Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - An-Hui Ge
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xingzhu Ma
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, 150086, China
| | - Xiaolin Wang
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Qiujin Xie
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Like Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianwei Song
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengchen Jiang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Weibing Yang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jeremy D Murray
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ertao Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| |
Collapse
|
17
|
Stulanovic N, Kerdel Y, Rezende L, Deflandre B, Burguet P, Belde L, Denoel R, Tellatin D, Rigolet A, Hanikenne M, Quinton L, Ongena M, Rigali S. Nitrogen sources enhance siderophore-mediated competition for iron between potato common scab and late blight causative agents. Metallomics 2024; 16:mfae004. [PMID: 38244228 DOI: 10.1093/mtomcs/mfae004] [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: 10/05/2023] [Accepted: 01/18/2024] [Indexed: 01/22/2024]
Abstract
How do pathogens affecting the same host interact with each other? We evaluated here the types of microbe-microbe interactions taking place between Streptomyces scabiei and Phytophthora infestans, the causative agents of common scab and late blight diseases in potato crops, respectively. Under most laboratory culture conditions tested, S. scabiei impaired or completely inhibited the growth of P. infestans by producing either soluble and/or volatile compounds. Increasing peptone levels correlated with increased inhibition of P. infestans. Comparative metabolomics showed that production of S. scabiei siderophores (desferrioxamines, pyochelin, scabichelin, and turgichelin) increased with the quantity of peptone, thereby suggesting that they participate in the inhibition of the oomycete growth. Mass spectrometry imaging further uncovered that the zones of secreted siderophores and of P. infestans growth inhibition coincided. Moreover, either the repression of siderophore production or the neutralization of their iron-chelating activity led to a resumption of P. infestans growth. Replacement of peptone by natural nitrogen sources such as ammonium nitrate, sodium nitrate, ammonium sulfate, and urea also triggered siderophore production in S. scabiei. Interestingly, nitrogen source-induced siderophore production also inhibited the growth of Alternaria solani, the causative agent of the potato early blight. Overall, our work further emphasizes the importance of competition for iron between microorganisms that colonize the same niche. As common scab never alters the vegetative propagation of tubers, we propose that S. scabiei, under certain conditions, could play a protective role for its hosts against much more destructive pathogens through exploitative iron competition and volatile compound production.
Collapse
Affiliation(s)
- Nudzejma Stulanovic
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
| | - Yasmine Kerdel
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
| | - Lucas Rezende
- Hedera-22, Boulevard du Rectorat 27b, B-4000 Liège, Belgium
| | - Benoit Deflandre
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
| | - Pierre Burguet
- Molecular Systems (MolSys), Department of Chemistry, University of Liège, B-4000 Liège, Belgium
| | - Loïc Belde
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
| | - Romane Denoel
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
| | - Déborah Tellatin
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
| | - Augustin Rigolet
- Microbial Processes and Interactions, TERRA Teaching and Research Center, BioEcoAgro, Joint Research Unit/UMR transfrontalière 1158, University of Liège-Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Marc Hanikenne
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, B-4000 Liège, Belgium
| | - Loïc Quinton
- Molecular Systems (MolSys), Department of Chemistry, University of Liège, B-4000 Liège, Belgium
| | - Marc Ongena
- Microbial Processes and Interactions, TERRA Teaching and Research Center, BioEcoAgro, Joint Research Unit/UMR transfrontalière 1158, University of Liège-Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Sébastien Rigali
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
| |
Collapse
|
18
|
Gao M, Xiong C, Tsui CKM, Cai L. Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome. Mol Ecol 2024; 33:e17228. [PMID: 38037712 DOI: 10.1111/mec.17228] [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: 07/07/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
Soil and plant-associated protistan communities play a key role in shaping bacterial and fungal communities, primarily through their function as top-down predators. However, our understanding of how pathogen invasion influences these protistan communities and their relationships with bacterial and fungal communities remains limited. Here, we studied the protistan communities along the soil-plant continuum of healthy chilli peppers and those affected by Fusarium wilt disease (FWD), and integrated bacterial and fungal community data from our previous research. Our research showed that FWD was associated with a significant enrichment of phagotrophic protists in roots, and also increased the proportion and connectivity of these protists (especially Cercozoa and Ciliophora) in both intra- and inter-kingdom networks. Furthermore, the microbiome of diseased plants not only showed a higher relative abundance of functional genes related to bacterial anti-predator responses than healthy plants, but also contained a greater abundance of metagenome-assembled genomes with functional traits involved in this response. The increased microbial inter-kingdom associations between bacteria and protists, coupled with the notable bacterial anti-predator feedback in the microbiome of diseased plants, suggest that FWD may catalyse the associations between protists and their microbial prey. These findings highlight the potential role of predatory protists in influencing microbial assembly and functionality through top-down forces under pathogenic stress.
Collapse
Affiliation(s)
- Min Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Chao Xiong
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Clement K M Tsui
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- National Center for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
19
|
Guo S, Jiao Z, Yan Z, Yan X, Deng X, Xiong W, Tao C, Liu H, Li R, Shen Q, Kowalchuk GA, Geisen S. Predatory protists reduce bacteria wilt disease incidence in tomato plants. Nat Commun 2024; 15:829. [PMID: 38280866 PMCID: PMC10821857 DOI: 10.1038/s41467-024-45150-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/16/2024] [Indexed: 01/29/2024] Open
Abstract
Soil organisms are affected by the presence of predatory protists. However, it remains poorly understood how predatory protists can affect plant disease incidence and how fertilization regimes can affect these interactions. Here, we characterise the rhizosphere bacteria, fungi and protists over eleven growing seasons of tomato planting under three fertilization regimes, i.e conventional, organic and bioorganic, and with different bacterial wilt disease incidence levels. We find that predatory protists are negatively associated with disease incidence, especially two ciliophoran Colpoda OTUs, and that bioorganic fertilization enhances the abundance of predatory protists. In glasshouse experiments we find that the predatory protist Colpoda influences disease incidence by directly consuming pathogens and indirectly increasing the presence of pathogen-suppressive microorganisms in the soil. Together, we demonstrate that predatory protists reduce bacterial wilt disease incidence in tomato plants via direct and indirect reductions of pathogens. Our study provides insights on the role that predatory protists play in plant disease, which could be used to design more sustainable agricultural practices.
Collapse
Affiliation(s)
- Sai Guo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Zixuan Jiao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Zhiguang Yan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Xinyue Yan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, 6700 AA, Wageningen, The Netherlands
- Netherlands Department of Terrestrial Ecology, Netherlands Institute for Ecology, (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands
| |
Collapse
|
20
|
He X, Xiao X, Wei W, Li L, Zhao Y, Zhang N, Wang M. Soil rare microorganisms mediated the plant cadmium uptake: The central role of protists. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168505. [PMID: 37967623 DOI: 10.1016/j.scitotenv.2023.168505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023]
Abstract
Plants and microorganisms symbiotically mediate and/or catalyse the turnover of elements in rhizosphere soils, thus directly influencing the effectiveness of phytoremediation in addressing heavy metal contamination. Soil rare microbial communities are diverse but not well understood in terms of their importance for phytoremediation. In this study, we simulated the loss of rare microorganisms through dilution-to-extinction approach, and investigated the effects on integrated rhizosphere microbiome with soil microcosm experiments, including bacteria, fungi, protists, and microfauna. Additionally, we explored the implications for ryegrass (Lolium multiflorum Lam.) growth and its uptake of Cd (cadmium). Compared with the undiluted group, ryegrass exhibited a significant decrease in Cd uptake ranging from 52.34 % to 73.71 % in the rare species-loss soils, indicating a lack of functional redundancy in rhizosphere soil microbial community following rare species loss. Interestingly, these soils displayed a remarkable 1.79-fold increase in plant biomass and a 41.02 % increase in plant height. By sequencing the 16S, 18S, and ITS rRNA gene amplicons of rhizosphere microbes, we found that soil rare species loss decreased the rhizosphere microbial α-diversity, changed the community structures, and shifted the functional potential. Protists were particularly affected. Through the analysis of species co-occurrence networks, along with the partial least squares path modeling, we found that the diversity of protists and bacteria and the co-occurring network connectivity of protists and fungi contributed most to plant Cd uptake and growth. These results highlighted the potential significance of rare microorganisms, particularly protists, in phytoextraction of Cd-contaminated soils, owing to their central role in the microbial food web.
Collapse
Affiliation(s)
- Xingguo He
- School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China
| | - Xian Xiao
- School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China.
| | - Weiwei Wei
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Liangzhong Li
- Chongqing Huanyue Ecological Environment Technology Co., Ltd., Chongqing 400000, China
| | - Yuan Zhao
- School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China
| | - Na Zhang
- Hunan Soil and Fertilizer Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Mingyu Wang
- School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China
| |
Collapse
|
21
|
Ding L, Chen H, Wang M, Wang P. Shrub expansion raises both aboveground and underground multifunctionality on a subtropical plateau grassland: coupling multitrophic community assembly to multifunctionality and functional trade-off. Front Microbiol 2024; 14:1339125. [PMID: 38274762 PMCID: PMC10808678 DOI: 10.3389/fmicb.2023.1339125] [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: 11/15/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction Shrubs have expanded into grasslands globally. However, the relative importance of aboveground and underground diversity and the relative importance of underground community assembly and diversity in shaping multifunctionality and functional trade-offs over shrub expansion remains unknown. Methods In this study, aboveground and underground multitrophic communities (abundant and rare archaea, bacteria, fungi, nematodes, and protists) and 208 aboveground and underground ecosystem properties or indicators were measured at three stages (Grass, Mosaic, Shrub) of shrub expansion on the Guizhou subtropical plateau grassland to study multifunctionality and functional trade-offs. Results The results showed that shrub expansion significantly enhanced aboveground, underground, and entire ecosystem multifunctionality. The functional trade-off intensities of the aboveground, underground, and entire ecosystems showed significant V-shaped changes with shrub expansion. Shrub expansion improved plant species richness and changed the assembly process and species richness of soil abundant and rare subcommunities. Plant species diversity had a greater impact on multifunctionality than soil microbial diversity by more than 16%. The effect of plant species diversity on functional trade-offs was only one-fifth of the effect of soil microbial diversity. The soil microbial species richness did not affect multifunctionality, however, the assembly process of soil microbial communities did. Rather than the assembly process of soil microbial communities, the soil microbial species richness affected functional trade-offs. Discussion Our study is the first to couple multitrophic community assemblies to multifunctionality and functional trade-offs. Our results would boost the understanding of the role of aboveground and underground diversity in multifunctionality and functional trade-offs.
Collapse
Affiliation(s)
- Leilei Ding
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Hong Chen
- Guizhou Songbaishan Reservoir Management Office, Guiyang, Guizhou, China
| | - Mengya Wang
- College of Animal Science, Guizhou University, Guiyang, Guizhou, China
| | - Puchang Wang
- School of Life Science, Guizhou Normal University, Guiyang, Guizhou, China
| |
Collapse
|
22
|
Jia C, Zhou G, Ma L, Qiu X, Zhang J, Wang J, Zhang C, Chen L, Ma D, Zhao Z, Xue Z. The addition of discrimination inhibitors stimulations discrimination potential and N 2O emissions were linked to predation among microorganisms in long term nitrogen application and straw returning systems. Front Microbiol 2024; 14:1337507. [PMID: 38264480 PMCID: PMC10803610 DOI: 10.3389/fmicb.2023.1337507] [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: 11/13/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024] Open
Abstract
Introduction Ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) have been proven to be key microorganisms driving the ammonia oxidation process. However, under different fertilization practices, there is a lack of research on the impact of interaction between predators and AOA or AOB on nitrogen cycling at the multi-trophic level. Methods In this study, a network-oriented microscopic culture experiment was established based on four different long-term fertilization practices soils. We used the nitrification inhibitors 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxide-3-oxyl (PTIO) and 3, 4-Dimethylpyrazole phosphate (DMPP) inhibited AOA and AOB, respectively, to explore the impact of interaction between protists and AOA or AOB on nitrogen transformation. Results The results showed that long-term nitrogen application promoted the potential nitrification rate (PNR) and nitrous oxide (N2O) emission, and significantly increased the gene abundance of AOB, but had no obvious effect on AOA gene abundance. DMPP significantly reduced N2O emission and PNR, while PTIO had no obvious effect on them. Accordingly, in the multi-trophic microbial network, Cercozoa and Proteobacteria were identified as keystone taxa of protists and AOB, respectively, and were significantly positively correlated with N2O, PNR and nitrate nitrogen. However, Nitrososphaerota archaeon as the keystone species of AOA, had an obvious negative linkage to these indicators. The structural equation model (SEM) showed that AOA and AOB may be competitors to each other. Protists may promote AOB diversity through direct trophic interaction with AOA. Conclusion The interaction pattern between protists and ammonia-oxidizing microorganisms significantly affects potential nitrification rate and N2O emission, which has important implications for soil nitrogen cycle.
Collapse
Affiliation(s)
- Chunhua Jia
- Northeast Key Laboratory of Conservation and Improvement of Cultivated Land (Shenyang), Ministry of Agriculture and Rural Affairs, College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Guixiang Zhou
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ling Ma
- Northeast Key Laboratory of Conservation and Improvement of Cultivated Land (Shenyang), Ministry of Agriculture and Rural Affairs, College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xiuwen Qiu
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Jurong, China
| | - Jiabao Zhang
- Northeast Key Laboratory of Conservation and Improvement of Cultivated Land (Shenyang), Ministry of Agriculture and Rural Affairs, College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jingkuan Wang
- Northeast Key Laboratory of Conservation and Improvement of Cultivated Land (Shenyang), Ministry of Agriculture and Rural Affairs, College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Congzhi Zhang
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lin Chen
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Donghao Ma
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Zhanhui Zhao
- School of Geomatics and Urban Spatial Informatics, Henan University of Urban Construction, Pingdingshan, Henan, China
| | - Zaiqi Xue
- Fengqiu Experimental Station of National Ecosystem Research Network of China, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| |
Collapse
|
23
|
Ma L, Zhang L, Zhang S, Zhou M, Huang W, Zou X, He Z, Shu L. Soil protists are more resilient to the combined effect of microplastics and heavy metals than bacterial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167645. [PMID: 37806593 DOI: 10.1016/j.scitotenv.2023.167645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
Heavy metals and micro-/nanoplastic pollution seriously threaten the environment and ecosystems. While many studies investigated their effects on diverse microbes, few studies have focused on soil protists, and it is unclear how soil protists respond to the combined effect of micro-/nanoplastics and heavy metals. This study investigated how soil protistan and bacterial communities respond to single or combined copper and micro-/nanoplastics. The bacterial community exhibited an instantaneous response to single copper pollution, whereas the combined pollution resulted in a hysteresis effect on the protistan community. Single and combined pollution inhibited the predation of protists and changed the construction of ecological networks. Though single and combined pollution did not significantly affect the overall community structure, the exposure experiment indicated that combined pollution harmed soil amoeba's fitness. These findings offer valuable new insights into the toxic effects of single and combined pollution of copper and plastics on soil protistan and bacterial communities. Additionally, this study shows that sequencing-based analyses cannot fully reflect pollutants' adverse effects, and both culture-independent and dependent methods are needed to reveal the impact of pollutants on soil microbes.
Collapse
Affiliation(s)
- Lu Ma
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Lin Zhang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Siyi Zhang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Min Zhou
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Wei Huang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Xinyue Zou
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
| |
Collapse
|
24
|
Li Y, Chen Z, Wagg C, Castellano MJ, Zhang N, Ding W. Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism. GLOBAL CHANGE BIOLOGY 2024; 30:e17101. [PMID: 38273560 DOI: 10.1111/gcb.17101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/27/2024]
Abstract
Soil organic carbon (SOC) plays an essential role in mediating community structure and metabolic activities of belowground biota. Unraveling the evolution of belowground communities and their feedback mechanisms on SOC dynamics helps embed the ecology of soil microbiome into carbon cycling, which serves to improve biodiversity conservation and carbon management strategy under global change. Here, croplands with a SOC gradient were used to understand how belowground metabolisms and SOC decomposition were linked to the diversity, composition, and co-occurrence networks of belowground communities encompassing archaea, bacteria, fungi, protists, and invertebrates. As SOC decreased, the diversity of prokaryotes and eukaryotes also decreased, but their network complexity showed contrasting patterns: prokaryotes increased due to intensified niche overlap, while that of eukaryotes decreased possibly because of greater dispersal limitation owing to the breakdown of macroaggregates. Despite the decrease in biodiversity and SOC stocks, the belowground metabolic capacity was enhanced as indicated by increased enzyme activity and decreased enzymatic stoichiometric imbalance. This could, in turn, expedite carbon loss through respiration, particularly in the slow-cycling pool. The enhanced belowground metabolic capacity was dominantly driven by greater multitrophic network complexity and particularly negative (competitive and predator-prey) associations, which fostered the stability of the belowground metacommunity. Interestingly, soil abiotic conditions including pH, aeration, and nutrient stocks, exhibited a less significant role. Overall, this study reveals a greater need for soil C resources across multitrophic levels to maintain metabolic functionality as declining SOC results in biodiversity loss. Our researchers highlight the importance of integrating belowground biological processes into models of SOC turnover, to improve agroecosystem functioning and carbon management in face of intensifying anthropogenic land-use and climate change.
Collapse
Affiliation(s)
- Ye Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zengming Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Cameron Wagg
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada
| | | | - Nan Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| |
Collapse
|
25
|
Shangguan HY, Geisen S, Li ZP, Yao HF, Li G, Breed MF, Scheu S, Sun X. Urban greenspaces shape soil protist communities in a location-specific manner. ENVIRONMENTAL RESEARCH 2024; 240:117485. [PMID: 37907164 DOI: 10.1016/j.envres.2023.117485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/02/2023]
Abstract
The impacts of urbanization on aboveground biodiversity are well studied, and its impact on soil microorganisms are also receiving increased attention. However, the impact of urbanization on the soil protists are hardly investigated. Here, we studied how urbanization and distinct urban greenspaces affect protist communities. We used amplicon sequencing of the18 S rRNA gene of samples from five types of urban greenspaces (parks, greenbelts, industrial areas, residential areas and hospital lawns), neighboring natural forests and agricultural ecosystems in Ningbo, China. We found that urban greenspaces harbored higher protist α-diversity than forests, while protist β-diversity increased from agricultural systems to urban greenspaces to forests. Among the studied driving factors, soil bacterial α- and β-diversity best predicted phagotrophic protist α- and β-diversity in urban greenspaces, while differences in α- and β-diversity of phototrophic protists were best explained by soil carbon-to-nitrogen ratio and fungal β-diversity, respectively. Abiotic factors i.e., total phosphorus and carbon-to-nitrogen ratio, best predicted the α- and β-diversity of protist parasites in urban greenspaces, respectively. The results revealed that the composition and drivers of protist communities vary between functional groups and urban ecosystems. Overall, our findings contribute to a better understanding of drivers of soil protist communities and indicate that soil protist communities and associated soil functions could be managed in predictable ways in urban greenspaces.
Collapse
Affiliation(s)
- Hua-Yuan Shangguan
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB Wageningen, the Netherlands
| | - Zhi-Peng Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Hai-Feng Yao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Martin F Breed
- College of Science & Engineering, Flinders University, Bedford Park 5042 SA, Australia
| | - Stefan Scheu
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany; Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Xin Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| |
Collapse
|
26
|
Liao H, Hao X, Li Y, Ma S, Gao S, Cai P, Chen W, Huang Q. Protists regulate microbially mediated organic carbon turnover in soil aggregates. GLOBAL CHANGE BIOLOGY 2024; 30:e17102. [PMID: 38273557 DOI: 10.1111/gcb.17102] [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: 04/27/2023] [Revised: 11/05/2023] [Accepted: 11/09/2023] [Indexed: 01/27/2024]
Abstract
Soil protists, the major predator of bacteria and fungi, shape the taxonomic and functional structure of soil microbiome via trophic regulation. However, how trophic interactions between protists and their prey influence microbially mediated soil organic carbon turnover remains largely unknown. Here, we investigated the protistan communities and microbial trophic interactions across different aggregates-size fractions in agricultural soil with long-term fertilization regimes. Our results showed that aggregate sizes significantly influenced the protistan community and microbial hierarchical interactions. Bacterivores were the predominant protistan functional group and were more abundant in macroaggregates and silt + clay than in microaggregates, while omnivores showed an opposite distribution pattern. Furthermore, partial least square path modeling revealed positive impacts of omnivores on the C-decomposition genes and soil organic matter (SOM) contents, while bacterivores displayed negative impacts. Microbial trophic interactions were intensive in macroaggregates and silt + clay but were restricted in microaggregates, as indicated by the intensity of protistan-bacterial associations and network complexity and connectivity. Cercozoan taxa were consistently identified as the keystone species in SOM degradation-related ecological clusters in macroaggregates and silt + clay, indicating the critical roles of protists in SOM degradation by regulating bacterial and fungal taxa. Chemical fertilization had a positive effect on soil C sequestration through suppressing SOM degradation-related ecological clusters in macroaggregate and silt + clay. Conversely, the associations between the trophic interactions and SOM contents were decoupled in microaggregates, suggesting limited microbial contributions to SOM turnovers. Our study demonstrates the importance of protists-driven trophic interactions on soil C cycling in agricultural ecosystems.
Collapse
Affiliation(s)
- Hao Liao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, China
| | - Xiuli Hao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, China
| | - Yiting Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Silin Ma
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, China
| | - Shenghan Gao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, China
| | - Peng Cai
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, China
| | - Wenli Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, China
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Wuhan, China
| |
Collapse
|
27
|
Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [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] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
Collapse
Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | |
Collapse
|
28
|
Chen Y, Fu W, Xiao H, Zhai Y, Luo Y, Wang Y, Liu Z, Li Q, Huang J. A Review on Rhizosphere Microbiota of Tea Plant ( Camellia sinensis L): Recent Insights and Future Perspectives. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19165-19188. [PMID: 38019642 DOI: 10.1021/acs.jafc.3c02423] [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: 12/01/2023]
Abstract
Rhizosphere microbial colonization of the tea plant provides many beneficial functions for the host, But the factors that influence the composition of these rhizosphere microbes and their functions are still unknown. In order to explore the interaction between tea plants and rhizosphere microorganisms, we summarized the current studies. First, the review integrated the known rhizosphere microbial communities of tea tree, including bacteria, fungi, and arbuscular mycorrhizal fungi. Then, various factors affecting tea rhizosphere microorganisms were studied, including: endogenous factors, environmental factors, and agronomic practices. Finally, the functions of rhizosphere microorganisms were analyzed, including (a) promoting the growth and quality of tea trees, (b) alleviating biotic and abiotic stresses, and (c) improving soil fertility. Finally, we highlight the gaps in knowledge of tea rhizosphere microorganisms and the future direction of development. In summary, understanding rhizosphere microbial interactions with tea plants is key to promoting the growth, development, and sustainable productivity of tea plants.
Collapse
Affiliation(s)
- Yixin Chen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Wenjie Fu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Han Xiao
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Yuke Zhai
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Sciences, Zhejiang University, Hangzhou, Zhejiang 3100058, P.R. China
| | - Yingzi Wang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Zhonghua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Qin Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
- Institute of Soil and Water Resources and Environmental Sciences, Zhejiang University, Hangzhou, Zhejiang 3100058, P.R. China
| | - Jianan Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China
- Collaborative Innovation Centre of Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, China
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| |
Collapse
|
29
|
Guo P, Li C, Liu J, Chai B. Predation has a significant impact on the complexity and stability of microbial food webs in subalpine lakes. Microbiol Spectr 2023; 11:e0241123. [PMID: 37787559 PMCID: PMC10714739 DOI: 10.1128/spectrum.02411-23] [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: 06/08/2023] [Accepted: 08/18/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE As an important part of microbial food webs, protists transfer organic carbon and nutrients to higher trophic levels in aquatic ecosystems. Protist predation often influences the abundance and composition of bacterial communities. However, we still do not understand whether and how predation affects the complexity and stability of microbial food webs. This study assessed the seasonal dynamic characteristics and driving factors of microbial food webs in terms of complexity and stability. Our findings have implications for future surveys to reveal the effects of climate and environmental changes.
Collapse
Affiliation(s)
- Ping Guo
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
- Central Laboratory, Changzhi Medical College, Changzhi, China
| | - Cui Li
- Faculty of Environment Economics, Shanxi University of Finance and Economics, Taiyuan, China
| | - Jinxain Liu
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Baofeng Chai
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| |
Collapse
|
30
|
Zhang Z, Yang Y, Zhao J, Li Y, Stephenson SL, Qiu J, Liu P. Environmental factors influencing the diversity and distribution of dictyostelid cellular slime molds in forest and farmland soils of western China. Microbiol Spectr 2023; 11:e0173223. [PMID: 37962389 PMCID: PMC10715086 DOI: 10.1128/spectrum.01732-23] [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: 04/25/2023] [Accepted: 10/04/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Soil protists are an essential yet seriously understudied component of the soil microbiome. In this study, 11 new records of dictyostelids belonging to 2 orders, 3 families, and 4 genera were identified from 99 soil samples collected from different elevations and habitats in central Gansu and the southeastern and southcentral portions of Guizhou Province, China. We found that dictyostelid communities were significantly different between Gansu and Guizhou Provinces, apparently in response to different environmental factors. Moreover, dictyostelids were found to have the highest species diversity in mixed forests. Soil pH, temperature, and elevation were determined to be the primary factors that affect the distribution and occurrence of dictyostelids in Guizhou and Gansu Provinces. This work supplements the survey data available for dictyostelids elsewhere in China. These new findings have significant implications for our understanding of the diversity of soil microorganisms.
Collapse
Affiliation(s)
- Zhaojuan Zhang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yingkun Yang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jing Zhao
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Steven L. Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Junzhi Qiu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Pu Liu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| |
Collapse
|
31
|
Yue Y, Liu C, Xu B, Wang Y, Lv Q, Zhou Z, Li R, Kowalchuk GA, Jousset A, Shen Q, Xiong W. Rhizosphere shapes the associations between protistan predators and bacteria within microbiomes through the deterministic selection on bacterial communities. Environ Microbiol 2023; 25:3623-3629. [PMID: 37849426 DOI: 10.1111/1462-2920.16528] [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: 04/29/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023]
Abstract
The assembly of bacterial communities in the rhizosphere is well-documented and plays a crucial role in supporting plant performance. However, we have limited knowledge of how plant rhizosphere determines the assembly of protistan predators and whether the potential associations between protistan predators and bacterial communities shift due to rhizosphere selection. To address this, we examined bacterial and protistan taxa from 443 agricultural soil samples including bulk and rhizosphere soils. Our results presented distinct patterns of bacteria and protistan predators in rhizosphere microbiome assembly. Community assembly of protistan predators was determined by a stochastic process in the rhizosphere and the diversity of protistan predators was reduced in the rhizosphere compared to bulk soils, these may be attributed to the indirect impacts from the altered bacterial communities that showed deterministic process assembly in the rhizosphere. Interestingly, we observed that the plant rhizosphere facilitates more close interrelationships between protistan predators and bacterial communities, which might promote a healthy rhizosphere microbial community for plant growth. Overall, our findings indicate that the potential predator-prey relationships within the microbiome, mediated by plant rhizosphere, might contribute to plant performance in agricultural ecosystems.
Collapse
Affiliation(s)
- Yang Yue
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Chen Liu
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Boting Xu
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yijin Wang
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Qihui Lv
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Zeyuan Zhou
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Rong Li
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Alexandre Jousset
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Wu Xiong
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
32
|
Zhao J, Fan D, Guo W, Wu J, Zhang X, Zhuang X, Kong W. Precipitation Drives Soil Protist Diversity and Community Structure in Dry Grasslands. MICROBIAL ECOLOGY 2023; 86:2293-2304. [PMID: 37191674 DOI: 10.1007/s00248-023-02235-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/30/2023] [Indexed: 05/17/2023]
Abstract
Protists are essential components of soil microbial communities, mediating nutrient cycling and ecosystem functions in terrestrial ecosystems. However, their distribution patterns and driving factors, particularly, the relative importance of climate, plant and soil factors, remain largely unknown. This limits our understanding of soil protist roles in ecosystem functions and their responses to climate change. This is particularly a concern in dryland ecosystems where soil microbiomes are more important for ecosystem functions because plant diversity and growth are heavily constrained by environmental stresses. Here, we explored protist diversity and their driving factors in grassland soils on the Tibetan Plateau, which is a typical dryland region with yearly low temperatures. Soil protist diversity significantly decreased along the gradient of meadow, steppe, and desert. Soil protist diversity positively correlated with precipitation, plant biomass and soil nutrients, but these correlations were changed by grazing. Structural equation and random forest models demonstrated that precipitation dominated soil protist diversity directly and indirectly by influencing plant and soil factors. Soil protist community structure gradually shifted along meadow, steppe and desert, and was driven more by precipitation than by plant and soil factors. Soil protist community compositions were dominated by Cercozoa, Ciliophora and Chlorophyta. In particular, Ciliophora increased but Chlorophyta decreased in relative abundance along the gradient of meadow, steppe and desert. These results demonstrate that precipitation plays more important roles in driving soil protist diversity and community structure than plant and soil factors, suggesting that future precipitation change profoundly alters soil protist community and functions in dry grasslands.
Collapse
Affiliation(s)
- Jin Zhao
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Inner Mongolia University, Hohhot, 010021, China
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Dandan Fan
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Wei Guo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Inner Mongolia University, Hohhot, 010021, China
| | - Jianshuang Wu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianzhou Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuliang Zhuang
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, 100101, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100039, China.
| |
Collapse
|
33
|
Hu S, Li G, Berlinches de Gea A, Teunissen J, Geisen S, Wilschut RA, Schwelm A, Wang Y. Microbiome predators in changing soils. Environ Microbiol 2023; 25:2057-2067. [PMID: 37438930 DOI: 10.1111/1462-2920.16461] [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: 03/14/2023] [Accepted: 06/22/2023] [Indexed: 07/14/2023]
Abstract
Microbiome predators shape the soil microbiome and thereby soil functions. However, this knowledge has been obtained from small-scale observations in fundamental rather than applied settings and has focused on a few species under ambient conditions. Therefore, there are several unaddressed questions on soil microbiome predators: (1) What is the role of microbiome predators in soil functioning? (2) How does global change affect microbiome predators and their functions? (3) How can microbiome predators be applied in agriculture? We show that there is sufficient evidence for the vital role of microbiome predators in soils and stress that global changes impact their functions, something that urgently needs to be addressed to better understand soil functioning as a whole. We are convinced that there is a potential for the application of microbiome predators in agricultural settings, as they may help to sustainably increase plant growth. Therefore, we plea for more applied research on microbiome predators.
Collapse
Affiliation(s)
- Shunran Hu
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Guixin Li
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Alejandro Berlinches de Gea
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
| | - Joliese Teunissen
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Stefan Geisen
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
| | - Rutger A Wilschut
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
| | - Arne Schwelm
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
- Department of Environment, Soils and Landuse, Teagasc Johnstown Castle, Wexford, Ireland
| | - Yuxin Wang
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Geisen S, Lara E, Mitchell E. Contemporary issues, current best practice and ways forward in soil protist ecology. Mol Ecol Resour 2023; 23:1477-1487. [PMID: 37259890 DOI: 10.1111/1755-0998.13819] [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: 10/31/2022] [Revised: 02/23/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Soil protists are increasingly studied due to a release from previous methodological constraints and the acknowledgement of their immense diversity and functional importance in ecosystems. However, these studies often lack sufficient depth in knowledge, which is visible in the form of falsely used terms and false- or over-interpreted data with conclusions that cannot be drawn from the data obtained. As we welcome that also non-experts include protists in their still mostly bacterial and/or fungal-focused studies, our aim here is to help avoid some common errors. We provide suggestions for current terms to use when working on soil protists, like protist instead of protozoa, predator instead of grazer, microorganisms rather than microflora and other terms to be used to describe the prey spectrum of protists. We then highlight some dos and don'ts in soil protist ecology including challenges related to interpreting 18S rRNA gene amplicon sequencing data. We caution against the use of standard bioinformatic settings optimized for bacteria and the uncritical reliance on incomplete and partly erroneous reference databases. We also show why causal inferences cannot be drawn from sequence-based correlation analyses or any sampling/monitoring, study in the field without thorough experimental confirmation and sound understanding of the biology of taxa. Together, we envision this work to help non-experts to more easily include protists in their soil ecology analyses and obtain more reliable interpretations from their protist data and other biodiversity data that, in the end, will contribute to a better understanding of soil ecology.
Collapse
Affiliation(s)
- Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | | | - Edward Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| |
Collapse
|
36
|
Garrido-Sanz D, Čaušević S, Vacheron J, Heiman CM, Sentchilo V, van der Meer JR, Keel C. Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere. MICROBIOME 2023; 11:214. [PMID: 37770950 PMCID: PMC10540321 DOI: 10.1186/s40168-023-01660-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/31/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND Plant-beneficial bacterial inoculants are of great interest in agriculture as they have the potential to promote plant growth and health. However, the inoculation of the rhizosphere microbiome often results in a suboptimal or transient colonization, which is due to a variety of factors that influence the fate of the inoculant. To better understand the fate of plant-beneficial inoculants in complex rhizosphere microbiomes, composed by hundreds of genotypes and multifactorial selection mechanisms, controlled studies with high-complexity soil microbiomes are needed. RESULTS We analysed early compositional changes in a taxa-rich natural soil bacterial community under both exponential nutrient-rich and stationary nutrient-limited growth conditions (i.e. growing and stable communities, respectively) following inoculation with the plant-beneficial bacterium Pseudomonas protegens in a bulk soil or a wheat rhizosphere environment. P. protegens successfully established under all conditions tested and was more abundant in the rhizosphere of the stable community. Nutrient availability was a major factor driving microbiome composition and structure as well as the underlying assembly processes. While access to nutrients resulted in communities assembled mainly by homogeneous selection, stochastic processes dominated under the nutrient-deprived conditions. We also observed an increased rhizosphere selection effect under nutrient-limited conditions, resulting in a higher number of amplicon sequence variants (ASVs) whose relative abundance was enriched. The inoculation with P. protegens produced discrete changes, some of which involved other Pseudomonas. Direct competition between Pseudomonas strains partially failed to replicate the observed differences in the microbiome and pointed to a more complex interaction network. CONCLUSIONS The results of this study show that nutrient availability is a major driving force of microbiome composition, structure and diversity in both the bulk soil and the wheat rhizosphere and determines the assembly processes that govern early microbiome development. The successful establishment of the inoculant was facilitated by the wheat rhizosphere and produced discrete changes among other members of the microbiome. Direct competition between Pseudomonas strains only partially explained the microbiome changes, indicating that indirect interactions or spatial distribution in the rhizosphere or soil interface may be crucial for the survival of certain bacteria. Video Abstract.
Collapse
Affiliation(s)
- Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
| | - Senka Čaušević
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Clara M Heiman
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
| |
Collapse
|
37
|
Li J, Yang C, Jousset A, Yang K, Wang X, Xu Z, Yang T, Mei X, Zhong Z, Xu Y, Shen Q, Friman VP, Wei Z. Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants. eLife 2023; 12:e90726. [PMID: 37706503 PMCID: PMC10519709 DOI: 10.7554/elife.90726] [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: 07/04/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Abstract
While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth promotion in agricultural systems.
Collapse
Affiliation(s)
- Jingxuan Li
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Chunlan Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Alexandre Jousset
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Keming Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zhihui Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Tianjie Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xinlan Mei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zengtao Zhong
- College of Life Science, Nanjing Agricultural UniversityNanjingChina
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Ville-Petri Friman
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
- Department of Microbiology, University of HelsinkiHelsinkiFinland
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| |
Collapse
|
38
|
Yang J, Yun J, Liu X, Du W, Xiang M. Niche and ecosystem preference of earliest diverging fungi in soils. Mycology 2023; 14:239-255. [PMID: 37583459 PMCID: PMC10424602 DOI: 10.1080/21501203.2023.2237047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/11/2023] [Indexed: 08/17/2023] Open
Abstract
Within the supergroup Rotosphaeromycetes, or "Holomycota"/"Nucletmycea", there are several well-recognised unicellular clades in the earliest diverging fungi (EDF). However, we know little about their occurrence. Here, we investigated EDF in the rhizosphere and bulk soils from cropland, forest, orchard, and wetland ecosystems around the Beijing-Hebei area, China, to illustrate their niche and ecosystem preference. More than 500 new operational taxonomic units (OTUs) of EDF were detected based on the 18S rRNA genes. Microsporida and Aphelida constitute dominant groups, whereas Rozellosporida was quite rare. Although the EDF community was site-specific, the soil chemical characteristics, vegetation, and other eukaryotic microorganisms were the key factors driving the occurrence of EDF. Moreover, the stochastic process consisted the most of the EDF community assembly.
Collapse
Affiliation(s)
- Jiarui Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Juanli Yun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
39
|
Zheng W, Zheng X, Wu Y, Lv S, Ge C, Wang X, Wang Q, Cui J, Ren N, Chen Y. Diversity Temporal-Spatial Dynamics of Potato Rhizosphere Ciliates and Contribution to Nitrogen- and Carbon-Derived Nutrition in North-East China. PLANTS (BASEL, SWITZERLAND) 2023; 12:2260. [PMID: 37375886 DOI: 10.3390/plants12122260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023]
Abstract
Ciliates are an important component of the rhizosphere microorganism community, but their nutritional contribution to plants has not been fully revealed. In this paper, we investigated the rhizosphere ciliate community of potatoes during six growth stages, illustrated the spatial-temporal dynamics of composition and diversity, and analyzed the correlation between soil physicochemical properties. The contributions of ciliates to the carbon- and nitrogen-derived nutrition of potatoes were calculated. Fifteen species of ciliates were identified, with higher diversity in the top soil, which increased as the potatoes grew, while they were more abundant in the deep soil, and the number decreased as the potatoes grew. The highest number of species of ciliates appeared in July (seedling stage). Among the five core species of ciliates, Colpoda sp. was the dominant species in all six growth stages. Multiple physicochemical properties affected the rhizosphere ciliate community, with ammonium nitrogen (NH4+-N) and the soil water content (SWC) greatly influencing ciliate abundance. The key correlation factors of ciliates diversity were NH4+-N, available phosphorus (AP), and soil organic matter (SOM). The annual average contribution rates of carbon and nitrogen by rhizosphere ciliates to potatoes were 30.57% and 23.31%, respectively, with the highest C/N contribution rates reaching 94.36% and 72.29% in the seedling stage. This study established a method for estimating the contributions of carbon and nitrogen by ciliates to crops and found that ciliates could be potential organic fertilizer organisms. These results might be used to improve water and nitrogen management in potato cultivation and promote ecological agriculture.
Collapse
Affiliation(s)
- Weibin Zheng
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Xiaodan Zheng
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yuqing Wu
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Shaoyang Lv
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Chang Ge
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Xiang Wang
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Qiuhong Wang
- Crop Academy, Heilongjiang University, Harbin 150080, China
| | - Jingjing Cui
- Crop Academy, Heilongjiang University, Harbin 150080, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Ying Chen
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| |
Collapse
|
40
|
Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
Abstract
The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.
Collapse
Affiliation(s)
- Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian Jin
- Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| |
Collapse
|
41
|
Baldrian P, López-Mondéjar R, Kohout P. Forest microbiome and global change. Nat Rev Microbiol 2023:10.1038/s41579-023-00876-4. [PMID: 36941408 DOI: 10.1038/s41579-023-00876-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 03/23/2023]
Abstract
Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially fungi and bacteria. The effects of global change differ among boreal, temperate and tropical forests. The future of forests depends mostly on the performance and balance of fungal symbiotic guilds, saprotrophic fungi and bacteria, and fungal plant pathogens. Drought severely weakens forest resilience, as it triggers adverse processes such as pathogen outbreaks and fires that impact the microbial and forest performance for carbon storage and nutrient turnover. Nitrogen deposition also substantially affects forest microbial processes, with a pronounced effect in the temperate zone. Considering plant-microorganism interactions would help predict the future of forests and identify management strategies to increase ecosystem stability and alleviate climate change effects. In this Review, we describe the impact of global change on the forest ecosystem and its microbiome across different climatic zones. We propose potential approaches to control the adverse effects of global change on forest stability, and present future research directions to understand the changes ahead.
Collapse
Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| |
Collapse
|
42
|
Ren P, Sun A, Jiao X, Shen JP, Yu DT, Li F, Wu B, He JZ, Hu HW. Predatory protists play predominant roles in suppressing soil-borne fungal pathogens under organic fertilization regimes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160986. [PMID: 36528948 DOI: 10.1016/j.scitotenv.2022.160986] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Soil-borne fungal pathogens pose a major threat to global agricultural production and food security. Pathogen-suppressive bacteria and plant beneficial protists are important components of soil microbiomes and essential to plant health and performance, but it remains largely unknown regarding how agricultural management practices influence the relative importance of protists and bacteria in plant disease suppression. Here, we characterized soil microbiomes (including fungi, protists, and bacteria) in bulk and sorghum rhizosphere soils with various long-term inorganic and organic fertilization regimes, and linked the changes in fungal plant pathogens with the protistan and bacterial communities. We found that the relative abundances of fungal pathogens were significantly decreased by organic fertilization regimes, and there was a significant difference in the community composition of fungal pathogens between inorganic and organic fertilization regimes. Organic fertilization significantly enhanced predatory protists but reduced the proportions of protistan phototrophs. Co-occurrence network analysis revealed more intensive connections between fungal plant pathogens with protists, especially predatory protists, than with bacterial taxa, which was further supported by stronger associations between the community structure of fungal pathogens and predatory protists. We identified more protist consumer taxa than bacterial taxa as predictors of fungal plant pathogens, and structural equation modelling revealed a more important impact of protist consumers than bacteria on fungal pathogens. Altogether, we provide new evidence that the disease inhibitory effects of long-term organic fertilization regimes could be best explained by the potential predation pressure of protists. Our findings advance the mechanistic understanding of the role of predator-prey interactions in controlling fungal diseases, and have implications for novel biocontrol strategies to mitigate the consequences of fungal infections for plant performance.
Collapse
Affiliation(s)
- Peixin Ren
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Anqi Sun
- 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
| | - Xiaoyan Jiao
- College of Resource and Environment, Shanxi Agricultural University, Taiyuan, China
| | - Ju-Pei Shen
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Dan-Ting Yu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Fangfang Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Bingxue Wu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Ji-Zheng He
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Hang-Wei Hu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China; School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville 3010, Victoria, Australia.
| |
Collapse
|
43
|
Lv Z, Xu M, Liu Y, Rønn R, Rensing C, Liu S, Gao S, Liao H, Liu YR, Chen W, Zhu YG, Huang Q, Hao X. Phagotrophic Protists Modulate Copper Resistance of the Bacterial Community in Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:3590-3601. [PMID: 36811608 DOI: 10.1021/acs.est.2c07136] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Protist predation is a crucial biotic driver modulating bacterial populations and functional traits. Previous studies using pure cultures have demonstrated that bacteria with copper (Cu) resistance exhibited fitness advantages over Cu-sensitive bacteria under the pressure of protist predation. However, the impact of diverse natural communities of protist grazers on bacterial Cu resistance in natural environments remains unknown. Here, we characterized the communities of phagotrophic protists in long-term Cu-contaminated soils and deciphered their potential ecological impacts on bacterial Cu resistance. Long-term field Cu pollution increased the relative abundances of most of the phagotrophic lineages in Cercozoa and Amoebozoa but reduced the relative abundance of Ciliophora. After accounting for soil properties and Cu pollution, phagotrophs were consistently identified as the most important predictor of the Cu-resistant (CuR) bacterial community. Phagotrophs positively contributed to the abundance of a Cu resistance gene (copA) through influencing the cumulative relative abundance of Cu-resistant and -sensitive ecological clusters. Microcosm experiments further confirmed the promotion effect of protist predation on bacterial Cu resistance. Our results indicate that the selection by protist predation can have a strong impact on the CuR bacterial community, which broadens our understanding of the ecological function of soil phagotrophic protists.
Collapse
Affiliation(s)
- Zhenguang Lv
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Regin Rønn
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Song Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shenghan Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Liao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
44
|
Mitsi K, Richter DJ, Arroyo AS, López-Escardó D, Antó M, Oterino AG, Ruiz-Trillo I. Taxonomic composition, community structure and molecular novelty of microeukaryotes in a temperate oligomesotrophic lake as revealed by metabarcoding. Sci Rep 2023; 13:3119. [PMID: 36813945 PMCID: PMC9947120 DOI: 10.1038/s41598-023-30228-4] [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: 07/03/2022] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
Microbial eukaryotes are diverse and ecologically important organisms, yet sampling constraints have hindered the understanding of their distribution and diversity in freshwater ecosystems. Metabarcoding has provided a powerful complement to traditional limnological studies, revealing an unprecedented diversity of protists in freshwater environments. Here, we aim to expand our knowledge of the ecology and diversity of protists in lacustrine ecosystems by targeting the V4 hypervariable region of the 18S rRNA gene in water column, sediment and biofilm samples collected from Sanabria Lake (Spain) and surrounding freshwater ecosystems. Sanabria is a temperate lake, which are relatively understudied by metabarcoding in comparison to alpine and polar lakes. The phylogenetic diversity of microbial eukaryotes detected in Sanabria spans all currently recognized eukaryotic supergroups, with Stramenopiles being the most abundant and diverse supergroup in all sampling sites. Parasitic microeukaryotes account for 21% of the total protist ASVs identified in our study and were dominated by Chytridiomycota, both in terms of richness and abundance, in all sampling sites. Sediments, biofilms and water column samples harbour distinct microbial communities. Phylogenetic placement of poorly assigned and abundant ASVs indicates molecular novelty inside Rhodophyta, Bigyra, early-branching Nucletmycea and Apusomonadida. In addition, we report the first freshwater incidence of the previously exclusively marine genera Abeoforma and Sphaeroforma. Our results contribute to a deeper understanding of microeukaryotic communities in freshwater ecosystems, and provide the first molecular reference for future biomonitoring surveys in Sanabria Lake.
Collapse
Affiliation(s)
- Konstantina Mitsi
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033, Barcelona, Spain.
| | - Daniel J. Richter
- grid.507636.10000 0004 0424 5398Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain
| | - Alicia S. Arroyo
- grid.507636.10000 0004 0424 5398Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain
| | - David López-Escardó
- grid.418218.60000 0004 1793 765XInstitut de Ciències del Mar (CSIC), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain
| | - Meritxell Antó
- grid.507636.10000 0004 0424 5398Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain
| | | | - Iñaki Ruiz-Trillo
- grid.507636.10000 0004 0424 5398Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain ,grid.425902.80000 0000 9601 989XInstitució Catalana de Recerca I Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08010 Barcelona, Spain
| |
Collapse
|
45
|
Zheng X, Xu K, Naoum J, Lian Y, Wu B, He Z, Yan Q. Deciphering microeukaryotic-bacterial co-occurrence networks in coastal aquaculture ponds. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:44-55. [PMID: 37073331 PMCID: PMC10077187 DOI: 10.1007/s42995-022-00159-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 12/06/2022] [Indexed: 05/03/2023]
Abstract
Microeukaryotes and bacteria are key drivers of primary productivity and nutrient cycling in aquaculture ecosystems. Although their diversity and composition have been widely investigated in aquaculture systems, the co-occurrence bipartite network between microeukaryotes and bacteria remains poorly understood. This study used the bipartite network analysis of high-throughput sequencing datasets to detect the co-occurrence relationships between microeukaryotes and bacteria in water and sediment from coastal aquaculture ponds. Chlorophyta and fungi were dominant phyla in the microeukaryotic-bacterial bipartite networks in water and sediment, respectively. Chlorophyta also had overrepresented links with bacteria in water. Most microeukaryotes and bacteria were classified as generalists, and tended to have symmetric positive and negative links with bacteria in both water and sediment. However, some microeukaryotes with high density of links showed asymmetric links with bacteria in water. Modularity detection in the bipartite network indicated that four microeukaryotes and twelve uncultured bacteria might be potential keystone taxa among the module connections. Moreover, the microeukaryotic-bacterial bipartite network in sediment harbored significantly more nestedness than that in water. The loss of microeukaryotes and generalists will more likely lead to the collapse of positive co-occurrence relationships between microeukaryotes and bacteria in both water and sediment. This study unveils the topology, dominant taxa, keystone species, and robustness in the microeukaryotic-bacterial bipartite networks in coastal aquaculture ecosystems. These species herein can be applied for further management of ecological services, and such knowledge may also be very useful for the regulation of other eutrophic ecosystems. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00159-6.
Collapse
Affiliation(s)
- Xiafei Zheng
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, 315100 China
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization Technology, College of Life Sciences, Hubei Normal University, Huangshi, 435002 China
| | - Jonathan Naoum
- Department of Biological Sciences, Ecotoxicology of Aquatic Microorganisms Laboratory, GRIL-EcotoQ-TOXEN, Université Du Québec À Montréal, Succursale Centre-Ville, Montreal, QC Canada
| | - Yingli Lian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
- Animal Husbandry and Fisheries Research Center of Guangdong Haid Group CO., Ltd. Key Laboratory of Microecological Resources and Utilization in Breeding Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, 510006 China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| |
Collapse
|
46
|
Mishra A, Singh L, Singh D. Unboxing the black box-one step forward to understand the soil microbiome: A systematic review. MICROBIAL ECOLOGY 2023; 85:669-683. [PMID: 35112151 PMCID: PMC9957845 DOI: 10.1007/s00248-022-01962-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.
Collapse
Affiliation(s)
- Apurva Mishra
- Academy of Scientific and Innovative Research [AcSIR], Ghaziabad, 201002, India
- Environmental Biotechnology and Genomics Division, , CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Lal Singh
- Environmental Biotechnology and Genomics Division, , CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Dharmesh Singh
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Trogerstrasse 30, 81675, Munich, Bavaria, Germany.
| |
Collapse
|
47
|
Jiang Y, Wang Z, Liu Y, Han Y, Wang Y, Wang Q, Liu T. Nematodes and their bacterial prey improve phosphorus acquisition by wheat. THE NEW PHYTOLOGIST 2023; 237:974-986. [PMID: 36285379 DOI: 10.1111/nph.18569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Plant growth is greatly influenced by the rhizosphere microbiome, which has been traditionally investigated from a bottom-up perspective assessing how resources such as root exudates stimulate microbial growth and drive microbiome assembly. However, the importance of predation as top-down force on the soil microbiome remains largely underestimated. Here, we planted wheat both in natural and in sterilized soils inoculated with the key microbiome predators - bacterivorous nematodes - to assess how plant performance responds to top-down predation of the soil microbiome and specific plant growth-promoting bacteria, namely phosphate-solubilizing bacteria. We found that nematodes enriched certain groups (e.g. Actinobacteria, Chloroflexi, and Firmicutes) and strengthened microbial connectance (e.g. Actinobacteria and Proteobacteria). These changes in microbiome structure were associated with phosphate-solubilizing bacteria that facilitated phosphorus (P) cycling, leading to greater P uptake and biomass of wheat in both soils. However, the enhancement varied between nematode species, which may be attributed to the divergence of feeding behavior, as nematodes with weaker grazing intensity supported greater abundance of phosphate-solubilizing bacteria and better plant performance compared with nematodes with greater grazing intensity. These results confirmed the ecological importance of soil nematodes for ecosystem functions via microbial co-occurrence networks and suggested that the predation strength of nematodes determines the soil bacteria contribution to P biogeochemical cycling and plant growth.
Collapse
Affiliation(s)
- Ying Jiang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhonghua Wang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ye Liu
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yanlai Han
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yi Wang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qiang Wang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ting Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
48
|
Nguyen BT, Dumack K, Trivedi P, Islam Z, Hu H. Plant associated protists-Untapped promising candidates for agrifood tools. Environ Microbiol 2023; 25:229-240. [PMID: 36482161 PMCID: PMC10108267 DOI: 10.1111/1462-2920.16303] [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: 10/10/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
The importance of host-associated microorganisms and their biotic interactions for plant health and performance has been increasingly acknowledged. Protists, main predators and regulators of bacteria and fungi, are abundant and ubiquitous eukaryotes in terrestrial ecosystems. Protists are considered to benefit plant health and performance, but the community structure and functions of plant-associated protists remain surprisingly underexplored. Harnessing plant-associated protists and other microbes can potentially enhance plant health and productivity and sustain healthy food and agriculture systems. In this review, we summarize the knowledge of multifunctionality of protists and their interactions with other microbes in plant hosts, and propose a future framework to study plant-associated protists and utilize protists as agrifood tools for benefiting agricultural production.
Collapse
Affiliation(s)
- Bao‐Anh Thi Nguyen
- School of Agriculture and Food, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia
| | - Kenneth Dumack
- Terrestrial EcologyInstitute of Zoology, University of CologneKölnGermany
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Zahra Islam
- School of Agriculture and Food, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia
- ARC Hub for Smart FertilisersThe University of MelbourneParkvilleVictoriaAustralia
| | - Hang‐Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia
- ARC Hub for Smart FertilisersThe University of MelbourneParkvilleVictoriaAustralia
| |
Collapse
|
49
|
Hirayama T, Mochida K. Plant Hormonomics: A Key Tool for Deep Physiological Phenotyping to Improve Crop Productivity. PLANT & CELL PHYSIOLOGY 2023; 63:1826-1839. [PMID: 35583356 PMCID: PMC9885943 DOI: 10.1093/pcp/pcac067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/07/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Agriculture is particularly vulnerable to climate change. To cope with the risks posed by climate-related stressors to agricultural production, global population growth, and changes in food preferences, it is imperative to develop new climate-smart crop varieties with increased yield and environmental resilience. Molecular genetics and genomic analyses have revealed that allelic variations in genes involved in phytohormone-mediated growth regulation have greatly improved productivity in major crops. Plant science has remarkably advanced our understanding of the molecular basis of various phytohormone-mediated events in plant life. These findings provide essential information for improving the productivity of crops growing in changing climates. In this review, we highlight the recent advances in plant hormonomics (multiple phytohormone profiling) and discuss its application to crop improvement. We present plant hormonomics as a key tool for deep physiological phenotyping, focusing on representative plant growth regulators associated with the improvement of crop productivity. Specifically, we review advanced methodologies in plant hormonomics, highlighting mass spectrometry- and nanosensor-based plant hormone profiling techniques. We also discuss the applications of plant hormonomics in crop improvement through breeding and agricultural management practices.
Collapse
Affiliation(s)
- Takashi Hirayama
- *Corresponding authors: Takashi Hirayama, E-mail, ; Keiichi Mochida, E-mail,
| | - Keiichi Mochida
- *Corresponding authors: Takashi Hirayama, E-mail, ; Keiichi Mochida, E-mail,
| |
Collapse
|
50
|
Kane JL, Kotcon JB, Freedman ZB, Morrissey EM. Fungivorous nematodes drive microbial diversity and carbon cycling in soil. Ecology 2023; 104:e3844. [PMID: 35960179 DOI: 10.1002/ecy.3844] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/06/2022] [Accepted: 07/01/2022] [Indexed: 02/01/2023]
Abstract
Soil bacteria and fungi mediate terrestrial biogeochemical cycling, but we know relatively little about how trophic interactions influence their community composition, diversity, and function. Specifically, it is unclear how consumer populations affect the activity of microbial taxa they consume, and therefore the interaction of those taxa with other members of the microbial community. Due to its extreme diversity, studying trophic dynamics in soil is a complex feat. Seeking to address these challenges, we performed a microcosm-based consumer manipulation experiment to determine the impact of a common fungal-feeding nematode (Aphelenchus avenae) on soil microbial community composition, diversity, and activity (e.g., C cycling parameters). Fungivory decreased fungal and bacterial α-diversity and stimulated C and N cycling, possibly via cascading impacts of fungivory on bacterial communities. Our results present experimental evidence that soil trophic dynamics are intimately linked with microbial diversity and function, factors that are key in understanding global patterns in biogeochemical cycling.
Collapse
Affiliation(s)
- Jennifer L Kane
- Division of Plant and Soil Science, Davis College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia, USA
| | - James B Kotcon
- Division of Plant and Soil Science, Davis College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia, USA
| | - Zachary B Freedman
- Department of Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ember M Morrissey
- Division of Plant and Soil Science, Davis College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia, USA
| |
Collapse
|