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Fernández-Triana I, Rubilar O, Parada J, Fincheira P, Benavides-Mendoza A, Durán P, Fernández-Baldo M, Seabra AB, Tortella GR. Metal nanoparticles and pesticides under global climate change: Assessing the combined effects of multiple abiotic stressors on soil microbial ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 942:173494. [PMID: 38810746 DOI: 10.1016/j.scitotenv.2024.173494] [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: 03/12/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
The soil is a vital resource that hosts many microorganisms crucial in biogeochemical cycles and ecosystem health. However, human activities such as the use of metal nanoparticles (MNPs), pesticides and the impacts of global climate change (GCCh) can significantly affect soil microbial communities (SMC). For many years, pesticides and, more recently, nanoparticles have contributed to sustainable agriculture to ensure continuous food production to sustain the significant growth of the world population and, therefore, the demand for food. Pesticides have a recognized pest control capacity. On the other hand, nanoparticles have demonstrated a high ability to improve water and nutrient retention, promote plant growth, and control pests. However, it has been reported that their accumulation in agricultural soils can also adversely affect the environment and soil microbial health. In addition, climate change, with its variations in temperature and extreme water conditions, can lead to drought and increased soil salinity, modifying both soil conditions and the composition and function of microbial communities. Abiotic stressors can interact and synergistically or additively affect soil microorganisms, significantly impacting soil functioning and the capacity to provide ecosystem services. Therefore, this work reviewed the current scientific literature to understand how multiple stressors interact and affect the SMC. In addition, the importance of molecular tools such as metagenomics, metatranscriptomics, proteomics, or metabolomics in the study of the responses of SMC to exposure to multiple abiotic stressors was examined. Future research directions were also proposed, focusing on exploring the complex interactions between stressors and their long-term effects and developing strategies for sustainable soil management. These efforts will contribute to the preservation of soil health and the promotion of sustainable agricultural practices.
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Affiliation(s)
- I Fernández-Triana
- Doctoral Program in Science of Natural Resources, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile
| | - O Rubilar
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, 4811230 Temuco, Chile; Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile
| | - J Parada
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, 4811230 Temuco, Chile
| | - P Fincheira
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, 4811230 Temuco, Chile
| | - A Benavides-Mendoza
- Departamento de Horticultura, Universidad Autónoma Agraria Antonio Narro, 25315 Saltillo, Mexico
| | - P Durán
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
| | - Martín Fernández-Baldo
- Department of Animal and Plant Biology, University of Londrina, PR 445, km 380, CEP 86047-970 Londrina, PR, Brazil
| | - A B Seabra
- Center for Natural and Human Sciences, Universidade Federal do ABC, Santo André, Brazil
| | - G R Tortella
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, 4811230 Temuco, Chile; Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile.
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2
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Baker NR, Zhalnina K, Yuan M, Herman D, Ceja-Navarro JA, Sasse J, Jordan JS, Bowen BP, Wu L, Fossum C, Chew A, Fu Y, Saha M, Zhou J, Pett-Ridge J, Northen TR, Firestone MK. Nutrient and moisture limitations reveal keystone metabolites linking rhizosphere metabolomes and microbiomes. Proc Natl Acad Sci U S A 2024; 121:e2303439121. [PMID: 39093948 PMCID: PMC11317588 DOI: 10.1073/pnas.2303439121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/03/2024] [Indexed: 08/04/2024] Open
Abstract
Plants release a wealth of metabolites into the rhizosphere that can shape the composition and activity of microbial communities in response to environmental stress. The connection between rhizodeposition and rhizosphere microbiome succession has been suggested, particularly under environmental stress conditions, yet definitive evidence is scarce. In this study, we investigated the relationship between rhizosphere chemistry, microbiome dynamics, and abiotic stress in the bioenergy crop switchgrass grown in a marginal soil under nutrient-limited, moisture-limited, and nitrogen (N)-replete, phosphorus (P)-replete, and NP-replete conditions. We combined 16S rRNA amplicon sequencing and LC-MS/MS-based metabolomics to link rhizosphere microbial communities and metabolites. We identified significant changes in rhizosphere metabolite profiles in response to abiotic stress and linked them to changes in microbial communities using network analysis. N-limitation amplified the abundance of aromatic acids, pentoses, and their derivatives in the rhizosphere, and their enhanced availability was linked to the abundance of bacterial lineages from Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. Conversely, N-amended conditions increased the availability of N-rich rhizosphere compounds, which coincided with proliferation of Actinobacteria. Treatments with contrasting N availability differed greatly in the abundance of potential keystone metabolites; serotonin and ectoine were particularly abundant in N-replete soils, while chlorogenic, cinnamic, and glucuronic acids were enriched in N-limited soils. Serotonin, the keystone metabolite we identified with the largest number of links to microbial taxa, significantly affected root architecture and growth of rhizosphere microorganisms, highlighting its potential to shape microbial community and mediate rhizosphere plant-microbe interactions.
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Affiliation(s)
- Nameer R. Baker
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA94720
| | - Kateryna Zhalnina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Mengting Yuan
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA94720
| | - Don Herman
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA94720
| | - Javier A. Ceja-Navarro
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ86011
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Joelle Sasse
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Institute for Plant and Microbial Biology, University of Zurich, CH-8008Zurich, Switzerland
| | - Jacob S. Jordan
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Department of Chemistry, University of California, Berkeley, CA94720
| | - Benjamin P. Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK73019
| | - Christina Fossum
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA94720
| | - Aaron Chew
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA94720
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA94550
| | - Ying Fu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK73019
| | - Malay Saha
- Noble Research Institute, Ardmore, OK73401
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK73019
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA94550
- Life and Environmental Sciences Department, University of California Merced, Merced, CA95343
| | - Trent R. Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Mary K. Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA94720
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3
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Liu H, Li J, Singh BK. Harnessing co-evolutionary interactions between plants and Streptomyces to combat drought stress. NATURE PLANTS 2024; 10:1159-1171. [PMID: 39048724 DOI: 10.1038/s41477-024-01749-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 06/25/2024] [Indexed: 07/27/2024]
Abstract
Streptomyces is a drought-tolerant bacterial genus in soils, which forms close associations with plants to provide host resilience to drought stress. Here we synthesize the emerging research that illuminates the multifaceted interactions of Streptomyces spp. in both plant and soil environments. It also explores the potential co-evolutionary relationship between plants and Streptomyces spp. to forge mutualistic relationships, providing drought tolerance to plants. We propose that further advancement in fundamental knowledge of eco-evolutionary interactions between plants and Streptomyces spp. is crucial and holds substantial promise for developing effective strategies to combat drought stress, ensuring sustainable agriculture and environmental sustainability in the face of climate change.
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Affiliation(s)
- Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, Australia.
| | - Jiayu Li
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, Australia.
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Bandopadhyay S, Li X, Bowsher AW, Last RL, Shade A. Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought. Nat Commun 2024; 15:6347. [PMID: 39068162 PMCID: PMC11283566 DOI: 10.1038/s41467-024-50463-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 07/11/2024] [Indexed: 07/30/2024] Open
Abstract
Mitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers. Differences in community structure were observed between crops and between drought and watered and planted and unplanted treatments within crops. Despite crop-specific communities, drought rhizobiome dynamics were similar across the two crops. The presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought observed only for the bean rhizobiome. The switchgrass rhizobiome was stable despite changes in rhizosphere metabolite profiles between planted and unplanted treatments. We conclude that rhizobiome responses to short-term drought are crop-specific, with possible decoupling of plant exudation from rhizobiome responses.
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Affiliation(s)
- Sreejata Bandopadhyay
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
- U.S. Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
| | - Xingxing Li
- U.S. Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Alan W Bowsher
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Robert L Last
- U.S. Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Ashley Shade
- Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Laboratoire d'Ecologie Microbienne LEM, CNRS UMR5557, INRAE UMR1418, Villeurbanne, F-69100, France.
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5
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Lin R, Li H, Wu H, Ren H, Kong X, Lu Z. Resting for viability: Gordonia polyisoprenivorans ZM27, a robust generalist for petroleum bioremediation under hypersaline stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 360:124618. [PMID: 39067736 DOI: 10.1016/j.envpol.2024.124618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/15/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
The intrinsic issue associated with the application of microbes for practical pollution remediation involves maintaining the expected activity of engaged strains or consortiums as effectively as that noted under laboratory conditions. Faced with various stress factors, degraders with dormancy ability are more likely to survive and exhibit degradation activity. In this study, a hydrocarbonoclastic and halotolerant strain, Gordonia polyisoprenivorans ZM27, was isolated via stimulation with resuscitation-promoting factor (Rpf). Long-term exposure to dual stresses of 10% NaCl and starvation induced ZM27 to enter a viable but nonculturable (VBNC)-like state, and ZM27 cells could be resuscitated upon Rpf stimulation. Notable changes in both morphological and physiological characteristics between VBNC-like ZM27 cells and resuscitated cells confirmed the response to Rpf and their robust resistance against harsh environments. Whole-genome sequencing and analysis indicated ZM27 could be a generalist degrader with dormancy ability. Subsequently, VBNC-like ZM27 was applied in a soil microcosm experiment to investigate the practical application potential under harsh conditions. VBNC-like ZM27 combined with Rpf stimulation exhibited the most effective biodegradation performance, and the initial n-hexadecane content (1000 mg kg-1) decreased by 63.29% after 14-day incubation. Based on 16S rRNA amplicon sequencing and analysis, Gordonia exhibited a positive response to Rpf stimulation. The relative abundance of genus Gordonia was negatively correlated with that of Alcanivorax, a genus of obligate hydrocarbon degrader with the greatest abundance during soil incubation. Based on the degradation profile and community analysis, generalist Gordonia may be more efficient in hydrocarbon degradation than specialist Alcanivorax under harsh conditions. The characteristics of ZM27, including its sustainable culturability under long-term stress, response to Rpf and robust performance in soil microcosms, are valuable for the remediation of petroleum pollution under stressful conditions. Our work validated the importance of dormancy and highlighted the underestimated role of low-activity degraders in petroleum remediation.
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Affiliation(s)
- Renzhang Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Hao Li
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Hao Ren
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Xiangyu Kong
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China.
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Huang H, Li M, Guo Q, Zhang R, Zhang Y, Luo K, Chen Y. Influence of Drought Stress on the Rhizosphere Bacterial Community Structure of Cassava ( Manihot esculenta Crantz). Int J Mol Sci 2024; 25:7326. [PMID: 39000433 PMCID: PMC11242396 DOI: 10.3390/ijms25137326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Drought presents a significant abiotic stress that threatens crop productivity worldwide. Rhizosphere bacteria play pivotal roles in modulating plant growth and resilience to environmental stresses. Despite this, the extent to which rhizosphere bacteria are instrumental in plant responses to drought, and whether distinct cassava (Manihot esculenta Crantz) varieties harbor specific rhizosphere bacterial assemblages, remains unclear. In this study, we measured the growth and physiological characteristics, as well as the physical and chemical properties of the rhizosphere soil of drought-tolerant (SC124) and drought-sensitive (SC8) cassava varieties under conditions of both well-watered and drought stress. Employing 16S rDNA high-throughput sequencing, we analyzed the composition and dynamics of the rhizosphere bacterial community. Under drought stress, biomass, plant height, stem diameter, quantum efficiency of photosystem II (Fv/Fm), and soluble sugar of cassava decreased for both SC8 and SC124. The two varieties' rhizosphere bacterial communities' overall taxonomic structure was highly similar, but there were slight differences in relative abundance. SC124 mainly relied on Gamma-proteobacteria and Acidobacteriae in response to drought stress, and the abundance of this class was positively correlated with soil acid phosphatase. SC8 mainly relied on Actinobacteria in response to drought stress, and the abundance of this class was positively correlated with soil urease and soil saccharase. Overall, this study confirmed the key role of drought-induced rhizosphere bacteria in improving the adaptation of cassava to drought stress and clarified that this process is significantly related to variety.
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Affiliation(s)
- Huling Huang
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Mingchao Li
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Qiying Guo
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Rui Zhang
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yindong Zhang
- Key Laboratory of Plant Disease and Pest Control of Hainan Province, Institute of Plant Protection, Hainan Academy of Agricultural Sciences, Haikou 571100, China;
| | - Kai Luo
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yinhua Chen
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
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Pearman WS, Duffy GA, Gemmell NJ, Morales SE, Fraser CI. Long-distance movement dynamics shape host microbiome richness and turnover. FEMS Microbiol Ecol 2024; 100:fiae089. [PMID: 38857884 PMCID: PMC11212666 DOI: 10.1093/femsec/fiae089] [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: 10/06/2023] [Revised: 05/22/2024] [Accepted: 06/08/2024] [Indexed: 06/12/2024] Open
Abstract
Host-associated microbial communities are shaped by host migratory movements. These movements can have contrasting impacts on microbiota, and understanding such patterns can provide insight into the ecological processes that contribute to community diversity. Furthermore, long-distance movements to new environments are anticipated to occur with increasing frequency due to host distribution shifts resulting from climate change. Understanding how hosts transport their microbiota with them could be of importance when examining biological invasions. Although microbial community shifts are well-documented, the underlying mechanisms that lead to the restructuring of these communities remain relatively unexplored. Using literature and ecological simulations, we develop a framework to elucidate the major factors that lead to community change. We group host movements into two types-regular (repeated/cyclical migratory movements, as found in many birds and mammals) and irregular (stochastic/infrequent movements that do not occur on a cyclical basis, as found in many insects and plants). Ecological simulations and prior research suggest that movement type and frequency, alongside environmental exposure (e.g. internal/external microbiota) are key considerations for understanding movement-associated community changes. From our framework, we derive a series of testable hypotheses, and suggest means to test them, to facilitate future research into host movement and microbial community dynamics.
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Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Grant A Duffy
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
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Wei F, Feng Z, Yang C, Zhao L, Zhang Y, Zhou J, Feng H, Zhu H, Xu X. Genetic control of rhizosphere microbiome of the cotton plants under field conditions. Appl Microbiol Biotechnol 2024; 108:371. [PMID: 38861165 PMCID: PMC11166756 DOI: 10.1007/s00253-024-13143-0] [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: 12/08/2023] [Revised: 03/24/2024] [Accepted: 04/09/2024] [Indexed: 06/12/2024]
Abstract
Understanding the extent of heritability of a plant-associated microbiome (phytobiome) is critically important for exploitation of phytobiomes in agriculture. Two crosses were made between pairs of cotton cultivars (Z2 and J11, L1 and Z49) with differential resistance to Verticillium wilt. F2 plants were grown in a field, together with the four parents to study the heritability of cotton rhizosphere microbiome. Amplicon sequencing was used to profile bacterial and fungal communities in the rhizosphere. F2 offspring plants of both crosses had higher average alpha diversity indices than the two parents; parents differed significantly from F2 offspring in Bray-Curtis beta diversity indices as well. Two types of data were used to study the heritability of rhizosphere microbiome: principal components (PCs) and individual top microbial operational taxonomic units (OTUs). For the L1 × Z49 cross, the variance among the F2 progeny genotypes (namely, genetic variance, VT) was significantly greater than the random variability (VE) for 12 and 34 out of top 100 fungal and bacterial PCs, respectively. For the Z2 × J11 cross, the corresponding values were 10 and 20 PCs. For 29 fungal OTUs and 10 bacterial OTUs out of the most abundant 100 OTUs, genetic variance (VT) was significantly greater than VE for the L1 × Z49 cross; the corresponding values for the Z2 × J11 cross were 24 and one. The estimated heritability was mostly in the range of 40% to 60%. These results suggested the existence of genetic control of polygenic nature for specific components of rhizosphere microbiome in cotton. KEY POINTS: • F2 offspring cotton plants differed significantly from parents in rhizosphere microbial diversity. • Specific rhizosphere components are likely to be genetically controlled by plants. • Common PCs and specific microbial groups are significant genetic components between the two crosses.
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Affiliation(s)
- Feng Wei
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zili Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
| | - Chuanzhen Yang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lihong Zhao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yalin Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
| | - Jinglong Zhou
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Hongjie Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Heqin Zhu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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Sun RZ, Wang YY, Liu XQ, Yang ZL, Deng X. Structure and dynamics of microbial communities associated with the resurrection plant Boea hygrometrica in response to drought stress. PLANTA 2024; 260:24. [PMID: 38858226 DOI: 10.1007/s00425-024-04459-2] [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: 03/14/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024]
Abstract
MAIN CONCLUSION The resurrection plant Boea hygrometrica selectively recruits and assembles drought-specific microbial communities across the plant-soil compartments, which may benefit plant growth and fitness under extreme drought conditions. Plant-associated microbes are essential for facilitating plant growth and fitness under drought stress. The resurrection plant Boea hygrometrica in natural habitats with seasonal rainfall can survive rapid desiccation, yet their interaction with microbiomes under drought conditions remains unexplored. This study examined the bacterial and fungal microbiome structure and drought response across plant-soil compartments of B. hygrometrica by high-throughput amplicon sequencing of 16S rRNA gene and internal transcribed spacer. Our results demonstrated that the diversity, composition, and functional profile of the microbial community varied considerably across the plant-soil compartments and were strongly affected by drought stress. Bacterial and fungal diversity was significantly reduced from soil to endosphere and belowground to aboveground compartments. The compartment-specific enrichment of the dominant bacteria phylum Cyanobacteriota and genus Methylorubrum in leaf endosphere, genera Pseudonocardia in rhizosphere soil and Actinoplanes in root endosphere, and fungal phylum Ascomycota in the aboveground compartments and genera Knufia in root endosphere and Cladosporium in leaf endosphere composed part of the core microbiota with corresponding enrichment of beneficial functions for plant growth and fitness. Moreover, the recruitment of dominant microbial genera Sphingosinicella and Plectosphaerella, Ceratobasidiaceae mycorrhizal fungi, and numerous plant growth-promoting bacteria involving nutrient supply and auxin regulation was observed in desiccated B. hygrometrica plants. Our results suggest that the stable assembled drought-specific microbial community of B. hygrometrica may contribute to plant survival under extreme environments and provide valuable microbial resources for the microbe-mediated drought tolerance enhancement in crops.
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Affiliation(s)
- Run-Ze Sun
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.
- China National Botanical Garden, 100093, Beijing, China.
| | - Yuan-Yuan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiao-Qiang Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhao-Lin Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xin Deng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.
- China National Botanical Garden, 100093, Beijing, China.
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10
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Qiao Y, Wang Z, Sun H, Guo H, Song Y, Zhang H, Ruan Y, Xu Q, Huang Q, Shen Q, Ling N. Synthetic community derived from grafted watermelon rhizosphere provides protection for ungrafted watermelon against Fusarium oxysporum via microbial synergistic effects. MICROBIOME 2024; 12:101. [PMID: 38840214 DOI: 10.1186/s40168-024-01814-z] [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: 12/01/2023] [Accepted: 04/11/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Plant microbiota contributes to plant growth and health, including enhancing plant resistance to various diseases. Despite remarkable progress in understanding diseases resistance in plants, the precise role of rhizosphere microbiota in enhancing watermelon resistance against soil-borne diseases remains unclear. Here, we constructed a synthetic community (SynCom) of 16 core bacterial strains obtained from the rhizosphere of grafted watermelon plants. We further simplified SynCom and investigated the role of bacteria with synergistic interactions in promoting plant growth through a simple synthetic community. RESULTS Our results demonstrated that the SynCom significantly enhanced the growth and disease resistance of ungrafted watermelon grown in non-sterile soil. Furthermore, analysis of the amplicon and metagenome data revealed the pivotal role of Pseudomonas in enhancing plant health, as evidenced by a significant increase in the relative abundance and biofilm-forming pathways of Pseudomonas post-SynCom inoculation. Based on in vitro co-culture experiments and bacterial metabolomic analysis, we selected Pseudomonas along with seven other members of the SynCom that exhibited synergistic effects with Pseudomonas. It enabled us to further refine the initially constructed SynCom into a simplified SynCom comprising the eight selected bacterial species. Notably, the plant-promoting effects of simplified SynCom were similar to those of the initial SynCom. Furthermore, the simplified SynCom protected plants through synergistic effects of bacteria. CONCLUSIONS Our findings suggest that the SynCom proliferate in the rhizosphere and mitigate soil-borne diseases through microbial synergistic interactions, highlighting the potential of synergistic effects between microorganisms in enhancing plant health. This study provides a novel insight into using the functional SynCom as a promising solution for sustainable agriculture. Video Abstract.
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Affiliation(s)
- Yizhu Qiao
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhendong Wang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong Sun
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hanyue Guo
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Song
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - He Zhang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Ruan
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qicheng Xu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Qiwei Huang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ning Ling
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
- Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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11
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Cao Y, Li Z, Du P, Ji J, Sun W, Xu J, Liang B. Effects of different dwarfing interstocks on the rhizosphere, endophytic bacteria, and drought resistance of apple trees. Microbiol Res 2024; 283:127690. [PMID: 38461571 DOI: 10.1016/j.micres.2024.127690] [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: 01/05/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/12/2024]
Abstract
Rootstock is commonly used to enhance plant resistance to drought stress. However, it is necessary to investigate the effects of different rootstock, interstock, and scion combinations on rhizosphere and root endophytic bacteria under drought stress. We conducted a pot experiment to investigate how interstock [SH40, Jizhen 1 (J1), and Jizhen 2 (J2)] affects the drought tolerance and nitrogen (N) uptake and utilization of apple trees under drought stress. The results showed that the total dry weight, total chlorophyll content, carotenoid content, photosynthesis rate, and N absorption and utilization efficiency of apple trees decreased significantly, whereas relative electrolyte leakage increased significantly under drought stress. Membership function analysis showed that the apple plants with the J1 interstock had the greatest drought resistance. In addition, drought treatment significantly affected the diversity and composition of rhizosphere and root endophytic communities in all three rootstock/interstock/scion combinations. Further analysis revealed that the relative abundance of the plant pathogen Ralstonia was significantly increased in J2 drought-treated roots, compared to the other groups, whereas those of some potentially beneficial bacteria (0134_terrestrial_group, Phenylobacterium, Ellin6067, Kribbella, Chloronema, and Streptomyces) increased significantly in the J1 drought-treated sample. Co-occurrence network analysis showed that some potentially beneficial bacteria (Ellin6067, S0134_terrestrial_group, Pedomicrobium, and Subgroup_10) were significantly positively correlated with N content. These modifications of the rhizosphere and endophytic bacterial communities may influence the drought resilience and N uptake efficiency of different combinations of interstocks and scions. This study is a much-needed step towards understanding the stress response mechanism of scion-rootstock combinations.
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Affiliation(s)
- Yang Cao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zhongyong Li
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Peihua Du
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Jiahao Ji
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Wei Sun
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Jizhong Xu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Bowen Liang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China.
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12
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Gholizadeh S, Nemati I, Vestergård M, Barnes CJ, Kudjordjie EN, Nicolaisen M. Harnessing root-soil-microbiota interactions for drought-resilient cereals. Microbiol Res 2024; 283:127698. [PMID: 38537330 DOI: 10.1016/j.micres.2024.127698] [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: 01/16/2024] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 04/17/2024]
Abstract
Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.
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Affiliation(s)
- Somayeh Gholizadeh
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Iman Nemati
- Department of Plant Production and Genetics Engineering, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Mette Vestergård
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Christopher James Barnes
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Enoch Narh Kudjordjie
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Mogens Nicolaisen
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark.
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13
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Legeay J, Errafii K, Ziami A, Hijri M. The rhizosphere of a drought-tolerant plant species in Morocco: A refuge of high microbial diversity with no taxon preference. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13254. [PMID: 38725134 PMCID: PMC11082428 DOI: 10.1111/1758-2229.13254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/14/2024] [Indexed: 05/13/2024]
Abstract
Arid and semi-arid areas are facing increasingly severe water deficits that are being intensified by global climate changes. Microbes associated with plants native to arid regions provide valuable benefits to plants, especially in water-stressed environments. In this study, we used 16S rDNA metabarcoding analysis to examine the bacterial communities in the bulk soil, rhizosphere and root endosphere of the plant Malva sylvestris L. in Morocco, along a gradient of precipitation. We found that the rhizosphere of M. sylvestris did not show significant differences in beta-diversity compared to bulk soil, although, it did display an increased degree of alpha-diversity. The endosphere was largely dominated by the genus Rhizobium and displayed remarkable variation between plants, which could not be attributed to any of the variables observed in this study. Overall, the effects of precipitation level were relatively weak, which may be related to the intense drought in Morocco at the time of sampling. The dominance of Rhizobium in a non-leguminous plant is particularly noteworthy and may permit the utilization of this bacterial taxon to augment drought tolerance; additionally, the absence of any notable selection of the rhizosphere of M. sylvestris suggests that it is not significatively affecting its soil environment.
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Affiliation(s)
- Jean Legeay
- African Genome CenterUniversity Mohammed VI Polytechnic (UM6P)Ben GuerirMorocco
| | - Khaoula Errafii
- African Genome CenterUniversity Mohammed VI Polytechnic (UM6P)Ben GuerirMorocco
| | - Abdelhadi Ziami
- African Genome CenterUniversity Mohammed VI Polytechnic (UM6P)Ben GuerirMorocco
| | - Mohamed Hijri
- African Genome CenterUniversity Mohammed VI Polytechnic (UM6P)Ben GuerirMorocco
- Institut de Recherche en Biologie VégétaleDépartement de Sciences Biologiques, Université de MontréalMontrealQuebecCanada
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14
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Hagen M, Dass R, Westhues C, Blom J, Schultheiss SJ, Patz S. Interpretable machine learning decodes soil microbiome's response to drought stress. ENVIRONMENTAL MICROBIOME 2024; 19:35. [PMID: 38812054 PMCID: PMC11138018 DOI: 10.1186/s40793-024-00578-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/10/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND Extreme weather events induced by climate change, particularly droughts, have detrimental consequences for crop yields and food security. Concurrently, these conditions provoke substantial changes in the soil bacterial microbiota and affect plant health. Early recognition of soil affected by drought enables farmers to implement appropriate agricultural management practices. In this context, interpretable machine learning holds immense potential for drought stress classification of soil based on marker taxa. RESULTS This study demonstrates that the 16S rRNA-based metagenomic approach of Differential Abundance Analysis methods and machine learning-based Shapley Additive Explanation values provide similar information. They exhibit their potential as complementary approaches for identifying marker taxa and investigating their enrichment or depletion under drought stress in grass lineages. Additionally, the Random Forest Classifier trained on a diverse range of relative abundance data from the soil bacterial micobiome of various plant species achieves a high accuracy of 92.3 % at the genus rank for drought stress prediction. It demonstrates its generalization capacity for the lineages tested. CONCLUSIONS In the detection of drought stress in soil bacterial microbiota, this study emphasizes the potential of an optimized and generalized location-based ML classifier. By identifying marker taxa, this approach holds promising implications for microbe-assisted plant breeding programs and contributes to the development of sustainable agriculture practices. These findings are crucial for preserving global food security in the face of climate change.
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Affiliation(s)
- Michelle Hagen
- Computomics GmbH, Eisenbahnstraße 1, 72072, Tübingen, Baden-Württemberg, Germany
| | - Rupashree Dass
- Computomics GmbH, Eisenbahnstraße 1, 72072, Tübingen, Baden-Württemberg, Germany
| | - Cathy Westhues
- Computomics GmbH, Eisenbahnstraße 1, 72072, Tübingen, Baden-Württemberg, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Gießen, Heinrich-Buff-Ring 58, 35390, Gießen, Hesse, Germany
| | | | - Sascha Patz
- Computomics GmbH, Eisenbahnstraße 1, 72072, Tübingen, Baden-Württemberg, Germany.
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15
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Zai X, Cordovez V, Zhu F, Zhao M, Diao X, Zhang F, Raaijmakers JM, Song C. C4 cereal and biofuel crop microbiomes. Trends Microbiol 2024:S0966-842X(24)00093-3. [PMID: 38772810 DOI: 10.1016/j.tim.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/23/2024]
Abstract
Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.
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Affiliation(s)
- Xiaoyu Zai
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China
| | - Meicheng Zhao
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Chunxu Song
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China.
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16
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Bamba M, Akyol TY, Azuma Y, Quilbe J, Andersen SU, Sato S. Synergistic effects of plant genotype and soil microbiome on growth in Lotus japonicus. FEMS Microbiol Ecol 2024; 100:fiae056. [PMID: 38678008 PMCID: PMC11068475 DOI: 10.1093/femsec/fiae056] [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: 10/25/2022] [Revised: 03/25/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024] Open
Abstract
The biological interactions between plants and their root microbiomes are essential for plant growth, and even though plant genotype (G), soil microbiome (M), and growth conditions (environment; E) are the core factors shaping root microbiome, their relationships remain unclear. In this study, we investigated the effects of G, M, and E and their interactions on the Lotus root microbiome and plant growth using an in vitro cross-inoculation approach, which reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. Results suggested that a large proportion of the root microbiome composition is determined by M and E, while G-related (G, G × M, and G × E) effects were significant but small. In contrast, the interaction between G and M had a more pronounced effect on plant shoot growth than M alone. Our findings also indicated that most microbiome variations controlled by M have little effect on plant phenotypes, whereas G × M interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention to optimize crop yield and resilience.
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Affiliation(s)
- Masaru Bamba
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Turgut Yigit Akyol
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Yusuke Azuma
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Johan Quilbe
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Stig Uggerhøj Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
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Ben Zineb A, Lamine M, Khallef A, Hamdi H, Ahmed T, Al-Jabri H, Alsafran M, Mliki A, Sayadi S, Gargouri M. Harnessing rhizospheric core microbiomes from arid regions for enhancing date palm resilience to climate change effects. Front Microbiol 2024; 15:1362722. [PMID: 38646634 PMCID: PMC11027745 DOI: 10.3389/fmicb.2024.1362722] [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: 12/28/2023] [Accepted: 03/11/2024] [Indexed: 04/23/2024] Open
Abstract
Date palm cultivation has thrived in the Gulf Cooperation Council region since ancient times, where it represents a vital sector in agricultural and socio-economic development. However, climate change conditions prevailing for decades in this area, next to rarefication of rain, hot temperatures, intense evapotranspiration, rise of sea level, salinization of groundwater, and intensification of cultivation, contributed to increase salinity in the soil as well as in irrigation water and to seriously threaten date palm cultivation sustainability. There are also growing concerns about soil erosion and its repercussions on date palm oases. While several reviews have reported on solutions to sustain date productivity, including genetic selection of suitable cultivars for the local harsh environmental conditions and the implementation of efficient management practices, no systematic review of the desertic plants' below-ground microbial communities and their potential contributions to date palm adaptation to climate change has been reported yet. Indeed, desert microorganisms are expected to address critical agricultural challenges and economic issues. Therefore, the primary objectives of the present critical review are to (1) analyze and synthesize current knowledge and scientific advances on desert plant-associated microorganisms, (2) review and summarize the impacts of their application on date palm, and (3) identify possible gaps and suggest relevant guidance for desert plant microbes' inoculation approach to sustain date palm cultivation within the Gulf Cooperation Council in general and in Qatar in particular.
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Affiliation(s)
- Ameni Ben Zineb
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mariem Lamine
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Ahlem Khallef
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Helmi Hamdi
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Talaat Ahmed
- Environmental Science Center, Qatar University, Doha, Qatar
| | - Hareb Al-Jabri
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mohammed Alsafran
- Agricultural Research Station, Office of VP for Research and Graduate Studies, Qatar University, Doha, Qatar
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Sami Sayadi
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mahmoud Gargouri
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
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18
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Zhang H, Liu H, Han X. Traits-based approach: leveraging genome size in plant-microbe interactions. Trends Microbiol 2024; 32:333-341. [PMID: 37925351 DOI: 10.1016/j.tim.2023.10.004] [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: 06/21/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
Trait-based approaches have gained growing interest in studying plant-microbe interactions. However, current traits normally considered (e.g., morphological, physiological, or chemical traits) are biased towards those showing large intraspecific variations, necessitating the identification of fewer plastic traits that differ between species. Here, we propose using genome size (the amount of DNA in the nucleus of a cell) as a suitable trait for studying plant-microbiome interactions due to its relatively stable nature, minimally affected by external environmental variations. Emerging evidence suggests that plant genome size affects the plant-associated microbial community, and tissue-specific environments select microbes based on their genome size. These findings pinpoint environmental selection in genome size as an emerging driver of plant-microbiome interactions, potentially impacting ecosystem functions and productivity.
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Affiliation(s)
- Haiyang Zhang
- College of Life Sciences, Hebei University, Baoding, China.
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2753, Australia
| | - Xingguo Han
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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19
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Caldara M, Gullì M, Graziano S, Riboni N, Maestri E, Mattarozzi M, Bianchi F, Careri M, Marmiroli N. Microbial consortia and biochar as sustainable biofertilisers: Analysis of their impact on wheat growth and production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170168. [PMID: 38244628 DOI: 10.1016/j.scitotenv.2024.170168] [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: 09/05/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/22/2024]
Abstract
The European Union is among the top wheat producers in the world, but its productivity relies on adequate soil fertilisation. Biofertilisers, either alone or in combination with biochar, can be a preferable alternative to chemical fertilisers. However, the addition of biofertilisers, specifically plant growth promoting microbes (PGPM), could modify grain composition, and/or deteriorate the soil composition. In this study, the two wheat cultivars Triticum aestivum (Bramante) and T. durum (Svevo) were cultivated in open fields for two consecutive years in the presence of a commercial PGPM mix supplied alone or in combination with biochar. An in-depth analysis was conducted by collecting physiological and agronomic data throughout the growth period. The effects of PGPM and biochar were investigated in detail; specifically, soil chemistry and rhizosphere microbial composition were characterized, along with the treatment effects on seed storage proteins. The results demonstrated that the addition of commercial microbial consortia and biochar, alone or in combination, did not modify the rhizospheric microbial community; however, it increased grain yield, especially in the cultivar Svevo (increase of 6.8 %-13.6 %), even though the factors driving the most variations were associated with both climate and cultivar. The total gluten content of the flours was not affected, whereas the main effect of the treatments was a variation in gliadins and low-molecular-weight-glutenin subunits in both cultivars when treated with PGPM and biochar. This suggested improved grain quality, especially regarding the viscoelastic properties of the dough, when the filling period occurred in a dry climate. The results indicate that the application of biofertilisers and biochar may aid the effective management of sustainable wheat cultivation, to support environmental health without altering the biodiversity of the resident microbiome.
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Affiliation(s)
- Marina Caldara
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Mariolina Gullì
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Sara Graziano
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Nicolò Riboni
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Elena Maestri
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; National Interuniversity Consortium for Environmental Sciences (CINSA), Parco Area delle Scienze, 43124 Parma, Italy
| | - Monica Mattarozzi
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Federica Bianchi
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Center CIDEA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Maria Careri
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Nelson Marmiroli
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; National Interuniversity Consortium for Environmental Sciences (CINSA), Parco Area delle Scienze, 43124 Parma, Italy.
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20
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Agunbiade VF, Babalola OO. Drought Stress Amelioration Attributes of Plant-Associated Microbiome on Agricultural Plants. Bioinform Biol Insights 2024; 18:11779322241233442. [PMID: 38464334 PMCID: PMC10924568 DOI: 10.1177/11779322241233442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 02/01/2024] [Indexed: 03/12/2024] Open
Abstract
The future global food security depends on the availability of water for agriculture. Yet, the ongoing rise in nonagricultural uses for water, such as urban and industrial uses, and growing environmental quality concerns have increased pressure of irrigation water demand and posed danger to food security. Nevertheless, its severity and duration are predicted to rise shortly. Drought pressure causes stunted growth, severe damage to photosynthesis activity, loss in crop yield, reduced seed germination, and reduced nutrient intake by plants. To overcome the effects of a devastating drought on plants, it is essential to think about the causes, mechanisms of action, and long-term agronomy management and genetics. As a result, there is an urgent need for long-term medication to deal with the harmful effects of drought pressure. The review focuses on the adverse impact of drought on the plant, physiological, and biochemical aspects, and management measures to control the severity of drought conditions. This article reviews the role of genome editing (GE) technologies such as CRISPR 9 (CRISPR-Cas9) related spaces and short palindromic relapse between proteins in reducing the effects of phytohormones, osmolytes, external compounds, proteins, microbes (plant growth-promoting microorganism [PGPM]), approach omics, and drought on plants that support plant growth. This research is to examine the potential of using the microbiome associated with plants for drought resistance and sustainable agriculture. Researchers also advocate using a mix of biotechnology, agronomic, and advanced GE technologies to create drought-tolerant plant varieties.
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Affiliation(s)
- Victor Funso Agunbiade
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
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21
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Igwe AN, Pearse IS, Aguilar JM, Strauss SY, Vannette RL. Plant species within Streptanthoid Complex associate with distinct microbial communities that shift to be more similar under drought. Ecol Evol 2024; 14:e11174. [PMID: 38529025 PMCID: PMC10961476 DOI: 10.1002/ece3.11174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/19/2024] [Accepted: 03/07/2024] [Indexed: 03/27/2024] Open
Abstract
Prolonged water stress can shift rhizoplane microbial communities, yet whether plant phylogenetic relatedness or drought tolerance predicts microbial responses is poorly understood. To explore this question, eight members of the Streptanthus clade with varying affinity to serpentine soil were subjected to three watering regimes. Rhizoplane bacterial communities were characterized using 16S rRNA gene amplicon sequencing and we compared the impact of watering treatment, soil affinity, and plant species identity on bacterial alpha and diversity. We determined which taxa were enriched among drought treatments using DESeq2 and identified features of soil affinity using random forest analysis. We show that water stress has a greater impact on microbial community structure than soil affinity or plant identity, even within a genus. Drought reduced alpha diversity overall, but plant species did not strongly differentiate alpha diversity. Watering altered the relative abundance of bacterial genera within Proteobacteria, Firmicutes, Bacteroidetes, Planctomycetes, and Acidobacteria, which responded similarly in the rhizoplane of most plant species. In addition, bacterial communities were more similar when plants received less water. Pseudarthrobacter was identified as a feature of affinity to serpentine soil while Bradyrhizobium, Chitinophaga, Rhodanobacter, and Paenibacillus were features associated with affinity to nonserpentine soils among Streptanthus. The homogenizing effect of drought on microbial communities and the increasing prevalence of Gram-negative bacteria across all plant species suggest that effects of water stress on root-associated microbiome structure may be predictable among closely related plant species that inhabit very different soil environments. The functional implications of observed changes in microbiome composition remain to be studied.
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Affiliation(s)
- Alexandria N. Igwe
- Entomology and NematologyUniversity of California – DavisDavisCaliforniaUSA
- Department of Biological SciencesVirginia TechBlacksburgVirginiaUSA
| | - Ian S. Pearse
- Evolution and EcologyUniversity of California – DavisDavisCaliforniaUSA
| | | | - Sharon Y. Strauss
- Evolution and EcologyUniversity of California – DavisDavisCaliforniaUSA
| | - Rachel L. Vannette
- Entomology and NematologyUniversity of California – DavisDavisCaliforniaUSA
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22
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Deng Y, Kong W, Zhang X, Zhu Y, Xie T, Chen M, Zhu L, Sun J, Zhang Z, Chen C, Zhu C, Yin H, Huang S, Gu Y. Rhizosphere microbial community enrichment processes in healthy and diseased plants: implications of soil properties on biomarkers. Front Microbiol 2024; 15:1333076. [PMID: 38505554 PMCID: PMC10949921 DOI: 10.3389/fmicb.2024.1333076] [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: 11/04/2023] [Accepted: 02/01/2024] [Indexed: 03/21/2024] Open
Abstract
Plant health states may influence the distribution of rhizosphere microorganisms, which regulate plant growth and development. In this study, the response of rhizosphere bacteria and fungi of healthy and diseased plants compared to bulk microbes was analyzed using high-throughput sequencing. Plant adaptation strategies of plants under potato virus Y (PVY) infection have been studied from a microbial perspective. The diversity and community structure of bacteria and fungi varied between bulk and rhizosphere soils, but not between healthy and diseased rhizosphere soils. A LEfSe analysis revealed the significant differences between different treatments on bacterial and fungal community compositions and identified Roseiflexaceae, Sphingomonas, and Sphingobium as the bacterial biomarkers of bulk (BCK), healthy rhizosphere (BHS), and diseased rhizosphere (BIS) soils, respectively; Rhodotorula and Ascomycota_unidentified_1_1 were identified as the fungal biomarkers of bulk (FCK) and healthy rhizosphere (FHS) soils. Bacterial networks were found to be more complex and compact than fungal networks and revealed the roles of biomarkers as network keystone taxa. PVY infection further increased the connectedness among microbial taxa to improve rhizosphere microbial community stability and resistance to environmental stress. Additionally, water content (WC) played an apparent influence on bacterial community structure and diversity, and pH showed significant effects on fungal community diversity. WC and pH greatly affected the biomarkers of bacterial rhizosphere communities, whereas the biomarkers of bulk bacterial communities were significantly affected by soil nutrients, especially for Sphingobium. Overall, the rhizosphere microbial community enrichment processes were different between healthy and diseased plants by changing the community compositions and identifying different biomarkers. These findings provide insight into the assemblage of rhizosphere microbial communities and soil physicochemical properties, which contributes to a deeper understanding of the establishment of an artificial core root microbiota to facilitate plant growth and bolstering resistance mechanisms. This knowledge contributes to a deeper understanding of the establishment of an artificial core root microbiota, thereby facilitating plant growth and bolstering resistance mechanisms.
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Affiliation(s)
- Yong Deng
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Wuyuan Kong
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Xiaoming Zhang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Yi Zhu
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Tian Xie
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Ming Chen
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Li Zhu
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Jingzhao Sun
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Zhihua Zhang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Chaoyong Chen
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Chongwen Zhu
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Songqing Huang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Yabing Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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23
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Liu Z, Zhang C, Ma J, Peng Q, Du X, Sun S, Cheng J, Peng W, Chen L, Gu Z, Zhang W, Su P, Zhang D. Extraction Methods Determine the Quality of Soil Microbiota Acquisition. Microorganisms 2024; 12:403. [PMID: 38399807 PMCID: PMC10891820 DOI: 10.3390/microorganisms12020403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The soil microbiome plays a key role in plant health. Native soil microbiome inoculation, metagenomic profiling, and high-throughput cultivation require efficient microbe extraction. Sonication and oscillation are the most common methods used to extract soil microbiomes. However, the extraction efficiency of these methods has not been investigated in full. In this study, we compared the culturable microbe numbers, community structures, and alpha diversities among the different methods, including sonication, oscillation, and centrifugation, and their processing times. The study results showed that sonication significantly increases the culturable colony number compared with oscillation and centrifugation. Furthermore, the sonication strategy was found to be the main factor influencing extraction efficiency, but increased sonication time can aid in recovery from this impact. Finally, the extraction processing times were found to have a significant negative relationship with α-diversity among the extracted microbiota. In conclusion, sonication is the main factor for enriching in situ microbiota, and increased extraction time significantly decreases the α-diversity of the extracted microbiota. The results of this study provide insights into the isolation and utilization of different microorganism sources.
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Affiliation(s)
- Zhuoxin Liu
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Chi Zhang
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jiejia Ma
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Qianze Peng
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya 572024, China
| | - Xiaohua Du
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Shu'e Sun
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ju'e Cheng
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Weiye Peng
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lijie Chen
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Zepei Gu
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Weixing Zhang
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Pin Su
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya 572024, China
| | - Deyong Zhang
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya 572024, China
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24
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He H, Tang C, Cao Z, Wang T, He M, Xiao M, Xiao L, Li Y, Li X. Revealing Medicinal Constituents of Bistorta vivipara Based on Non-Targeted Metabolomics and 16S rDNA Gene Sequencing Technology. Molecules 2024; 29:860. [PMID: 38398612 PMCID: PMC10892765 DOI: 10.3390/molecules29040860] [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: 12/30/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Bistorta vivipara is a medicinal plant with a long history, but there are few studies on the effects of its medicinal components and endophytic bacteria on the accumulation of secondary metabolites. Therefore, in this study, non-targeted metabolomics techniques and 16s rDNA techniques were used to study B. vivipara from different regions. A total of 1290 metabolites and 437 differential metabolites were identified from all samples. Among them, flavonoids, isoflavonoids, and benzopyrans are the main medicinal components of B. vivipara; these have potential anticancer, antiviral, and antioxidant properties, as well as potential applications for the treatment of atrial fibrillation. In addition, irigenin, an important medicinal component, was identified for the first time. The endophytic bacterial communities in the root tissues of B. vivipara from different regions were also different in composition and richness. Hierarchical clustering heat map analysis showed that Proteobacteria and Actinobacteriota bacteria significantly affected the accumulation of many medicinal components in the roots of B. vivipara.
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Affiliation(s)
- Hui He
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining 810016, China; (H.H.); (C.T.); (Z.C.); (T.W.); (M.H.); (M.X.)
| | - Chuyu Tang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining 810016, China; (H.H.); (C.T.); (Z.C.); (T.W.); (M.H.); (M.X.)
| | - Zhengfei Cao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining 810016, China; (H.H.); (C.T.); (Z.C.); (T.W.); (M.H.); (M.X.)
| | - Tao Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining 810016, China; (H.H.); (C.T.); (Z.C.); (T.W.); (M.H.); (M.X.)
| | - Min He
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining 810016, China; (H.H.); (C.T.); (Z.C.); (T.W.); (M.H.); (M.X.)
| | - Mengjun Xiao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining 810016, China; (H.H.); (C.T.); (Z.C.); (T.W.); (M.H.); (M.X.)
| | - Licheng Xiao
- Animal Husbandry and Veterinary Workstation in Yushu City, Yushu 815000, China;
| | - Yuling Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining 810016, China; (H.H.); (C.T.); (Z.C.); (T.W.); (M.H.); (M.X.)
| | - Xiuzhang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining 810016, China; (H.H.); (C.T.); (Z.C.); (T.W.); (M.H.); (M.X.)
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25
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Sharma V, Mohammed SA, Devi N, Vats G, Tuli HS, Saini AK, Dhir YW, Dhir S, Singh B. Unveiling the dynamic relationship of viruses and/or symbiotic bacteria with plant resilience in abiotic stress. STRESS BIOLOGY 2024; 4:10. [PMID: 38311681 PMCID: PMC10838894 DOI: 10.1007/s44154-023-00126-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/22/2023] [Indexed: 02/06/2024]
Abstract
In the ecosphere, plants interact with environmental biotic and abiotic partners, where unbalanced interactions can induce unfavourable stress conditions. Abiotic factors (temperature, water, and salt) are primarily required for plants healthy survival, and any change in their availability is reflected as a stress signal. In certain cases, the presence of infectious pathogens such as viruses, bacteria, fungi, protozoa, nematodes, and insects can also create stress conditions in plants, leading to the emergence of disease or deficiency symptoms. While these symptoms are often typical of abiotic or biotic stress, however, there are instances where they can intensify under specific conditions. Here, we primarily summarize the viral interactions with plants during abiotic stress to understand how these associations are linked together during viral pathogenesis. Secondly, focus is given to the beneficial effects of root-associated symbiotic bacteria in fulfilling the basic needs of plants during normal as well as abiotic stress conditions. The modulations of plant functional proteins, and their occurrence/cross-talk, with pathogen (virus) and symbiont (bacteria) molecules are also discussed. Furthermore, we have highlighted the biochemical and systematic adaptations that develop in plants due to bacterial symbiosis to encounter stress hallmarks. Lastly, directions are provided towards exploring potential rhizospheric bacteria to maintain plant-microbes ecosystem and manage abiotic stress in plants to achieve better trait health in the horticulture crops.
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Affiliation(s)
- Vasudha Sharma
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Shakeel A Mohammed
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Nisha Devi
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Gourav Vats
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Hardeep S Tuli
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Adesh K Saini
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Yashika W Dhir
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| | - Sunny Dhir
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| | - Bharat Singh
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
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26
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Afridi MS, Kumar A, Javed MA, Dubey A, de Medeiros FHV, Santoyo G. Harnessing root exudates for plant microbiome engineering and stress resistance in plants. Microbiol Res 2024; 279:127564. [PMID: 38071833 DOI: 10.1016/j.micres.2023.127564] [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: 08/28/2023] [Revised: 11/02/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.
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Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil.
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030 Morelia, Mexico.
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27
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Li J, Hou L, Zhang G, Cheng L, Liu Y. Comparative Analysis of Rhizosphere and Endosphere Fungal Communities in Healthy and Diseased Faba Bean Plants. J Fungi (Basel) 2024; 10:84. [PMID: 38276030 PMCID: PMC10817651 DOI: 10.3390/jof10010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
This study used the ITS approach based on Illumina MiSeq sequencing to assess the endosphere and rhizosphere fungal communities in healthy and diseased faba bean plants. The findings indicate that the most predominant phyla in all samples were Ascomycota (49.89-99.56%) and Basidiomycota (0.33-25.78%). In healthy endosphere samples, Glomeromycota (0.08-1.17%) was the only predominant phylum. In diseased endosphere samples, Olpidiomycota (0.04-1.75%) was the only predominant phylum. At the genus level, Penicillium (0.47-35.21%) was more abundant in rhizosphere soil, while Paraphoma (3.48-91.16%) was predominant in the endosphere roots of faba bean plants. Significant differences were observed in the alpha diversity of rhizosphere samples from different germplasm resources (p < 0.05). The fungal community structures were clearly distinguished between rhizosphere and endosphere samples and between healthy and diseased endosphere samples (p < 0.05). Saccharomyces was significantly enriched in diseased endosphere samples, whereas Apiotrichum was enriched in healthy endosphere samples. Vishniacozyma and Phialophora were enriched in diseased rhizosphere samples, while Pseudogymnoascus was enriched in healthy rhizosphere samples. Diseased samples displayed more strongly correlated genera than healthy samples. Saprotrophs accounted for a larger proportion of the fungal microbes in rhizosphere soil than in endosphere roots. This study provides a better understanding of the composition and diversity of fungal communities in the rhizosphere and endosphere of faba bean plants as well as a theoretical guidance for future research on the prevention or control of faba bean root rot disease.
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Affiliation(s)
- Juan Li
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Lu Hou
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Gui Zhang
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Liang Cheng
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yujiao Liu
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
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Leal CM, Geiger A, Molnár A, Váczy KZ, Kgobe G, Zsófi Z, Geml J. Disentangling the effects of terroir, season, and vintage on the grapevine fungal pathobiome. Front Microbiol 2024; 14:1322559. [PMID: 38298541 PMCID: PMC10829339 DOI: 10.3389/fmicb.2023.1322559] [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: 10/16/2023] [Accepted: 12/19/2023] [Indexed: 02/02/2024] Open
Abstract
The composition, diversity and dynamics of microbial communities associated with grapevines may be influenced by various environmental factors, including terroir, vintage, and season. Among these factors, terroir stands out as a unique possible determinant of the pathobiome, the community of plant-associated pathogens. This study employed high-throughput molecular techniques, including metabarcoding and network analysis, to investigate the compositional dynamics of grapevine fungal pathobiome across three microhabitats (soil, woody tissue, and bark) using the Furmint cultivar. Samples were collected during late winter and late summer in 2020 and 2021, across three distinct terroirs in Hungary's Tokaj wine region. Of the 123 plant pathogenic genera found, Diplodia, Phaeomoniella, and Fusarium displayed the highest richness in bark, wood, and soil, respectively. Both richness and abundance exhibited significant disparities across microhabitats, with plant pathogenic fungi known to cause grapevine trunk diseases (GTDs) demonstrating highest richness and abundance in wood and bark samples, and non-GTD pathogens prevailed soil. Abundance and richness, however, followed distinct patterns Terroir accounted for a substantial portion of the variance in fungal community composition, ranging from 14.46 to 24.67%. Season and vintage also contributed to the variation, explaining 1.84 to 2.98% and 3.67 to 6.39% of the variance, respectively. Notably, significant compositional differences in fungi between healthy and diseased grapevines were only identified in wood and bark samples. Cooccurrence networks analysis, using both unweighted and weighted metrics, revealed intricate relationships among pathogenic fungal genera. This involved mostly positive associations, potentially suggesting synergism, and a few negative relationships, potentially suggesting antagonistic interactions. In essence, the observed differences among terroirs may stem from environmental filtering due to varied edaphic and mesoclimatic conditions. Temporal weather and vine management practices could explain seasonal and vintage fungal dynamics. This study provides insights into the compositional dynamics of grapevine fungal pathobiome across different microhabitats, terroirs, seasons, and health statuses. The findings emphasize the importance of considering network-based approaches in studying microbial communities and have implications for developing improved viticultural plant health strategies.
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Affiliation(s)
- Carla Mota Leal
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Gödöllő, Hungary
| | - Adrienn Geiger
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Gödöllő, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Anna Molnár
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Kálmán Z. Váczy
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Glodia Kgobe
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Gödöllő, Hungary
| | - Zsolt Zsófi
- Institute for Viticulture and Enology, Eszterházy Károly Catholic University, Eger, Hungary
| | - József Geml
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
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Yan K, Lu DS, Ding CJ, Wang Y, Tian YR, Su XH, Dong YF, Wang YP. Rare and abundant bacterial communities in poplar rhizosphere soils respond differently to genetic effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168216. [PMID: 37923276 DOI: 10.1016/j.scitotenv.2023.168216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Interactions between plants and soil microbes are important to plant hybrid breeding under global change. However, the relationship between host plants and rhizosphere soil microorganisms has not been fully elucidated. Understanding the rhizosphere microbial structure of parents and progenies would provide a deeper insight into how genetic effects modulate the relationship between plants and soil. In this study, two family groups of poplar trees (A: parents and their two progenies; B: parents and their one progeny) with different genetic backgrounds (including seven genotypes) were selected from a common garden, and their rhizobacterial communities were analyzed to explore parent-progeny relationships. Our results showed significant differences in phylogenetic diversity, the number of 16S genes and the structure of rhizosphere bacterial communities (Adonis: R2 = 0.166, P < 0.01) between different family groups. Rhizosphere bacterial community structure was significantly dominated by genetic effects. Compared with abundant taxa, genetic effects were more powerful drivers of rare taxa. In addition, bacterial communities of hybrid progenies were all significantly more similar to their parents compared to the other group of parents, especially among rare taxa. The two poplar family groups exhibited differences between their rhizosphere bacterial co-occurrence networks. Group B had a relatively complex network with 2380 edges and 468 nodes, while group A had 1829 edges and 304 nodes. Soil organic carbon and carbon to nitrogen ratio (C/N) also influenced the rhizosphere bacterial community assembly. This was especially true for soil C/N, which explained 23 % of the β-nearest taxon index (βNTI) variation in rare taxa. Our results reveal the relationship of rhizosphere microorganisms between parents and progenies. This can help facilitate an understanding of the combination of plant breeding with microbes resource utilization and provide a theoretical basis for scientific advancement to support the development of forestry industry.
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Affiliation(s)
- Kun Yan
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - De Shan Lu
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Chang Jun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yan Wang
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Yong Ren Tian
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Xiao Hua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | | | - Yan Ping Wang
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China.
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Lee SM, Thapa Magar R, Jung MK, Kong HG, Song JY, Kwon JH, Choi M, Lee HJ, Lee SY, Khan R, Kim JF, Lee SW. Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health. THE ISME JOURNAL 2024; 18:wrae120. [PMID: 38952008 PMCID: PMC11253211 DOI: 10.1093/ismejo/wrae120] [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: 05/14/2024] [Revised: 06/17/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remain poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp. RD1 strain exhibited weak respiration and elongated cell morphology without forming bacterial colonies. A transposon mutant of H3 in a gene encoding succinate-semialdehyde dehydrogenase displayed much attenuated support of RD1 colony formation. Through the subsequent addition of succinate to the media, we found that succinate serves as a public good that supports RD1 growth. Comparative genome analysis highlighted that RD1 lacked the gene for sufficient succinate, suggesting its evolution as a beneficiary of succinate biosynthesis. The syntrophic interaction between RD1 and H3 efficiently protected tomato plants from bacterial wilt and promoted tomato growth. The addition of succinate to the medium restored complex II-dependent respiration in RD1 and facilitated the cultivation of various bacterial isolates from the rhizosphere. Taken together, we delineate energy auxotrophic beneficiaries ubiquitous in the microbial community, and these beneficiaries could benefit host plants with the aid of helpers in the rhizosphere.
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Affiliation(s)
- Sang-Moo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Roniya Thapa Magar
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Min Kyeong Jung
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Hyun Gi Kong
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
- Department of Plant Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ju Yeon Song
- Department of Systems Biology and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Joo Hwan Kwon
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Minseo Choi
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Hyoung Ju Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Seung Yeup Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
- Department of Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Jihyun F Kim
- Department of Systems Biology and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Microbiome Initiative, Yonsei University, Seoul 03722, Republic of Korea
| | - Seon-Woo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Republic of Korea
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
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31
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Wu L, Ren C, Jiang H, Zhang W, Chen N, Zhao X, Wei G, Shu D. Land abandonment transforms soil microbiome stability and functional profiles in apple orchards of the Chinese Losses Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167556. [PMID: 37804979 DOI: 10.1016/j.scitotenv.2023.167556] [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: 08/01/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 10/09/2023]
Abstract
Land abandonment is considered an effective strategy for ecological restoration on a global scale. However, few studies have focused on how environmental heterogeneity associated with the age of land abandonment affects the assembly and potential functions of the soil microbial community. In the present study, we investigated the community assembly of soil bacteria and fungi as well as the stability of soil networks and their potential functions in the chronosequence of abandoned apple orchards. We elucidated that the Shannon diversity of bacteria and the richness of fungi increased as land abandonment progressed. In addition, land abandonment destabilized the microbial network stability but increased network complexity. Soil available nitrogen, total carbon, and moisture are the potentially important factors in shaping the soil microbial assembly. Importantly, we showed that the microbial community diversity and functional diversity presented a synchronization effect in response to the different stages of land abandonment. Furthermore, specific bacterial taxa related to carbon fixation, dissimilatory nitrate reduction, and organic phosphorus mineralization were significantly enriched during the early abandonment stage. Collectively, these results indicate that land abandonment significantly transformed soil microbiome assembly and functional adaptation during the restoration process. These findings provide valuable insights into the influence of ecological restoration on soil microbiome and ecosystem functions in arable areas.
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Affiliation(s)
- Likun Wu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Chengyao Ren
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Hai Jiang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenyu Zhang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Ni Chen
- The Department of Agriculture and Rural Affairs of Shaanxi Province, Xi'an, Shaanxi 710000, China
| | - Xining Zhao
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, 712100 Yangling, Shaanxi Province, China; Institute of Soil and Water Conservation, Northwest A&F University, 712100 Yangling, Shaanxi Province, China
| | - Gehong Wei
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
| | - Duntao Shu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
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32
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He H, Zhou J, Wang Y, Jiao S, Qian X, Liu Y, Liu J, Chen J, Delgado-Baquerizo M, Brangarí AC, Chen L, Cui Y, Pan H, Tian R, Liang Y, Tan W, Ochoa-Hueso R, Fang L. Deciphering microbiomes dozens of meters under our feet and their edaphoclimatic and spatial drivers. GLOBAL CHANGE BIOLOGY 2024; 30:e17028. [PMID: 37955302 DOI: 10.1111/gcb.17028] [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: 08/15/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
Microbes inhabiting deep soil layers are known to be different from their counterpart in topsoil yet remain under investigation in terms of their structure, function, and how their diversity is shaped. The microbiome of deep soils (>1 m) is expected to be relatively stable and highly independent from climatic conditions. Much less is known, however, on how these microbial communities vary along climate gradients. Here, we used amplicon sequencing to investigate bacteria, archaea, and fungi along fifteen 18-m depth profiles at 20-50-cm intervals across contrasting aridity conditions in semi-arid forest ecosystems of China's Loess Plateau. Our results showed that bacterial and fungal α diversity and bacterial and archaeal community similarity declined dramatically in topsoil and remained relatively stable in deep soil. Nevertheless, deep soil microbiome still showed the functional potential of N cycling, plant-derived organic matter degradation, resource exchange, and water coordination. The deep soil microbiome had closer taxa-taxa and bacteria-fungi associations and more influence of dispersal limitation than topsoil microbiome. Geographic distance was more influential in deep soil bacteria and archaea than in topsoil. We further showed that aridity was negatively correlated with deep-soil archaeal and fungal richness, archaeal community similarity, relative abundance of plant saprotroph, and bacteria-fungi associations, but increased the relative abundance of aerobic ammonia oxidation, manganese oxidation, and arbuscular mycorrhizal in the deep soils. Root depth, complexity, soil volumetric moisture, and clay play bridging roles in the indirect effects of aridity on microbes in deep soils. Our work indicates that, even microbial communities and nutrient cycling in deep soil are susceptible to changes in water availability, with consequences for understanding the sustainability of dryland ecosystems and the whole-soil in response to aridification. Moreover, we propose that neglecting soil depth may underestimate the role of soil moisture in dryland ecosystems under future climate scenarios.
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Affiliation(s)
- Haoran He
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Jingxiong Zhou
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | - Yunqiang Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Earth and Environmental Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
| | - Yurong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Ji Liu
- Hubei Province Key Laboratory for Geographical Process Analysis and Simulation, Central China Normal University, Wuhan, China
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Albert C Brangarí
- Institute for Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Li Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongxing Cui
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Haibo Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Renmao Tian
- Institute for Food Safety and Health (IFSH), Illinois Institute of Technology, Bedford Park, Illinois, USA
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Wenfeng Tan
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Raúl Ochoa-Hueso
- Department of Biology, IVAGRO, University of Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Campus del Rio San Pedro, Cádiz, Spain
| | - Linchuan Fang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Green Utilization of Critical Non-Metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan, China
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Jarrar H, El-Keblawy A, Ghenai C, Abhilash PC, Bundela AK, Abideen Z, Sheteiwy MS. Seed enhancement technologies for sustainable dryland restoration: Coating and scarification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166150. [PMID: 37595910 DOI: 10.1016/j.scitotenv.2023.166150] [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: 02/10/2023] [Revised: 08/06/2023] [Accepted: 08/06/2023] [Indexed: 08/20/2023]
Abstract
High temperatures, soil salinity, a lack of available water, loose soils with reduced water holding, and low soil fertility are obstacles to restoration efforts in degraded drylands and desert ecosystems. Improved soil physical and chemical properties, seed germination and seedling recruitment, and plant growth are all proposed as outcomes of seed enhancement technologies (SETs). Seed priming, seed coating, and seed scarification are three SETs' methods for promoting seed germination and subsequent plant development under unfavorable environmental conditions. Various subtypes can be further classified within these three broad groups. The goals of this review are to (1) develop a general classification of coating and scarification SETs, (2) facilitate the decision-making process to adopt suitable SETs for arid lands environments, and (3) highlight the benefits of coating and scarification SETs in overcoming biotic and abiotic challenges in ecological restoring degraded dryland. For rehabilitating degraded lands and restoring drylands, it is recommended to 1) optimize SETs that have been used effectively for a long time, particularly those associated with seed physiological enhancement and seed microenvironment, 2) integrate coating and scarification to overcome different biotic and abiotic constraints, and 3) apply SET(s) to a mixture of seeds from various species and sizes. However, more research should be conducted on developing SETs for large-scale use to provide the required seed tonnages for dryland restoration.
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Affiliation(s)
- Heba Jarrar
- Renewable Energy and Energy Efficiency Research Group, Research Institute for Sciences and Engineering, University of Sharjah, Sharjah 27272, United Arab Emirates.
| | - Ali El-Keblawy
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates.
| | - Chaouki Ghenai
- Department of Sustainable and Renewable Energy Engineering, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - P C Abhilash
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Amit Kumar Bundela
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Zainul Abideen
- Dr. Muhammad Ajmal Khan Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi 75270, Pakistan
| | - Mohamed S Sheteiwy
- Department of Agronomy, Faculty of Agriculture, Mansoura University, Mansoura 35516, Egypt
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Fan W, Xiao Y, Dong J, Xing J, Tang F, Shi F. Variety-driven rhizosphere microbiome bestows differential salt tolerance to alfalfa for coping with salinity stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1324333. [PMID: 38179479 PMCID: PMC10766110 DOI: 10.3389/fpls.2023.1324333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
Soil salinization is a global environmental issue and a significant abiotic stress that threatens crop production. Root-associated rhizosphere microbiota play a pivotal role in enhancing plant tolerance to abiotic stresses. However, limited information is available concerning the specific variations in rhizosphere microbiota driven by different plant genotypes (varieties) in response to varying levels of salinity stress. In this study, we compared the growth performance of three alfalfa varieties with varying salt tolerance levels in soils with different degrees of salinization. High-throughput 16S rRNA and ITS sequencing were employed to analyze the rhizosphere microbial communities. Undoubtedly, the increasing salinity significantly inhibited alfalfa growth and reduced rhizosphere microbial diversity. However, intriguingly, salt-tolerant varieties exhibited relatively lower susceptibility to salinity, maintaining more stable rhizosphere bacterial community structure, whereas the reverse was observed for salt-sensitive varieties. Bacillus emerged as the dominant species in alfalfa's adaptation to salinity stress, constituting 21.20% of the shared bacterial genera among the three varieties. The higher abundance of Bacillus, Ensifer, and Pseudomonas in the rhizosphere of salt-tolerant alfalfa varieties is crucial in determining their elevated salt tolerance. As salinity levels increased, salt-sensitive varieties gradually accumulated a substantial population of pathogenic fungi, such as Fusarium and Rhizoctonia. Furthermore, rhizosphere bacteria of salt-tolerant varieties exhibited increased activity in various metabolic pathways, including biosynthesis of secondary metabolites, carbon metabolism, and biosynthesis of amino acids. It is suggested that salt-tolerant alfalfa varieties can provide more carbon sources to the rhizosphere, enriching more effective plant growth-promoting bacteria (PGPB) such as Pseudomonas to mitigate salinity stress. In conclusion, our results highlight the variety-mediated enrichment of rhizosphere microbiota in response to salinity stress, confirming that the high-abundance enrichment of specific dominant rhizosphere microbes and their vital roles play a significant role in conferring high salt adaptability to these varieties.
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Affiliation(s)
- Wenqiang Fan
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanzi Xiao
- College of Agriculture and Forestry, Hulunbuir University, Hulunber, China
| | - Jiaqi Dong
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Xing
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Fang Tang
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Fengling Shi
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High-Efficiency Utilization of the Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
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35
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Maestro‐Gaitán I, Granado‐Rodríguez S, Redondo‐Nieto M, Battaglia A, Poza‐Viejo L, Matías J, Bolaños L, Reguera M. Unveiling changes in rhizosphere-associated bacteria linked to the genotype and water stress in quinoa. Microb Biotechnol 2023; 16:2326-2344. [PMID: 37712602 PMCID: PMC10686115 DOI: 10.1111/1751-7915.14337] [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: 06/02/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
Drought is among the main abiotic factors causing agronomical losses worldwide. To minimize its impact, several strategies have been proposed, including the use of plant growth-promoting bacteria (PGPBs), as they have demonstrated roles in counteracting abiotic stress. This aspect has been little explored in emergent crops such as quinoa, which has the potential to contribute to reducing food insecurity. Thus, here we hypothesize that the genotype, water environment and the type of inoculant are determining factors in shaping quinoa rhizosphere bacterial communities, affecting plant performance. To address this, two different quinoa cultivars (with contrasting water stress tolerance), two water conditions (optimal and limiting water conditions) and different soil infusions were used to define the relevance of these factors. Different bacterial families that vary among genotypes and water conditions were identified. Certain families were enriched under water stress conditions, such as the Nocardioidaceae, highly present in the water-sensitive cultivar F15, or the Pseudomonadaceae, Burkholderiaceae and Sphingomonadaceae, more abundant in the tolerant cultivar F16, which also showed larger total polyphenol content. These changes demonstrate that the genotype and environment highly contribute to shaping the root-inhabiting bacteria in quinoa, and they suggest that this plant species is a great source of PGPBs for utilization under water-liming conditions.
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Affiliation(s)
| | | | | | | | - Laura Poza‐Viejo
- Departamento de BiologíaUniversidad Autónoma de MadridMadridSpain
| | - Javier Matías
- Agrarian Research Institute “La Orden‐Valdesequera” of Extremadura (CICYTEX)BadajozSpain
| | - Luis Bolaños
- Departamento de BiologíaUniversidad Autónoma de MadridMadridSpain
| | - Maria Reguera
- Departamento de BiologíaUniversidad Autónoma de MadridMadridSpain
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36
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Martins BR, Siani R, Treder K, Michałowska D, Radl V, Pritsch K, Schloter M. Cultivar-specific dynamics: unravelling rhizosphere microbiome responses to water deficit stress in potato cultivars. BMC Microbiol 2023; 23:377. [PMID: 38036970 PMCID: PMC10691024 DOI: 10.1186/s12866-023-03120-4] [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] [Accepted: 11/10/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Growing evidence suggests that soil microbes can improve plant fitness under drought. However, in potato, the world's most important non-cereal crop, the role of the rhizosphere microbiome under drought has been poorly studied. Using a cultivation independent metabarcoding approach, we examined the rhizosphere microbiome of two potato cultivars with different drought tolerance as a function of water regime (continuous versus reduced watering) and manipulation of soil microbial diversity (i.e., natural (NSM), vs. disturbed (DSM) soil microbiome). RESULTS Water regime and soil pre-treatment showed a significant interaction with bacterial community composition of the sensitive (HERBST) but not the resistant cultivar (MONI). Overall, MONI had a moderate response to the treatments and its rhizosphere selected Rhizobiales under reduced watering in NSM soil, whereas Bradyrhizobium, Ammoniphilus, Symbiobacterium and unclassified Hydrogenedensaceae in DSM soil. In contrast, HERBST response to the treatments was more pronounced. Notably, in NSM soil treated with reduced watering, the root endophytic fungus Falciphora and many Actinobacteriota members (Streptomyces, Glycomyces, Marmoricola, Aeromicrobium, Mycobacterium and others) were largely represented. However, DSM soil treatment resulted in no fungal taxa and fewer enrichment of these Actinobacteriota under reduced watering. Moreover, the number of bacterial core amplicon sequence variants (core ASVs) was more consistent in MONI regardless of soil pre-treatment and water regimes as opposed to HERBST, in which a marked reduction of core ASVs was observed in DSM soil. CONCLUSIONS Besides the influence of soil conditions, our results indicate a strong cultivar-dependent relationship between the rhizosphere microbiome of potato cultivars and their capacity to respond to perturbations such as reduced soil moisture. Our study highlights the importance of integrating soil conditions and plant genetic variability as key factors in future breeding programs aiming to develop drought resistance in a major food crop like potato. Elucidating the molecular mechanisms how plants recruit microbes from soil which help to mitigate plant stress and to identify key microbial taxa, which harbour the respective traits might therefore be an important topic for future research.
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Affiliation(s)
- Benoit Renaud Martins
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.
| | - Roberto Siani
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Chair for Environmental Microbiology, Technical University of Munich, Freising, Germany
| | - Krzysztof Treder
- Plant Breeding and Acclimatization Institute - National Research Institute in Radzików, Bonin Division, Department of Potato Protection and Seed Science at Bonin, 76-009, Bonin, Bonin Str 3, Poland
| | - Dorota Michałowska
- Plant Breeding and Acclimatization Institute - National Research Institute in Radzików, Bonin Division, Department of Potato Protection and Seed Science at Bonin, 76-009, Bonin, Bonin Str 3, Poland
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Karin Pritsch
- Research Unit for Environmental Simulation (EUS), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Chair for Environmental Microbiology, Technical University of Munich, Freising, Germany
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37
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Wu R, Davison MR, Nelson WC, Smith ML, Lipton MS, Jansson JK, McClure RS, McDermott JE, Hofmockel KS. Hi-C metagenome sequencing reveals soil phage-host interactions. Nat Commun 2023; 14:7666. [PMID: 37996432 PMCID: PMC10667309 DOI: 10.1038/s41467-023-42967-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023] Open
Abstract
Bacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome conformation capture (Hi-C) to directly capture phage-host relationships. Some hosts have high centralities in bacterial community co-occurrence networks, suggesting phage infections have an important impact on the soil bacterial community interactions. We observe increased average viral copies per host (VPH) and decreased viral transcriptional activity following a two-week soil-drying incubation, indicating an increase in lysogenic infections. Soil drying also alters the observed phage host range. A significant negative correlation between VPH and host abundance prior to drying indicates more lytic infections result in more host death and inversely influence host abundance. This study provides empirical evidence of phage-mediated bacterial population dynamics in soil by directly capturing specific phage-host interactions.
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Affiliation(s)
- Ruonan Wu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Michelle R Davison
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - William C Nelson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Montana L Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mary S Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ryan S McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason E McDermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
- Department of Agronomy, Iowa State University, Ames, IA, USA.
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38
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Wu SH, Luo MX, Chang JT, Chen Y, Liao PC. Unravelling the dynamics of soil microbial communities under the environmental selection and range shift process in afforestation ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165476. [PMID: 37454863 DOI: 10.1016/j.scitotenv.2023.165476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/30/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
The process of forest range shift not only affects the vegetation aboveground but also influences the dynamics of belowground microbial communities. To investigate the changes in soil under forest range shift, we examined the natural forest soil microbiome along with its corresponding physicochemical properties, as well as the afforestation of natural forest by seedlings and sowing. By utilizing natural forests and employing different afforestation methods, we simulated the three stages of forest range shift: the staging stage, regeneration, and colonization. We employed network analysis and phylogenetic assemblages to examine the structure of soil microbial communities during these three stages in a macro-environmental change context. Ordination and regression analyses were also used to explore the correlation between microorganisms, environmental factors, and changes in their niches. The findings revealed that different afforestation (range shift) types led to distinct microbial compositions. Seedling afforestation exhibited similarities to mature forests, suggesting a significant influence on below-ground microorganisms. In contrast, sowing-based afforestation resulted in small changes in soil microbes, indicating a legacy effect on grassland soils. The impact of the rhizosphere on microbial composition remained consistent across the three forest types. Overall, this study underscores the significance of forest range shift in shaping soil microbial communities and emphasizes the need to consider these dynamics in forest management and restoration endeavours.
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Affiliation(s)
- Shu-Hong Wu
- School of Ecology and Nature Conservation, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing 100083, China.
| | - Min-Xin Luo
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei 116, Taiwan.
| | - Jui-Tse Chang
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei 116, Taiwan.
| | - Ye Chen
- School of Grassland, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing 100083, China
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei 116, Taiwan.
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39
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Oldstone-Jackson C, Huang F, Bergelson J. Microbe-associated molecular pattern recognition receptors have little effect on endophytic Arabidopsis thaliana microbiome assembly in the field. FRONTIERS IN PLANT SCIENCE 2023; 14:1276472. [PMID: 38023837 PMCID: PMC10663345 DOI: 10.3389/fpls.2023.1276472] [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: 08/12/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023]
Abstract
Plant microbiome structure affects plant health and productivity. A limited subset of environmental microbes successfully establishes within plant tissues, but the forces underlying this selectivity remain poorly characterized. Transmembrane pattern recognition receptors (PRRs), used by plants to detect microbe-associated molecular patterns (MAMPs), are strong candidates for achieving this selectivity because PRRs can potentially interact with many members of the microbiome. Indeed, MAMPs found in many microbial taxa, including beneficials and commensals, can instigate a robust immune response that affects microbial growth. Surprisingly, we found that MAMP-detecting PRRs have little effect on endophytic bacterial and fungal microbiome structure in the field. We compared the microbiomes of four PRR knockout lines of Arabidopsis thaliana to wild-type plants in multiple tissue types over several developmental stages and detected only subtle shifts in fungal, but not bacterial, β-diversity in one of the four PRR mutants. In one developmental stage, lore mutants had slightly altered fungal β-diversity, indicating that LORE may be involved in plant-fungal interactions in addition to its known role in detecting certain bacterial lipids. No other effects of PRRs on α-diversity, microbiome variability, within-individual homogeneity, or microbial load were found. The general lack of effect suggests that individual MAMP-detecting PRRs are not critical in shaping the endophytic plant microbiome. Rather, we suggest that MAMP-detecting PRRs must either act in concert and/or are individually maintained through pleiotropic effects or interactions with coevolved mutualists or pathogens. Although unexpected, these results offer insights into the role of MAMP-detecting PRRs in plant-microbe interactions and help direct future efforts to uncover host genetic elements that control plant microbiome assembly.
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Affiliation(s)
| | - Feng Huang
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Joy Bergelson
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
- Center for Genomics and Systems Biology, Department of Biology, College of Arts and Science, New York University, New York, NY, United States
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40
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Zheng Q, Hu Y, Kosina SM, Van Goethem MW, Tringe SG, Bowen BP, Northen TR. Conservation of beneficial microbes between the rhizosphere and the cyanosphere. THE NEW PHYTOLOGIST 2023; 240:1246-1258. [PMID: 37668195 DOI: 10.1111/nph.19225] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/26/2023] [Indexed: 09/06/2023]
Abstract
Biocrusts are phototroph-driven communities inhabiting arid soil surfaces. Like plants, most photoautotrophs (largely cyanobacteria) in biocrusts are thought to exchange fixed carbon for essential nutrients like nitrogen with cyanosphere bacteria. Here, we aim to compare beneficial interactions in rhizosphere and cyanosphere environments, including finding growth-promoting strains for hosts from both environments. To examine this, we performed a retrospective analysis of 16S rRNA gene sequencing datasets, host-microbe co-culture experiments between biocrust communities/biocrust isolates and a model grass (Brachypodium distachyon) or a dominant biocrust cyanobacterium (Microcoleus vaginatus), and metabolomic analysis. All 18 microbial phyla in the cyanosphere were also present in the rhizosphere, with additional 17 phyla uniquely found in the rhizosphere. The biocrust microbes promoted the growth of the model grass, and three biocrust isolates (Bosea sp._L1B56, Pseudarthrobacter sp._L1D14 and Pseudarthrobacter picheli_L1D33) significantly promoted the growth of both hosts. Moreover, pantothenic acid was produced by Pseudarthrobacter sp._L1D14 when grown on B. distachyon exudates, and supplementation of plant growth medium with this metabolite increased B. distachyon biomass by over 60%. These findings suggest that cyanobacteria and other diverse photoautotrophic hosts can be a source for new plant growth-promoting microbes and metabolites.
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Affiliation(s)
- Qing Zheng
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuntao Hu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Marc W Van Goethem
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Susannah G Tringe
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint Genome Institute, Berkeley, CA, 94720, USA
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41
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Li J, Wang J, Liu H, Macdonald CA, Singh BK. Microbial inoculants with higher capacity to colonize soils improved wheat drought tolerance. Microb Biotechnol 2023; 16:2131-2144. [PMID: 37815273 PMCID: PMC10616649 DOI: 10.1111/1751-7915.14350] [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: 07/11/2023] [Revised: 09/16/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023] Open
Abstract
Microbial inoculants have gained increasing attention worldwide as an eco-friendly solution for improving agriculture productivity. Several studies have demonstrated their potential benefits, such as enhanced resistance to drought, salinity, and pathogens. However, the beneficial impacts of inoculants remain inconsistent. This variability is attributed to limited knowledge of the mechanisms by which microbial inoculants affect crop growth and a lack of ecological characteristics of these inoculants that limit our ability to predict their beneficial effects. The first important step is believed to be the evaluation of the inoculant's ability to colonize new habitats (soils and plant roots), which could provide crops with beneficial functions and improve the consistency and efficiency of the inoculants. In this study, we aimed to investigate the impact of three microbial inoculants (two bacterial: P1 and P2, and one fungal: P3) on the growth and stress responses of three wheat varieties in two different soil types under drought conditions. Furthermore, we investigated the impact of microbial inoculants on soil microbial communities. Plant biomass and traits were measured, and high-throughput sequencing was used to characterize bulk and rhizosphere soil microbiomes after exposure to drought stress. Under drought conditions, plant shoot weight significantly increased (11.37%) under P1 treatments compared to uninoculated controls. In addition, total nitrogen enzyme activity increased significantly under P1 in sandy soil but not in clay soil. Importantly, network analyses revealed that P1, consisting of Bacillus paralicheniformis and Bacillus subtilis, emerged as the keystone taxa in sandy soil. Conversely, P2 and P3 failed to establish as keystone taxa, which may explain their insignificant impact on wheat performance under drought conditions. In conclusion, our study emphasizes the importance of effective colonization by microbial inoculants in promoting crop growth under drought conditions. Our findings support the development of microbial inoculants that robustly colonize plant roots for improved agricultural productivity.
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Affiliation(s)
- Jiayu Li
- Hawkesbury Institute for the Environment, Western Sydney University, New South Wales, Penrith, Australia
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, New South Wales, Penrith, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, New South Wales, Penrith, Australia
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, New South Wales, Penrith, Australia
| | - Catriona A Macdonald
- Hawkesbury Institute for the Environment, Western Sydney University, New South Wales, Penrith, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, New South Wales, Penrith, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, New South Wales, Penrith, Australia
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42
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Liu X, Wang Y, Han L, Xia Y, Xie J. A virus induces alterations in root morphology while exerting minimal effects on the rhizosphere and endosphere microorganisms in rice. FEMS Microbiol Ecol 2023; 99:fiad113. [PMID: 37742208 DOI: 10.1093/femsec/fiad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023] Open
Abstract
The highly destructive southern rice black-streaked dwarf virus (SRBSDV) causes significant losses in rice production. To understand its impact on rice root, we studied fibrous root development and root microbiota variation (rhizosphere and endosphere) after SRBSDV infection. SRBSDV infection reduced the number and length of fibrous roots in rice. Interestingly, the rhizosphere had higher bacterial diversity and abundance at the initial (0 days) and 30-day postinfection stages, while 30-day-old roots showed increased diversity and abundance. However, there were no significant differences in microbiota diversity between infected and noninfected rice plants. The major rhizosphere microbiota included Proteobacteria, Bacteroidota, Acidobacteriota, and Planctomycetota, comprising about 80% of the community. The endosphere was dominated by Proteobacteria and Cyanobacteria, constituting over 90%, with Bacteroidota as the next most prominent group. Further, we identified differentially expressed genes related to plant-pathogen interactions, plant hormone signal, and ABC transporters, potentially affecting root morphology. Notably, specific bacteria (e.g. Inquilinus and Actinoplanes) showed correlations with these pathways. In conclusion, SRBSDV primarily influences root growth through host metabolism, rather than exerting direct effects on the root microbiota. These insights into the interactions among the pathogen, rice plant, and associated microbiota could have implications for managing SRBSDV's detrimental effects on rice production.
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Affiliation(s)
- Xuewei Liu
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Yirong Wang
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Lijuan Han
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Yuxian Xia
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
| | - Jiaqin Xie
- School of Life Sciences, Genetic Engineering Research Center, Chongqing University, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Chongqing Engineering Research Center for Fungal Insecticides, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
- Key Laboratory of Gene Function and Regulation Technology under Chongqing Municipal Education Commission, Daxuecheng South Road No. 55, Shapingba District 401331, Chongqing, China
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43
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Russ D, Fitzpatrick CR, Teixeira PJPL, Dangl JL. Deep discovery informs difficult deployment in plant microbiome science. Cell 2023; 186:4496-4513. [PMID: 37832524 DOI: 10.1016/j.cell.2023.08.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 10/15/2023]
Abstract
Plant-associated microbiota can extend plant immune system function, improve nutrient acquisition and availability, and alleviate abiotic stresses. Thus, naturally beneficial microbial therapeutics are enticing tools to improve plant productivity. The basic definition of plant microbiota across species and ecosystems, combined with the development of reductionist experimental models and the manipulation of plant phenotypes with microbes, has fueled interest in its translation to agriculture. However, the great majority of microbes exhibiting plant-productivity traits in the lab and greenhouse fail in the field. Therapeutic microbes must reach détente, the establishment of uneasy homeostasis, with the plant immune system, invade heterogeneous pre-established plant-associated communities, and persist in a new and potentially remodeled community. Environmental conditions can alter community structure and thus impact the engraftment of therapeutic microbes. We survey recent breakthroughs, challenges, and opportunities in translating beneficial microbes from the lab to the field.
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Affiliation(s)
- Dor Russ
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paulo J P L Teixeira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Bei Q, Reitz T, Schnabel B, Eisenhauer N, Schädler M, Buscot F, Heintz-Buschart A. Extreme summers impact cropland and grassland soil microbiomes. THE ISME JOURNAL 2023; 17:1589-1600. [PMID: 37419993 PMCID: PMC10504347 DOI: 10.1038/s41396-023-01470-5] [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: 01/23/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023]
Abstract
The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond to such disturbances. Here, metagenomics was used to investigate the effects of future climate scenarios (+0.6 °C warming and altered precipitation) on soil microbiomes during the summers of 2014-2019. Unexpectedly, Central Europe experienced extreme heatwaves and droughts during 2018-2019, causing significant impacts on the structure, assembly, and function of soil microbiomes. Specifically, the relative abundance of Actinobacteria (bacteria), Eurotiales (fungi), and Vilmaviridae (viruses) was significantly increased in both cropland and grassland. The contribution of homogeneous selection to bacterial community assembly increased significantly from 40.0% in normal summers to 51.9% in extreme summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), and sporulation (spoIID, spoVK) were identified as potential contributors to drought-enriched taxa, and their expressions were confirmed by metatranscriptomics in 2022. The impact of extreme summers was further evident in the taxonomic profiles of 721 recovered metagenome-assembled genomes (MAGs). Annotation of contigs and MAGs suggested that Actinobacteria may have a competitive advantage in extreme summers due to the biosynthesis of geosmin and 2-methylisoborneol. Future climate scenarios caused a similar pattern of changes in microbial communities as extreme summers, but to a much lesser extent. Soil microbiomes in grassland showed greater resilience to climate change than those in cropland. Overall, this study provides a comprehensive framework for understanding the response of soil microbiomes to extreme summers.
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Affiliation(s)
- Qicheng Bei
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany.
| | - Thomas Reitz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Beatrix Schnabel
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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45
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Calvert J, McTaggart A, Carvalhais LC, Rensink S, Dennis PG, Drenth A, Shivas R. Divergent rainforest tree microbiomes between phases of the monsoon cycle, host plants and tissues. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:860-870. [PMID: 37647418 DOI: 10.1111/plb.13569] [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: 01/09/2023] [Accepted: 07/26/2023] [Indexed: 09/01/2023]
Abstract
The Australian Monsoon Tropics (AMT) contain some of the most biodiverse forests on the continent. Little is known about the dynamics of rainforest plant microbiomes in general, and there have been no community-level studies on Australian rainforest endophytes, their seasonality, tissue and host specificity. We tested whether community composition of tropical tree endophytes (fungi and bacteria) differs: (i) at different points during a monsoon cycle, (ii) between leaf and stem tissues, (iii) between forest microclimates (gully/ridge), and between (iv) host plant species, and (v) host plant clade, using amplicon sequencing of the bacterial 16S and fungal ITS2 gene regions. Results indicated that the composition of rainforest plant microbiomes differs between wet and dry seasons, which may be explained by physiological shifts in host plants due to annual climate fluctuations from mesic to xeric. Endophyte microbiomes differed between leaves and stems. Distinct fungal communities were associated with host species and clades, with some trees enriched in a number of fungal taxa compared to host plants in other clades. Diversity of bacterial endophytes in plant stems increased in the dry season. We conclude that the microbiomes of tropical plants are responsive to monsoonal climate variation, are highly compartmentalised between plant tissues, and may be partly shaped by the relatedness of their host plants.
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Affiliation(s)
- J Calvert
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - A McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - L C Carvalhais
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - S Rensink
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - P G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - A Drenth
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - R Shivas
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
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Metze D, Schnecker J, Canarini A, Fuchslueger L, Koch BJ, Stone BW, Hungate BA, Hausmann B, Schmidt H, Schaumberger A, Bahn M, Kaiser C, Richter A. Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions. Nat Commun 2023; 14:5895. [PMID: 37736743 PMCID: PMC10516970 DOI: 10.1038/s41467-023-41524-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO2 levels). For this purpose, we combined 18O-water vapor equilibration with quantitative stable isotope probing (termed 'vapor-qSIP') to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO2) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.
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Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria.
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Benjamin J Koch
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Schaumberger
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Irdning, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- International Institute for Applied Systems Analysis, Advancing Systems Analysis Program, Laxenburg, Austria.
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Liu J, Xu H, Wang Z, Liu J, Gong X. Core Endophytic Bacteria and Their Roles in the Coralloid Roots of Cultivated Cycas revoluta (Cycadaceae). Microorganisms 2023; 11:2364. [PMID: 37764208 PMCID: PMC10537169 DOI: 10.3390/microorganisms11092364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
As a gymnosperm group, cycads are known for their ancient origin and specialized coralloid root, which can be used as an ideal system to explore the interaction between host and associated microorganisms. Previous studies have revealed that some nitrogen-fixing cyanobacteria contribute greatly to the composition of the endophytic microorganisms in cycad coralloid roots. However, the roles of host and environment in shaping the composition of endophytic bacteria during the recruitment process remain unclear. Here, we determined the diversity, composition, and function prediction of endophytic bacteria from the coralloid roots of a widely cultivated cycad, Cycas revoluta Thunb. Using next-generation sequencing techniques, we comprehensively investigated the diversity and community structure of the bacteria in coralloid roots and bulk soils sampled from 11 sites in China, aiming to explore the variations in core endophytic bacteria and to predict their potential functions. We found a higher microbe diversity in bulk soils than in coralloid roots. Meanwhile, there was no significant difference in the diversity and composition of endophytic bacteria across different localities, and the same result was found after removing cyanobacteria. Desmonostoc was the most dominant in coralloid roots, followed by Nostoc, yet these two cyanobacteria were not shared by all samples. Rhodococcus, Edaphobacter, Niastella, Nordella, SH-PL14, and Virgisporangium were defined as the core microorganisms in coralloid roots. A function prediction analysis revealed that endophytic bacteria majorly participated in the plant uptake of phosphorus and metal ions and in disease resistance. These results indicate that the community composition of the bacteria in coralloid roots is affected by both the host and environment, in which the host is more decisive. Despite the very small proportion of core microbes, their interactions are significant and likely contribute to functions related to host survival. Our study contributes to an understanding of microbial diversity and composition in cycads, and it expands the knowledge on the association between hosts and symbiotic microbes.
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Affiliation(s)
- Jiating Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Xu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Zhaochun Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Jian Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Xun Gong
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
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Rodríguez R, Barra PJ, Larama G, Carrion VJ, de la Luz Mora M, Hale L, Durán P. Microbiome engineering optimized by Antarctic microbiota to support a plant host under water deficit. FRONTIERS IN PLANT SCIENCE 2023; 14:1241612. [PMID: 37780522 PMCID: PMC10541027 DOI: 10.3389/fpls.2023.1241612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023]
Abstract
Climate change challenges modern agriculture to develop alternative and eco-friendly solutions to alleviate abiotic and/or biotic stresses. The use of soil microbiomes from extreme environments opens new avenues to discover novel microorganisms and microbial functions to protect plants. In this study we confirm the ability of a bioinoculant, generated by natural engineering, to promote host development under water stress. Microbiome engineering was mediated through three factors i) Antarctic soil donation, ii) water deficit and iii) multigenerational tomato host selection. We revealed that tomato plants growing in soils supplemented with Antarctic microbiota were tolerant to water deficit stress after 10 generations. A clear increase in tomato seedling tolerance against water deficit stress was observed in all soils over generations of Host Mediated Microbiome Engineering, being Fildes mixture the most representatives, which was evidenced by an increased survival time, plant stress index, biomass accumulation, and decreased leaf proline content. Microbial community analysis using 16s rRNA gene amplicon sequencing data suggested a microbiome restructuring that could be associated with increased tolerance of water deficit. Additionally, the results showed a significant increase in the relative abundance of Candidatus Nitrosocosmicus and Bacillus spp. which could be key taxa associated with the observed tolerance improvement. We proposed that in situ microbiota engineering through the evolution of three factors (long-standing extreme climate adaption and host and stress selection) could represent a promising strategy for novel generation of microbial inoculants.
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Affiliation(s)
- Rodrigo Rodríguez
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
- Agroscientific SpA, Temuco, Chile
| | - Patricio J. Barra
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Giovanni Larama
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
| | | | - María de la Luz Mora
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Lauren Hale
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Paola Durán
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
- Facultad de Ciencias Agropecuarias y Medioambiente, Departamento de Producción Agropecuaria, Universidad de La Frontera, Temuco, Chile
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Fang J, Wei S, Gao Y, Zhang X, Cheng Y, Wang J, Ma J, Shi G, Bai L, Xie R, Zhao X, Ren Y, Lu Z. Character variation of root space microbial community composition in the response of drought-tolerant spring wheat to drought stress. Front Microbiol 2023; 14:1235708. [PMID: 37779714 PMCID: PMC10541208 DOI: 10.3389/fmicb.2023.1235708] [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: 06/06/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
Drought is the most prevalent environmental stress in crop production, posing a significant danger to food security. Microorganisms in the crop root zone affect crop growth and development, enhance effective nutrient use, and resist adversity hazards. To analyze the changes and functional differences of root space microbial (endosphere-rhizosphere-bulk soil) communities in spring wheat under drought stress. In this study, the root, rhizosphere, and bulk soil of the drought-tolerant group (DTG, three varieties) and drought-sensitive group (DSG, three varieties) were collected. The control (CK, 25-28%), moderate drought (MD, 15-18%), and severe drought (SD, 9-12%) were analyzed by high-throughput sequencing and bioinformatics. The results showed significant differences in the diversity of Bacteria and Fungi in the root space of spring wheat under drought stress (P < 0.05), with the drought-tolerant group exhibiting higher microbial diversity. The microbial community change in spring wheat root space was mainly determined by the niche differentiation of endosphere, rhizosphere, and bulk soil and declined from endosphere to bulk soil due to drought. The antagonism between microbial and root-space species increased, and the community's complexity and stability deteriorated. Enriching drought-resistant preference groups like Actinobaciota, Variovorax, Streptomyces, and Conocybe altered the structure and function of the microbial community in the root space of spring wheat. Spring wheat's root space Bacteria and Fungi have different strategies to respond to drought.
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Affiliation(s)
- Jing Fang
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Shuli Wei
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Yanrong Gao
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Xiangqian Zhang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuchen Cheng
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Jianguo Wang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Jie Ma
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Gongfu Shi
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Lanfang Bai
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot, China
| | - Rui Xie
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Xiaoqing Zhao
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Yongfeng Ren
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Zhanyuan Lu
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
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50
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Dao J, Xing Y, Chen C, Chen M, Wang Z. Adaptation of rhizosphere bacterial communities of drought-resistant sugarcane varieties under different degrees of drought stress. Microbiol Spectr 2023; 11:e0118423. [PMID: 37698408 PMCID: PMC10580969 DOI: 10.1128/spectrum.01184-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 07/12/2023] [Indexed: 09/13/2023] Open
Abstract
Sugarcane is highly sensitive to changes in moisture, and increased drought severely restricts its growth and productivity. Recent studies have shown that plant growth-promoting microorganisms are essential to reduce the adverse effects of environmental stresses, especially drought. However, our knowledge about the dynamics of rhizosphere microbial community structure in sugarcane under varying degrees of drought stress is limited. We analyzed the effects of different degrees of drought stress on the rhizosphere microbial communities of Zhongzhe 1(ZZ1) and Zhongzhe 6(ZZ6) with differences in drought resistance, by combining soil enzyme activity, nutrient content, and physiological and morphological characteristics of sugarcane roots. The results showed that rhizosphere bacterial community began to change at a field capacity of 50%, enriching the sugarcane rhizosphere with drought-resistant bacteria. The core strains of ZZ1 and ZZ6 rhizosphere enrichment were mainly Streptomycetales, Sphingomonadales, and Rhizobiales. However, compared to ZZ1, the changes in rhizosphere bacterial abundance in ZZ6 were primarily associated with the abundance of Streptomycetales as drought levels increased. Rhizobiales and Streptomycetales, enriched in the rhizosphere of ZZ6 under drought, were positively correlated with root tip number and total root length (TRL), increasing the distribution area of roots and, thus, improving water and nutrient uptake by the roots thereby enhancing the resistance of sugarcane to drought stress. This research enhances our understanding of the composition of the rhizosphere microbial community in sugarcane under different levels of drought stress and its interaction with the roots, thereby providing valuable insights for enhancing drought resistance in sugarcane. IMPORTANCE Drought stress is expected to further increase in intensity, frequency, and duration, causing substantial losses in sugarcane yields. Here, we exposed sugarcane to varying degrees of drought treatment during growth and quantified the eventual composition of the resulting sugarcane rhizosphere bacterial community groups. We found that sugarcane rhizosphere under mild drought began to recruit specific bacterial communities to resist drought stress and used the interactions of root tip number, total root length, and drought-resistant strains to improve sugarcane survival under drought. This research provides a theoretical basis for the rhizosphere microbiome to help sugarcane improve its resistance under different levels of drought stress.
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Affiliation(s)
- Jicao Dao
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, Guangxi, China
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
| | - Yuanjun Xing
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, Guangxi, China
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
| | - Chunyi Chen
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, Guangxi, China
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
| | - Mianhe Chen
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, Guangxi, China
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
| | - Ziting Wang
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, Guangxi, China
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
- College of Agronomy, Guangxi University, Nanning, Guangxi, China
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