1
|
Caravaca F, Torres P, Díaz G, Roldán A. Selective shifts in the rhizosphere microbiome during the drought season could explain the success of the invader Nicotiana glauca in semiarid ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174444. [PMID: 38964394 DOI: 10.1016/j.scitotenv.2024.174444] [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: 03/21/2024] [Revised: 06/28/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
The rhizosphere microbiome plays a crucial role in the ability of plants to colonize and thrive in stressful conditions such as drought, which could be decisive for the success of exotic plant invasion in the context of global climate change. The aim of this investigation was to examine differences in the composition, structure, and functional traits of the microbial community of the invader Nicotiana glauca R.C. Graham and native species growing at seven different Mediterranean semiarid locations under two distinct levels of water availability, corresponding to the wet and dry seasons. The results show that the phylum Actinobacteriota was an indicator phylum of the dry season as well as for the community of N. glauca. The dominant indicator bacterial families of the dry season were 67-14 (unclassified family), Pseudonocardiaceae, and Sphingomonadaceae, being relatively more abundant in the invasive rhizosphere. The relative abundances of the indicator fungal families Aspergillaceae (particularly the indicator genus Aspergillus), Glomeraceae, and Claroideoglomeraceae were higher in the invasive rhizosphere. The relative abundance of mycorrhizal fungi was higher in the invasive rhizosphere in the dry season (by about 40 % in comparison to that of native plants), without significant differences between invasive and native plants in the wet season. Bacterial potential functional traits related to energy and precursor metabolites production and also biosynthesis of cell wall, cofactors, vitamins, and amino acids as well as catabolic enzymes involved in the P cycle prevailed in the invasive rhizosphere under drought conditions. This study shows that the pronounced and beneficial shifts in the microbiome assembly and functions in the rhizosphere of N. glauca under conditions of low soil water availability can represent a clear advantage for its establishment.
Collapse
Affiliation(s)
- F Caravaca
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, P.O. Box 164, Campus de Espinardo 30100, Murcia, Spain.
| | - P Torres
- Universidad Miguel Hernández de Elche, Department of Applied Biology, Avda. Ferrocarril, s/n. Edf. Laboratorios-03202-Elche, Alicante, Spain
| | - G Díaz
- Universidad Miguel Hernández de Elche, Department of Applied Biology, Avda. Ferrocarril, s/n. Edf. Laboratorios-03202-Elche, Alicante, Spain
| | - A Roldán
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, P.O. Box 164, Campus de Espinardo 30100, Murcia, Spain
| |
Collapse
|
2
|
Liu J, Xu W, Zhang Q, Liao W, Li L, Chen S, Yang J, Wang Z, Xu F. OsPHR2-mediated recruitment of Pseudomonadaceae enhances rice phosphorus uptake. PLANT COMMUNICATIONS 2024; 5:100930. [PMID: 38685708 DOI: 10.1016/j.xplc.2024.100930] [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: 11/21/2023] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
Plants can shape their root microbiome to promote growth and nutrient uptake. PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) is a central regulator of phosphate signaling in rice, but whether OsPHR2 can shape the root microbiome to promote phosphorus uptake is unclear. Here, we investigate the role of OsPHR2 in recruiting microbiota for phosphorus uptake using high-throughput sequencing and metabolite analysis. OsPHR2-overexpressing (OsPHR2 OE) rice showed 69.8% greater shoot P uptake in natural soil compared with sterilized soil under high-phosphorus (HP) conditions, but there was only a 54.8% increase in the wild-type (WT). The abundance of the family Pseudomonadaceae was significantly enriched in OsPHR2 OE roots relative to those of WT rice. Compared with the WT, OsPHR2 OE rice had a relatively higher abundance of succinic acid and methylmalonic acid, which could stimulate the growth of Pseudomonas sp. (P6). After inoculation with P6, phosphorus uptake in WT and OsPHR2 OE rice was higher than that in uninoculated rice under low-phosphorus (LP) conditions. Taken together, our results suggest that OsPHR2 can increase phosphorus use in rice through root exudate-mediated recruitment of Pseudomonas. This finding reveals a cooperative contribution of the OsPHR2-modulated root microbiome, which is important for improving phosphorus use in agriculture.
Collapse
Affiliation(s)
- Jianping Liu
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weifeng Xu
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Qian Zhang
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wencheng Liao
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liang Li
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shu Chen
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jinyong Yang
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhengrui Wang
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Feiyun Xu
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| |
Collapse
|
3
|
Kozaeva E, Eida AA, Gunady EF, Dangl JL, Conway JM, Brophy JA. Roots of synthetic ecology: microbes that foster plant resilience in the changing climate. Curr Opin Biotechnol 2024; 88:103172. [PMID: 39029405 DOI: 10.1016/j.copbio.2024.103172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/11/2024] [Accepted: 06/26/2024] [Indexed: 07/21/2024]
Abstract
Microbes orchestrate nearly all major biogeochemical processes. The ability to program their influence on plant growth and development is attractive for sustainable agriculture. However, the complexity of microbial ecosystems and our limited understanding of the mechanisms by which plants and microbes interact with each other and the environment make it challenging to use microbiomes to influence plant growth. Novel technologies at the intersection of microbial ecology, systems biology, and bioengineering provide new tools to probe the role of plant microbiomes across environments. Here, we summarize recent studies on plant and microbe responses to abiotic stresses, showcasing key molecules and micro-organisms that are important for plant health. We highlight opportunities to use synthetic microbial communities to understand the complexity of plant-microbial interactions and discuss future avenues of programming ecology to improve plant and ecosystem health.
Collapse
Affiliation(s)
- Ekaterina Kozaeva
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Abdul Aziz Eida
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ella F Gunady
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Jeffery L Dangl
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jonathan M Conway
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
| | | |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Liu H, Li J, Singh BK. Harnessing co-evolutionary interactions between plants and Streptomyces to combat drought stress. NATURE PLANTS 2024:10.1038/s41477-024-01749-1. [PMID: 39048724 DOI: 10.1038/s41477-024-01749-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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.
Collapse
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.
| |
Collapse
|
6
|
Wang F, Jia M, Li K, Cui Y, An L, Sheng H. Sphingomonas sp. Hbc-6 alters Arabidopsis metabolites to improve plant growth and drought resistance by manipulating the microbiome. Microbiol Res 2024; 287:127852. [PMID: 39084119 DOI: 10.1016/j.micres.2024.127852] [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: 05/15/2024] [Revised: 07/08/2024] [Accepted: 07/17/2024] [Indexed: 08/02/2024]
Abstract
Drought significantly affects crop productivity and poses a considerable threat to agricultural ecosystems. Plant growth-promoting bacteria (PGPB) and plant microbiome play important roles in improving drought resistance and plant performance. However, the response of the rhizosphere microbiota to PGPB during the development of plants and the interaction between inoculum, microbiota, and plants under drought stress remain to be explored. In the present study, we used culturomic, microbiomic, and metabonomic analyses to uncover the mechanisms by which Sphingomonas sp. Hbc-6, a PGPB, promotes Arabidopsis growth and enhances drought resistance. We found that the rhizosphere microbiome assembly was interactively influenced by developmental stage, Hbc-6, and drought; the bacterial composition exhibited three patterns of shifts with developmental stage: resilience, increase, and decrease. Drought diminished microbial diversity and richness, whereas Hbc-6 increased microbial diversity and helped plants recruit specific beneficial bacterial taxa at each developmental stage, particularly during the bolting stage. Some microorganisms enriched by Hbc-6 had the potential to promote carbon and nitrogen cycling processes, and 86.79 % of the isolated strains exhibited PGP characteristics (for example Pseudomonas sp. TA9). They jointly regulated plant physiological metabolism (i.e., upregulated drought resistant-facilitating substances and reduced harmful substances), thereby stimulating the growth of Arabidopsis and increasing plant biomass under drought stress conditions. Collectively, these results indicate that Hbc-6 mediates plant growth and drought resistance by affecting the microbiome. The study thus provides novel insights and strain resources for drought-resistant, high-yielding crop cultivation and breeding.
Collapse
Affiliation(s)
- Fang Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mingyue Jia
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Kun Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yafang Cui
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China; The College of Forestry, Beijing Forestry University, Beijing, China
| | - Hongmei Sheng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Zeng ZY, Huang JR, Liu ZQ, Yang AL, Li YX, Wang YL, Zhang HB. Distinct effects of phyllosphere and rhizosphere microbes on invader Ageratina adenophora during its early life stages. eLife 2024; 13:RP95502. [PMID: 38896455 PMCID: PMC11186635 DOI: 10.7554/elife.95502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024] Open
Abstract
Microbes strongly affect invasive plant growth. However, how phyllosphere and rhizosphere soil microbes distinctively affect seedling mortality and growth of invaders across ontogeny under varying soil nutrient levels remains unclear. In this study, we used the invader Ageratina adenophora to evaluate these effects. We found that higher proportions of potential pathogens were detected in core microbial taxa in leaf litter than rhizosphere soil and thus leaf inoculation had more adverse effects on seed germination and seedling survival than soil inoculation. Microbial inoculation at different growth stages altered the microbial community and functions of seedlings, and earlier inoculation had a more adverse effect on seedling survival and growth. The soil nutrient level did not affect microbe-mediated seedling growth and the relative abundance of the microbial community and functions involved in seedling growth. The effects of some microbial genera on seedling survival are distinct from those on growth. Moreover, the A. adenophora seedling-killing effects of fungal strains isolated from dead seedlings by non-sterile leaf inoculation exhibited significant phylogenetic signals, by which strains of Allophoma and Alternaria generally caused high seedling mortality. Our study stresses the essential role of A. adenophora litter microbes in population establishment by regulating seedling density and growth.
Collapse
Affiliation(s)
- Zhao-Ying Zeng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan UniversityKunmingChina
- School of Ecology and Environmental Science, Yunnan UniversityKunmingChina
| | - Jun-Rong Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan UniversityKunmingChina
| | - Zi-Qing Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan UniversityKunmingChina
| | - Ai-Ling Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan UniversityKunmingChina
- School of Ecology and Environmental Science, Yunnan UniversityKunmingChina
| | - Yu-Xuan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan UniversityKunmingChina
- School of Ecology and Environmental Science, Yunnan UniversityKunmingChina
| | - Yong-Lan Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan UniversityKunmingChina
| | - Han-Bo Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan UniversityKunmingChina
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Ali R, Chaluvadi SR, Wang X, Hazzouri KM, Sudalaimuthuasari N, Rafi M, Al-Nuaimi M, Sasi S, Antepenko E, Bennetzen JL, Amiri KMA. Microbiome properties in the root nodules of Prosopis cineraria, a leguminous desert tree. Microbiol Spectr 2024; 12:e0361723. [PMID: 38624222 PMCID: PMC11237379 DOI: 10.1128/spectrum.03617-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/14/2024] [Indexed: 04/17/2024] Open
Abstract
We conducted a comprehensive analysis of the total microbiome and transcriptionally active microbiome communities in the roots and root nodules of Prosopis cineraria, an important leguminous tree in arid regions of many Asian countries. Mature P. cineraria trees growing in the desert did not exhibit any detected root nodules. However, we observed root nodules on the roots of P. cineraria growing on a desert farm and on young plants growing in a growth chamber, when inoculated with rhizosphere soil, including with rhizosphere soil from near desert tree roots that had no nodules. Compared to nearby soil, non-nodulated roots were enriched with Actinobacteria (e.g., Actinophytocola sp.), whereas root nodules sampled from the desert farm and growth chamber had abundant Alphaproteobacteria (e.g., Ensifer sp.). These nodules yielded many microbes in addition to such nitrogen-fixing bacteria as Ensifer and Sinorhizobium species. Significant differences exist in the composition and abundance of microbial isolates between the nodule surface and the nodule endosphere. Shotgun metagenome analysis of nodule endospheres revealed that the root nodules comprised over 90% bacterial DNA, whereas metatranscriptome analysis showed that the plant produces vastly more transcripts than the microbes in these nodules. Control inoculations demonstrated that four out of six Rhizobium, Agrobacterium, or Ensifer isolates purified from P. cineraria nodules produced nodules in the roots of P. cineraria seedlings under greenhouse conditions. The best nodulation was achieved when seedlings were inoculated with a mixture of those bacterial strains. Though root nodulation could be achieved under water stress conditions, nodule number and nodule biomass increased with copious water availability. .IMPORTANCEMicrobial communities were investigated in roots and root nodules of Prosopis cineraria, a leguminous tree species in arid Asian regions that is responsible for exceptionally important contributions to soil fertility in these dramatically dry locations. Soil removed from regions near nodule-free roots on these mature plants contained an abundance of bacteria with the genetic ability to generate nodules and fix nitrogen but did not normally nodulate in their native rhizosphere environment, suggesting a very different co-evolved relationship than that observed for herbaceous legumes. The relative over-expression of the low-gene-density plant DNA compared to the bacterial DNA in the nodules was also unexpected, indicating a very powerful induction of host genetic contributions within the nodule. Finally, the water dependence of nodulation in inoculated seedlings suggested a possible link between early seedling growth (before a deep root system can be developed) and the early development of nitrogen-fixing capability.
Collapse
Affiliation(s)
- Rashid Ali
- Mitrix Bio., Inc., Farmington, Connecticut, USA
| | | | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Khaled M. Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | | | - Mohammed Rafi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | - Mariam Al-Nuaimi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | - Shina Sasi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | - Eric Antepenko
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | | | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, UAE
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Jia W, Huang P, Zhu K, Gao X, Chen Q, Chen J, Ran Y, Chen S, Ma M, Wu S. Zonation of bulk and rhizosphere soil bacterial communities and their covariation patterns along the elevation gradient in riparian zones of three Gorges reservoir, China. ENVIRONMENTAL RESEARCH 2024; 249:118383. [PMID: 38331152 DOI: 10.1016/j.envres.2024.118383] [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: 11/23/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Zonation is a typical pattern of soil distribution and species assembly across riparian habitats. Microorganisms are essential members of riparian ecosystems and whether soil microbial communities demonstrate similar zonation patterns and how bulk and rhizosphere soil microorganisms interact along the elevation (submergence stress) gradient remain largely unknown. In this study, bulk and rhizosphere (dominant plant) soil samples were collected and investigated across riparian zones where the submergence stress intensity increased as the elevation decreased. Results showed that the richness of bacterial communities in bulk and rhizosphere soil samples was significantly different and presented a zonation pattern along with the submergence stress gradient. Bulk soil at medium elevation that underwent moderate submergence stress had the most abundant bacterial communities, while the species richness of rhizobacteria at low elevation that experienced serious submergence stress was the highest. Additionally, principal coordinate analysis (PCoA) and significance tests showed that bulk and rhizosphere soil samples were distinguished according to the structure of bacterial communities, and so were bulk or rhizosphere soil samples from different elevations. Redundancy analysis (RDA) and Mantel test suggested that bacterial communities of bulk soil mainly relied on the contents of soil organic matter, total carbon (TC), total nitrogen (TN), sodium (Na), calcium (Ca) and magnesium (Mg). Contrastingly, the contents of Na and Mg were the main factors explaining the variation in rhizobacterial community composition. Correlation and microbial source tracking analyses showed thatthe relationship of bulk and rhizosphere soil bacteria became much stronger, and the rhizosphere soil may get more bacterial communities from bulk soil with the increase in submergence severity. Our results suggest that the abiotic and biotic components of the riparian ecosystem are closely covariant along the submergence stress gradient and imply that the bacterial community may be a key node linking soil physiochemical properties and vegetation communities.
Collapse
Affiliation(s)
- Weitao Jia
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Ping Huang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Kai Zhu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Xin Gao
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Qiao Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Jilong Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Yiguo Ran
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Shanshan Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Maohua Ma
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Shengjun Wu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China.
| |
Collapse
|
15
|
Zhang Y, Wu X, Wang X, Dai M, Peng Y. Crop root system architecture in drought response. J Genet Genomics 2024:S1673-8527(24)00100-0. [PMID: 38723744 DOI: 10.1016/j.jgg.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 07/27/2024]
Abstract
Drought is a natural disaster that profoundly impacts on global agricultural production, significantly reduces crop yields, and thereby poses a severe threat to worldwide food security. Addressing the challenge of effectively improving crop drought resistance (DR) to mitigate yield loss under drought conditions is a global issue. An optimal root system architecture (RSA) plays a pivotal role in enhancing crops' capacity to efficiently uptake water and nutrients, which consequently strengthens their resilience against environmental stresses. In this review, we discuss the compositions and roles of crop RSA and summarize the most recent developments in augmenting drought tolerance in crops by manipulating RSA-related genes. Based on the current research, we propose the potential optimal RSA configuration that could be helpful in enhancing crop DR. Lastly, we discussed the existing challenges and future directions for breeding crops with enhanced DR capabilities through genetic improvements targeting RSA.
Collapse
Affiliation(s)
- Yanjun Zhang
- College of Agronomy, Gansu Agricultural University, Lanzhou, Gansu 730070, China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu 730070, China; Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China; Key Laboratory of Crop Gene Resources and Germplasm Innovation in Northwest Cold and Arid Regions, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu 730070, China
| | - Xi Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, HuBei 430070, China
| | - Xingrong Wang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China; Key Laboratory of Crop Gene Resources and Germplasm Innovation in Northwest Cold and Arid Regions, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu 730070, China
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, HuBei 430070, China.
| | - Yunling Peng
- College of Agronomy, Gansu Agricultural University, Lanzhou, Gansu 730070, China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
| |
Collapse
|
16
|
Ludington WB. The importance of host physical niches for the stability of gut microbiome composition. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230066. [PMID: 38497267 PMCID: PMC10945397 DOI: 10.1098/rstb.2023.0066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/04/2023] [Indexed: 03/19/2024] Open
Abstract
Gut bacteria are prevalent throughout the Metazoa and form complex microbial communities associated with food breakdown, nutrient provision and disease prevention. How hosts acquire and maintain a consistent bacterial flora remains mysterious even in the best-studied animals, including humans, mice, fishes, squid, bugs, worms and flies. This essay visits the evidence that hosts have co-evolved relationships with specific bacteria and that some of these relationships are supported by specialized physical niches that select, sequester and maintain microbial symbionts. Genetics approaches could uncover the mechanisms for recruiting and maintaining the stable and consistent members of the microbiome. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
Collapse
Affiliation(s)
- William B. Ludington
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Baltimore, MD 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| |
Collapse
|
17
|
Zhao Q, Bertolli S, Park YJ, Tan Y, Cutler KJ, Srinivas P, Asfahl KL, Fonesca-García C, Gallagher LA, Li Y, Wang Y, Coleman-Derr D, DiMaio F, Zhang D, Peterson SB, Veesler D, Mougous JD. Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature 2024; 629:165-173. [PMID: 38632398 PMCID: PMC11062931 DOI: 10.1038/s41586-024-07298-z] [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: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive1. The production of these antibacterial molecules reflects the relentless competition Streptomyces engage in with other bacteria, including other Streptomyces species1,2. Here we show that in addition to small-molecule antibiotics, Streptomyces produce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein. A cryo-electron microscopy structure of these particles reveals an extended stalk topped by a ringed crown comprising the toxin repeats scaffolding five lectin-tipped spokes, which led us to name them umbrella particles. Streptomyces coelicolor encodes three umbrella particles with distinct toxin and lectin composition. Notably, supernatant containing these toxins specifically and potently inhibits the growth of select Streptomyces species from among a diverse collection of bacteria screened. For one target, Streptomyces griseus, inhibition relies on a single toxin and that intoxication manifests as rapid cessation of vegetative hyphal growth. Our data show that Streptomyces umbrella particles mediate competition among vegetative mycelia of related species, a function distinct from small-molecule antibiotics, which are produced at the onset of reproductive growth and act broadly3,4. Sequence analyses suggest that this role of umbrella particles extends beyond Streptomyces, as we identified umbrella loci in nearly 1,000 species across Actinobacteria.
Collapse
Affiliation(s)
- Qinqin Zhao
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Savannah Bertolli
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Yongjun Tan
- Department of Biology, St Louis University, St Louis, MO, USA
| | - Kevin J Cutler
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Pooja Srinivas
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kyle L Asfahl
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA
| | - Citlali Fonesca-García
- Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Larry A Gallagher
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Yaqiao Li
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Yaxi Wang
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Devin Coleman-Derr
- Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Dapeng Zhang
- Department of Biology, St Louis University, St Louis, MO, USA
- Program of Bioinformatic and Computational Biology, St Louis University, St Louis, MO, USA
| | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - David Veesler
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA.
| |
Collapse
|
18
|
Su X, Zhang L, Meng H, Wang H, Zhao J, Sun X, Song X, Zhang X, Mao L. Long-term conservation tillage increase cotton rhizosphere sequestration of soil organic carbon by changing specific microbial CO 2 fixation pathways in coastal saline soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120743. [PMID: 38626484 DOI: 10.1016/j.jenvman.2024.120743] [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: 02/02/2024] [Revised: 02/27/2024] [Accepted: 03/19/2024] [Indexed: 04/18/2024]
Abstract
Coastal saline soil is an important reserve resource for arable land globally. Data from 10 years of continuous stubble return and subsoiling experiments have revealed that these two conservation tillage measures significantly improve cotton rhizosphere soil organic carbon sequestration in coastal saline soil. However, the contribution of microbial fixation of atmospheric carbon dioxide (CO2) has remained unclear. Here, metagenomics and metabolomics analyses were used to deeply explore the microbial CO2 fixation process in rhizosphere soil of coastal saline cotton fields under long-term stubble return and subsoiling. Metagenomics analysis showed that stubble return and subsoiling mainly optimized CO2 fixing microorganism (CFM) communities by increasing the abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi, and improving composition diversity. Conjoint metagenomics and metabolomics analyses investigated the effects of stubble return and subsoiling on the reverse tricarboxylic acid (rTCA) cycle. The conversion of citrate to oxaloacetate was inhibited in the citrate cleavage reaction of the rTCA cycle. More citrate was converted to acetyl-CoA, which enhanced the subsequent CO2 fixation process of acetyl-CoA conversion to pyruvate. In the rTCA cycle reductive carboxylation reaction from 2-oxoglutarate to isocitrate, synthesis of the oxalosuccinate intermediate product was inhibited, with strengthened CO2 fixation involving the direct conversion of 2-oxoglutarate to isocitrate. The collective results demonstrate that stubble return and subsoiling optimizes rhizosphere CFM communities by increasing microbial diversity, in turn increasing CO2 fixation by enhancing the utilization of rTCA and 3-hydroxypropionate/4-hydroxybutyrate cycles by CFMs. These events increase the microbial CO2 fixation in the cotton rhizosphere, thereby promoting the accumulation of microbial biomass, and ultimately improving rhizosphere soil organic carbon. This study clarifies the impact of conservation tillage measures on microbial CO2 fixation in cotton rhizosphere of coastal saline soil, and provides fundamental data for the improvement of carbon sequestration in saline soil in agricultural ecosystems.
Collapse
Affiliation(s)
- Xunya Su
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Le Zhang
- China Agricultural University, Agronomy College, Beijing, 100193, China.
| | - Hao Meng
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Han Wang
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Jiaxue Zhao
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Xuezhen Sun
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Xianliang Song
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Xiaopei Zhang
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| | - Lili Mao
- Shandong Agricultural University, Agronomy College, Taian, Shandong, 271018, China.
| |
Collapse
|
19
|
Zheng Y, Cao X, Zhou Y, Ma S, Wang Y, Li Z, Zhao D, Yang Y, Zhang H, Meng C, Xie Z, Sui X, Xu K, Li Y, Zhang CS. Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress. Nat Commun 2024; 15:3520. [PMID: 38664402 PMCID: PMC11045775 DOI: 10.1038/s41467-024-47773-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The root-associated microbiota plays an important role in the response to environmental stress. However, the underlying mechanisms controlling the interaction between salt-stressed plants and microbiota are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean (Glycine soja), we demonstrate that highly conserved microbes dominated by Pseudomonas are enriched in the root and rhizosphere microbiota of salt-stressed plant. Two corresponding Pseudomonas isolates are confirmed to enhance the salt tolerance of wild soybean. Shotgun metagenomic and metatranscriptomic sequencing reveal that motility-associated genes, mainly chemotaxis and flagellar assembly, are significantly enriched and expressed in salt-treated samples. We further find that roots of salt stressed plants secreted purines, especially xanthine, which induce motility of the Pseudomonas isolates. Moreover, exogenous application for xanthine to non-stressed plants results in Pseudomonas enrichment, reproducing the microbiota shift in salt-stressed root. Finally, Pseudomonas mutant analysis shows that the motility related gene cheW is required for chemotaxis toward xanthine and for enhancing plant salt tolerance. Our study proposes that wild soybean recruits beneficial Pseudomonas species by exudating key metabolites (i.e., purine) against salt stress.
Collapse
Affiliation(s)
- Yanfen Zheng
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Xuwen Cao
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266200, China
| | - Yanan Zhou
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, 271018, China
| | - Siqi Ma
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Youqiang Wang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Zhe Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Donglin Zhao
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Yanzhe Yang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Han Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Chen Meng
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Zhihong Xie
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, 271018, China
| | - Xiaona Sui
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Kangwen Xu
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Yiqiang Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Cheng-Sheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| |
Collapse
|
20
|
Kawa D, Thiombiano B, Shimels MZ, Taylor T, Walmsley A, Vahldick HE, Rybka D, Leite MFA, Musa Z, Bucksch A, Dini-Andreote F, Schilder M, Chen AJ, Daksa J, Etalo DW, Tessema T, Kuramae EE, Raaijmakers JM, Bouwmeester H, Brady SM. The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection. Cell Rep 2024; 43:113971. [PMID: 38537644 PMCID: PMC11063626 DOI: 10.1016/j.celrep.2024.113971] [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: 01/26/2023] [Revised: 01/17/2024] [Accepted: 02/29/2024] [Indexed: 04/10/2024] Open
Abstract
Sorghum bicolor is among the most important cereals globally and a staple crop for smallholder farmers in sub-Saharan Africa. Approximately 20% of sorghum yield is lost annually in Africa due to infestation with the root parasitic weed Striga hermonthica. Existing Striga management strategies are not singularly effective and integrated approaches are needed. Here, we demonstrate the functional potential of the soil microbiome to suppress Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation and with depletion of haustorium-inducing factors, compounds required for the initial stages of Striga infection. We further identify specific bacterial taxa that trigger the observed Striga-suppressive traits. Collectively, our study describes the importance of the soil microbiome in the early stages of root infection by Striga and pinpoints mechanisms of Striga suppression. These findings open avenues to broaden the effectiveness of integrated Striga management practices.
Collapse
Affiliation(s)
- Dorota Kawa
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA; Plant Stress Resilience, Department of Biology, Utrecht University, 3508 TC Utrecht, the Netherlands; Environmental and Computational Plant Development, Department of Biology, Utrecht University, 3508 TC Utrecht, the Netherlands.
| | - Benjamin Thiombiano
- Plant Hormone Biology Group, Green Life Sciences Cluster, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Mahdere Z Shimels
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands
| | - Tamera Taylor
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA; Plant Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA
| | - Aimee Walmsley
- Plant Hormone Biology Group, Green Life Sciences Cluster, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Hannah E Vahldick
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Dominika Rybka
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands
| | - Marcio F A Leite
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands
| | - Zayan Musa
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Alexander Bucksch
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA; Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA
| | - Francisco Dini-Andreote
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands; Department of Plant Science, The Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mario Schilder
- Plant Hormone Biology Group, Green Life Sciences Cluster, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Alexander J Chen
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Jiregna Daksa
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Desalegn W Etalo
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands; Wageningen University and Research, Laboratory of Phytopathology, Wageningen, the Netherlands
| | - Taye Tessema
- Ethiopian Institute of Agricultural Research, 3G53+6XC Holeta, Ethiopia
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands; Ecology and Biodiversity, Department of Biology, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Jos M Raaijmakers
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 PB Wageningen, the Netherlands
| | - Harro Bouwmeester
- Plant Hormone Biology Group, Green Life Sciences Cluster, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA.
| |
Collapse
|
21
|
Zhang J, Zhang H, Luo S, Ye L, Wang C, Wang X, Tian C, Sun Y. Analysis and Functional Prediction of Core Bacteria in the Arabidopsis Rhizosphere Microbiome under Drought Stress. Microorganisms 2024; 12:790. [PMID: 38674734 PMCID: PMC11052302 DOI: 10.3390/microorganisms12040790] [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: 02/12/2024] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
The effects of global warming, population growth, and economic development are increasing the frequency of extreme weather events, such as drought. Among abiotic stresses, drought has the greatest impact on soil biological activity and crop yields. The rhizosphere microbiota, which represents a second gene pool for plants, may help alleviate the effects of drought on crops. In order to investigate the structure and diversity of the bacterial communities on drought stress, this study analyzed the differences in the bacterial communities by high-throughput sequencing and bioinformatical analyses in the rhizosphere of Arabidopsis thaliana under normal and drought conditions. Based on analysis of α and β diversity, the results showed that drought stress had no significant effect on species diversity between groups, but affected species composition. Difference analysis of the treatments showed that the bacteria with positive responses to drought stress were Burkholderia-Caballeronia-Paraburkholderia (BCP) and Streptomyces. Drought stress reduced the complexity of the rhizosphere bacterial co-occurrence network. Streptomyces was at the core of the network in both the control and drought treatments, whereas the enrichment of BCP under drought conditions was likely due to a decrease in competitors. Functional prediction showed that the core bacteria metabolized a wide range of carbohydrates, such as pentose, glycans, and aromatic compounds. Our results provide a scientific and theoretical basis for the use of rhizosphere microbial communities to alleviate plant drought stress and the further exploration of rhizosphere microbial interactions under drought stress.
Collapse
Affiliation(s)
- Jianfeng Zhang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (H.Z.); (L.Y.); (X.W.)
| | - Hengfei Zhang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (H.Z.); (L.Y.); (X.W.)
| | - Shouyang Luo
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (S.L.); (C.W.); (C.T.)
| | - Libo Ye
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (H.Z.); (L.Y.); (X.W.)
| | - Changji Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (S.L.); (C.W.); (C.T.)
| | - Xiaonan Wang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil, Conservation College of Life Science, The Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (H.Z.); (L.Y.); (X.W.)
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (S.L.); (C.W.); (C.T.)
| | - Yu Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (S.L.); (C.W.); (C.T.)
| |
Collapse
|
22
|
Fan X, Ge AH, Wang E. Spatially distributed metabolites SWEETen the root for microbes. Cell Host Microbe 2024; 32:445-447. [PMID: 38604122 DOI: 10.1016/j.chom.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 04/13/2024]
Abstract
Limited understanding exists on the spatial configuration of underground plant-microbe interactions. In this issue of Cell Host & Microbe, Loo et al. illustrate the sugar transporter-involved interdependent interaction between root metabolites and microbial spatial colonization, providing insights into metabolic-associated organization of plant-microbe interactions.
Collapse
Affiliation(s)
- Xiaoyan Fan
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - An-Hui Ge
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ertao Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Shen J, Wang M, Wang E. Exploitation of the microbiome for crop breeding. NATURE PLANTS 2024; 10:533-534. [PMID: 38514786 DOI: 10.1038/s41477-024-01657-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Affiliation(s)
- Jiayong Shen
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Mingxing Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ertao Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Yang Z, Zhao T, Cheng H, Yang J. Microbiome-enabled genomic selection improves prediction accuracy for nitrogen-related traits in maize. G3 (BETHESDA, MD.) 2024; 14:jkad286. [PMID: 38113533 PMCID: PMC11090461 DOI: 10.1093/g3journal/jkad286] [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: 05/19/2023] [Revised: 05/19/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
Root-associated microbiomes in the rhizosphere (rhizobiomes) are increasingly known to play an important role in nutrient acquisition, stress tolerance, and disease resistance of plants. However, it remains largely unclear to what extent these rhizobiomes contribute to trait variation for different genotypes and if their inclusion in the genomic selection protocol can enhance prediction accuracy. To address these questions, we developed a microbiome-enabled genomic selection method that incorporated host SNPs and amplicon sequence variants from plant rhizobiomes in a maize diversity panel under high and low nitrogen (N) field conditions. Our cross-validation results showed that the microbiome-enabled genomic selection model significantly outperformed the conventional genomic selection model for nearly all time-series traits related to plant growth and N responses, with an average relative improvement of 3.7%. The improvement was more pronounced under low N conditions (8.4-40.2% of relative improvement), consistent with the view that some beneficial microbes can enhance N nutrient uptake, particularly in low N fields. However, our study could not definitively rule out the possibility that the observed improvement is partially due to the amplicon sequence variants being influenced by microenvironments. Using a high-dimensional mediation analysis method, our study has also identified microbial mediators that establish a link between plant genotype and phenotype. Some of the detected mediator microbes were previously reported to promote plant growth. The enhanced prediction accuracy of the microbiome-enabled genomic selection models, demonstrated in a single environment, serves as a proof-of-concept for the potential application of microbiome-enabled plant breeding for sustainable agriculture.
Collapse
Affiliation(s)
- Zhikai Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Tianjing Zhao
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Hao Cheng
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| |
Collapse
|
27
|
Yue H, Sun X, Wang T, Zhang A, Han D, Wei G, Song W, Shu D. Host genotype-specific rhizosphere fungus enhances drought resistance in wheat. MICROBIOME 2024; 12:44. [PMID: 38433268 PMCID: PMC10910722 DOI: 10.1186/s40168-024-01770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses. RESULTS Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum). CONCLUSIONS Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.
Collapse
Affiliation(s)
- Hong Yue
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xuming Sun
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tingting Wang
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ali Zhang
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dejun Han
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- College of Life Sciences, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
| | - Weining Song
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Duntao Shu
- College of Life Sciences, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
| |
Collapse
|
28
|
Kimotho RN, Maina S. Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1289-1313. [PMID: 37950741 PMCID: PMC10901211 DOI: 10.1093/jxb/erad448] [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: 05/26/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.
Collapse
Affiliation(s)
- Roy Njoroge Kimotho
- Hebei Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Solomon Maina
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales 2568, Australia
| |
Collapse
|
29
|
Wang M, Ge AH, Ma X, Wang X, Xie Q, Wang L, Song X, Jiang M, Yang W, Murray JD, Wang Y, Liu H, Cao X, Wang E. Dynamic root microbiome sustains soybean productivity under unbalanced fertilization. Nat Commun 2024; 15:1668. [PMID: 38395981 PMCID: PMC10891064 DOI: 10.1038/s41467-024-45925-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Root-associated microbiomes contribute to plant growth and health, and are dynamically affected by plant development and changes in the soil environment. However, how different fertilizer regimes affect quantitative changes in microbial assembly to effect plant growth remains obscure. Here, we explore the temporal dynamics of the root-associated bacteria of soybean using quantitative microbiome profiling (QMP) to examine its response to unbalanced fertilizer treatments (i.e., lacking either N, P or K) and its role in sustaining plant growth after four decades of unbalanced fertilization. We show that the root-associated bacteria exhibit strong succession during plant development, and bacterial loads largely increase at later stages, particularly for Bacteroidetes. Unbalanced fertilization has a significant effect on the assembly of the soybean rhizosphere bacteria, and in the absence of N fertilizer the bacterial community diverges from that of fertilized plants, while lacking P fertilizer impedes the total load and turnover of rhizosphere bacteria. Importantly, a SynCom derived from the low-nitrogen-enriched cluster is capable of stimulating plant growth, corresponding with the stabilized soybean productivity in the absence of N fertilizer. These findings provide new insights in the quantitative dynamics of the root-associated microbiome and highlight a key ecological cluster with prospects for sustainable agricultural management.
Collapse
Affiliation(s)
- Mingxing Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - An-Hui Ge
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xingzhu Ma
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, 150086, China
| | - Xiaolin Wang
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Qiujin Xie
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Like Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianwei Song
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengchen Jiang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Weibing Yang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jeremy D Murray
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ertao Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| |
Collapse
|
30
|
Chen L, Liu Y. The Function of Root Exudates in the Root Colonization by Beneficial Soil Rhizobacteria. BIOLOGY 2024; 13:95. [PMID: 38392313 PMCID: PMC10886372 DOI: 10.3390/biology13020095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
Soil-beneficial microbes in the rhizosphere play important roles in improving plant growth and health. Root exudates play key roles in plant-microbe interactions and rhizobacterial colonization. This review describes the factors influencing the dynamic interactions between root exudates and the soil microbiome in the rhizosphere, including plant genotype, plant development, and environmental abiotic and biotic factors. We also discuss the roles of specific metabolic mechanisms, regulators, and signals of beneficial soil bacteria in terms of colonization ability. We highlight the latest research progress on the roles of root exudates in regulating beneficial rhizobacterial colonization. Organic acids, amino acids, sugars, sugar alcohols, flavonoids, phenolic compounds, volatiles, and other secondary metabolites are discussed in detail. Finally, we propose future research objectives that will help us better understand the role of root exudates in root colonization by rhizobacteria and promote the sustainable development of agriculture and forestry.
Collapse
Affiliation(s)
- Lin Chen
- National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain, Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing 102300, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
31
|
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.
Collapse
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.
| |
Collapse
|
32
|
Gu Z, Hu C, Gan Y, Zhou J, Tian G, Gao L. Role of Microbes in Alleviating Crop Drought Stress: A Review. PLANTS (BASEL, SWITZERLAND) 2024; 13:384. [PMID: 38337917 PMCID: PMC10857462 DOI: 10.3390/plants13030384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 02/12/2024]
Abstract
Drought stress is an annual global phenomenon that has devastating effects on crop production, so numerous studies have been conducted to improve crop drought resistance. Plant-associated microbiota play a crucial role in crop health and growth; however, we have a limited understanding of the key processes involved in microbiome-induced crop adaptation to drought stress. In this review, we summarize the adverse effects of drought stress on crop growth in terms of germination, photosynthesis, nutrient uptake, biomass, and yield, with a focus on the response of soil microbial communities to drought stress and plant-microbe interactions under drought stress. Moreover, we review the morpho-physiological, biochemical, and molecular mechanisms underlying the mitigation effect of microbes on crop drought stress. Finally, we highlight future research directions, including the characterization of specific rhizosphere microbiome species with corresponding root exudates and the efficiency of rhizobacteria inoculants under drought conditions. Such research will advance our understanding of the complex interactions between crops and microbes and improve crop resistance to drought stress through the application of beneficial drought-adaptive microbes.
Collapse
Affiliation(s)
- Zechen Gu
- Engineering and Technical Center for Modern Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, China;
- Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, China; (C.H.); (Y.G.); (J.Z.); (G.T.)
| | - Chengji Hu
- Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, China; (C.H.); (Y.G.); (J.Z.); (G.T.)
| | - Yuxin Gan
- Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, China; (C.H.); (Y.G.); (J.Z.); (G.T.)
| | - Jinyan Zhou
- Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, China; (C.H.); (Y.G.); (J.Z.); (G.T.)
| | - Guangli Tian
- Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, China; (C.H.); (Y.G.); (J.Z.); (G.T.)
| | - Limin Gao
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, Nanjing 210014, China
| |
Collapse
|
33
|
Sher AW, Aufrecht JA, Herrera D, Zimmerman AE, Kim YM, Munoz N, Trejo JB, Paurus VL, Cliff JB, Hu D, Chrisler WB, Tournay RJ, Gomez-Rivas E, Orr G, Ahkami AH, Doty SL. Dynamic nitrogen fixation in an aerobic endophyte of Populus. THE ISME JOURNAL 2024; 18:wrad012. [PMID: 38365250 PMCID: PMC10833079 DOI: 10.1093/ismejo/wrad012] [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: 09/09/2023] [Revised: 11/11/2023] [Accepted: 11/21/2023] [Indexed: 02/18/2024]
Abstract
Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte-poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant-endophyte interactions.
Collapse
Affiliation(s)
- Andrew W Sher
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
| | - Jayde A Aufrecht
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Daisy Herrera
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Amy E Zimmerman
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Nathalie Munoz
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Jesse B Trejo
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Vanessa L Paurus
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - John B Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - William B Chrisler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Robert J Tournay
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
| | - Emma Gomez-Rivas
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, United States
| | - Sharon L Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, 98195-2100, United States
| |
Collapse
|
34
|
Wang W, Li D, Qiu X, Yang J, Liu L, Wang E, Yuan H. Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials. ENVIRONMENTAL MICROBIOME 2024; 19:2. [PMID: 38178261 PMCID: PMC10768371 DOI: 10.1186/s40793-023-00546-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/24/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND As part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic bacteria interaction with their host remain largely unknown. Here, 16S rRNA gene sequencing, transcriptomic analysis, and culture-based methods were used to reveal the underlying mechanisms. RESULTS WSHM reduced the alpha diversity of soybean endophytic bacteria, but increased the bacterial interactions and further selectively enriched the potentially beneficial bacteria. Meanwhile, WSHM regulated the expression of various genes related to the MAPK signaling pathway, plant-pathogen interaction, hormone signal transduction, and synthetic pathways in soybean root. Omics integration analysis showed that Sphingobium was the genus closest to the significantly changed genes in WSHM treatment. The inoculation of endophytic Sphingobium sp. TBBS4 isolated from soybean significantly improved soybean nodulation and growth by increasing della gene expression and reducing ethylene release. CONCLUSION All the results revealed that WSHM promotes soybean nodulation and growth by selectively regulating soybean gene expression and regulating the endophytic bacterial community, Sphingobium was the key bacterium involved in plant-microbe interaction. These findings refined our understanding of the mechanism of WSHM promoting soybean nodulation and growth and provided novel evidence for plant-endophyte interaction.
Collapse
Affiliation(s)
- Wenqian Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Dongmei Li
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Xiaoqian Qiu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Liang Liu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, C.P. 11340, Ciudad de México, México
| | - Hongli Yuan
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China.
| |
Collapse
|
35
|
Park JW, Braswell WE, Kunta M. Co-Occurrence Analysis of Citrus Root Bacterial Microbiota under Citrus Greening Disease. PLANTS (BASEL, SWITZERLAND) 2023; 13:80. [PMID: 38202388 PMCID: PMC10781011 DOI: 10.3390/plants13010080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 01/12/2024]
Abstract
Candidatus Liberibacter asiaticus (CLas) is associated with Citrus Huanglongbing (HLB), a devastating disease in the US. Previously, we conducted a two-year-long monthly HLB survey by quantitative real-time PCR using root DNA fractions prepared from 112 field grapefruit trees grafted on sour orange rootstock. Approximately 10% of the trees remained CLas-free during the entire survey period. This study conducted 16S metagenomics using the time-series root DNA fractions, monthly prepared during twenty-four consecutive months, followed by microbial co-occurrence network analysis to investigate the microbial factors contributing to the CLas-free phenotype of the aforementioned trees. Based on the HLB status and the time when the trees were first diagnosed as CLas-positive during the survey, the samples were divided into four groups, Stage H (healthy), Stage I (early), II (mid), and III (late) samples. The 16S metagenomics data using Silva 16S database v132 revealed that HLB compromised the diversity of rhizosphere microbiota. At the phylum level, Actinobacteria and Proteobacteria were the predominant bacterial phyla, comprising >93% of total bacterial phyla, irrespective of HLB status. In addition, a temporal change in the rhizosphere microbe population was observed during a two-year-long survey, from which we confirmed that some bacterial families differently responded to HLB disease status. The clustering of the bacterial co-occurrence network data revealed the presence of a subnetwork composed of Streptomycetaceae and bacterial families with plant growth-promoting activity in Stage H and III samples. These data implicated that the Streptomycetaceae subnetwork may act as a functional unit against HLB.
Collapse
Affiliation(s)
- Jong-Won Park
- Citrus Center, Texas A&M University-Kingsville, 312 N. International Blvd., Weslaco, TX 78599, USA
| | - W. Evan Braswell
- Insect Management and Molecular Diagnostic Laboratory, USDA APHIS PPQ S&T, Edinburg, TX 78541, USA
| | - Madhurababu Kunta
- Citrus Center, Texas A&M University-Kingsville, 312 N. International Blvd., Weslaco, TX 78599, USA
| |
Collapse
|
36
|
Sharma A, Choudhary P, Chakdar H, Shukla P. Molecular insights and omics-based understanding of plant-microbe interactions under drought stress. World J Microbiol Biotechnol 2023; 40:42. [PMID: 38105277 DOI: 10.1007/s11274-023-03837-4] [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: 09/29/2023] [Accepted: 11/11/2023] [Indexed: 12/19/2023]
Abstract
The detrimental effects of adverse environmental conditions are always challenging and remain a major concern for plant development and production worldwide. Plants deal with such constraints by physiological, biochemical, and morphological adaptations as well as acquiring mutual support of beneficial microorganisms. As many stress-responsive traits of plants are influenced by microbial activities, plants have developed a sophisticated interaction with microbes to cope with adverse environmental conditions. The production of numerous bioactive metabolites by rhizospheric, endo-, or epiphytic microorganisms can directly or indirectly alter the root system architecture, foliage production, and defense responses. Although plant-microbe interactions have been shown to improve nutrient uptake and stress resilience in plants, the underlying mechanisms are not fully understood. "Multi-omics" application supported by genomics, transcriptomics, and metabolomics has been quite useful to investigate and understand the biochemical, physiological, and molecular aspects of plant-microbe interactions under drought stress conditions. The present review explores various microbe-mediated mechanisms for drought stress resilience in plants. In addition, plant adaptation to drought stress is discussed, and insights into the latest molecular techniques and approaches available to improve drought-stress resilience are provided.
Collapse
Affiliation(s)
- Aditya Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Prassan Choudhary
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India
| | - Hillol Chakdar
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
| |
Collapse
|
37
|
Gao Y, Zhao Y, Li P, Qi X. Responses of the maize rhizosphere soil environment to drought-flood abrupt alternation stress. Front Microbiol 2023; 14:1295376. [PMID: 38170081 PMCID: PMC10760638 DOI: 10.3389/fmicb.2023.1295376] [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: 09/16/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
Changes in the soil environment in the root zone will affect the growth, development and resistance of plants. The mechanism underlying the effect of drought and flood stress on rhizosphere bacterial diversity, soil metabolites and soil enzyme activity is not clear and needs further study. To analyze the dynamic changes in bacteria, metabolites and enzyme activities in the rhizosphere soil of maize under different drought-flood abrupt alternation (DFAA) stresses, the barrel test method was used to set up the 'sporadic light rain' to flooding (referring to trace rainfall to heavy rain) (DFAA1) group, 'continuous drought' to flooding (DFAA2) group and normal irrigation (CK) group from the jointing to the tassel flowering stage of maize. The results showed that Actinobacteria was the most dominant phylum in the two DFAA groups during the drought period and the rewatering period, and Proteobacteria was the most dominant phylum during the flooding period and the harvest period. The alpha diversity index of rhizosphere bacteria in the DFAA2 group during the flooding period was significantly lower than that in other stages, and the relative abundance of Chloroflexi was higher. The correlation analysis between the differential genera and soil metabolites of the two DFAA groups showed that the relative abundance of Paenibacillus in the DFAA1 group was higher during the drought period, and it was significantly positively correlated with the bioactive lipid metabolites. The differential SJA-15 bacterium was enriched in the DFAA2 group during the flooding period and were strongly correlated with biogenic amine metabolites. The relative abundances of Arthrobacter, Alphaproteobacteria and Brevibacillus in the DFAA2 group were higher compared with DFAA1 group from rewatering to harvest and were significantly positively correlated with hydrocarbon compounds and steroid hormone metabolites. The acid phosphatase activity of the DFAA1 group was significantly higher than that of the DFAA2 group during the flooding period. The study suggests that there is a yield compensation phenomenon in the conversion of 'continuous drought' to flooding compared with 'sporadic light rain', which is related to the improvement in the flooding tolerance of maize by the dominant bacteria Chloroflexi, bacterium SJA-15 and biogenic amine metabolites. These rhizosphere bacteria and soil metabolites may have the potential function of helping plants adapt to the DFAA environment. The study revealed the response of the maize rhizosphere soil environment to DFAA stress and provided new ideas for exploring the potential mechanism of crop yield compensation under DFAA.
Collapse
Affiliation(s)
| | - Yulong Zhao
- Farmland Irrigation Research Institute of CAAS, Xinxiang, China
| | | | - Xuebin Qi
- Farmland Irrigation Research Institute of CAAS, Xinxiang, China
| |
Collapse
|
38
|
Benitez-Alfonso Y, Soanes BK, Zimba S, Sinanaj B, German L, Sharma V, Bohra A, Kolesnikova A, Dunn JA, Martin AC, Khashi U Rahman M, Saati-Santamaría Z, García-Fraile P, Ferreira EA, Frazão LA, Cowling WA, Siddique KHM, Pandey MK, Farooq M, Varshney RK, Chapman MA, Boesch C, Daszkowska-Golec A, Foyer CH. Enhancing climate change resilience in agricultural crops. Curr Biol 2023; 33:R1246-R1261. [PMID: 38052178 DOI: 10.1016/j.cub.2023.10.028] [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] [Indexed: 12/07/2023]
Abstract
Climate change threatens global food and nutritional security through negative effects on crop growth and agricultural productivity. Many countries have adopted ambitious climate change mitigation and adaptation targets that will exacerbate the problem, as they require significant changes in current agri-food systems. In this review, we provide a roadmap for improved crop production that encompasses the effective transfer of current knowledge into plant breeding and crop management strategies that will underpin sustainable agriculture intensification and climate resilience. We identify the main problem areas and highlight outstanding questions and potential solutions that can be applied to mitigate the impacts of climate change on crop growth and productivity. Although translation of scientific advances into crop production lags far behind current scientific knowledge and technology, we consider that a holistic approach, combining disciplines in collaborative efforts, can drive better connections between research, policy, and the needs of society.
Collapse
Affiliation(s)
| | - Beth K Soanes
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sibongile Zimba
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK; Horticulture Department, Lilongwe University of Agriculture and Natural Resources, P.O. Box 219, Lilongwe, Malawi
| | - Besiana Sinanaj
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Liam German
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Anastasia Kolesnikova
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - Jessica A Dunn
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK; Institute for Sustainable Food, University of Sheffield, Sheffield S10 2TN, UK
| | - Azahara C Martin
- Institute for Sustainable Agriculture (IAS-CSIC), Córdoba 14004, Spain
| | - Muhammad Khashi U Rahman
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca 37007, Spain; Institute for Agribiotechnology Research (CIALE), University of Salamanca, Villamayor de la Armuña 37185, Spain
| | - Zaki Saati-Santamaría
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca 37007, Spain; Institute for Agribiotechnology Research (CIALE), University of Salamanca, Villamayor de la Armuña 37185, Spain; Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | - Paula García-Fraile
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca 37007, Spain; Institute for Agribiotechnology Research (CIALE), University of Salamanca, Villamayor de la Armuña 37185, Spain
| | - Evander A Ferreira
- Institute of Agrarian Sciences, Federal University of Minas Gerais, Avenida Universitária 1000, 39404547, Montes Claros, Minas Gerais, Brazil
| | - Leidivan A Frazão
- Institute of Agrarian Sciences, Federal University of Minas Gerais, Avenida Universitária 1000, 39404547, Montes Claros, Minas Gerais, Brazil
| | - Wallace A Cowling
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Muhammad Farooq
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia; Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123, Oman
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - Christine Boesch
- School of Food Science and Nutrition, Faculty of Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| |
Collapse
|
39
|
Brescia F, Sillo F, Franchi E, Pietrini I, Montesano V, Marino G, Haworth M, Zampieri E, Fusini D, Schillaci M, Papa R, Santamarina C, Vita F, Chitarra W, Nerva L, Petruzzelli G, Mennone C, Centritto M, Balestrini R. The 'microbiome counterattack': Insights on the soil and root-associated microbiome in diverse chickpea and lentil genotypes after an erratic rainfall event. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:459-483. [PMID: 37226644 PMCID: PMC10667653 DOI: 10.1111/1758-2229.13167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023]
Abstract
Legumes maintain soil fertility thanks to their associated microbiota but are threatened by climate change that causes soil microbial community structural and functional modifications. The core microbiome associated with different chickpea and lentil genotypes was described after an unexpected climatic event. Results showed that chickpea and lentil bulk soil microbiomes varied significantly between two sampling time points, the first immediately after the rainfall and the second 2 weeks later. Rhizobia were associated with the soil of the more productive chickpea genotypes in terms of flower and fruit number. The root-associated bacteria and fungi were surveyed in lentil genotypes, considering that several parcels showed disease symptoms. The metabarcoding analysis revealed that reads related to fungal pathogens were significantly associated with one lentil genotype. A lentil core prokaryotic community common to all genotypes was identified as well as a genotype-specific one. A higher number of specific bacterial taxa and an enhanced tolerance to fungal diseases characterized a lentil landrace compared to the commercial varieties. This outcome supported the hypothesis that locally adapted landraces might have a high recruiting efficiency of beneficial soil microbes.
Collapse
Affiliation(s)
- Francesca Brescia
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Fabiano Sillo
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Elisabetta Franchi
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Ilaria Pietrini
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Vincenzo Montesano
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyBernalda (MT)Italy
| | - Giovanni Marino
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
| | - Matthew Haworth
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
| | - Elisa Zampieri
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Danilo Fusini
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Martino Schillaci
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Roberto Papa
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Chiara Santamarina
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Federico Vita
- Department of Bioscience, Biotechnology and EnvironmentUniversity of Bari Aldo MoroBariItaly
| | - Walter Chitarra
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and EconomicsConeglianoItaly
| | - Luca Nerva
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and EconomicsConeglianoItaly
| | | | - Carmelo Mennone
- Azienda Pantanello, ALSIA Research Center Metapontum AgrobiosBernalda (MT)Italy
| | - Mauro Centritto
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
- ENI‐CNR Water Research Center ‘Hypatia of Alexandria’ALSIA Research Center Metapontum AgrobiosBernaldaItaly
| | - Raffaella Balestrini
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
- ENI‐CNR Water Research Center ‘Hypatia of Alexandria’ALSIA Research Center Metapontum AgrobiosBernaldaItaly
| |
Collapse
|
40
|
Du C, Xu R, Zhao X, Liu Y, Zhou X, Zhang W, Zhou X, Hu N, Zhang Y, Sun Z, Wang Z. Association between host nitrogen absorption and root-associated microbial community in field-grown wheat. Appl Microbiol Biotechnol 2023; 107:7347-7364. [PMID: 37747613 DOI: 10.1007/s00253-023-12787-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/08/2023] [Accepted: 09/02/2023] [Indexed: 09/26/2023]
Abstract
Plant roots and rhizosphere soils assemble diverse microbial communities, and these root-associated microbiomes profoundly influence host development. Modern wheat has given rise to numerous cultivars for its wide range of ecological adaptations and commercial uses. Variations in nitrogen uptake by different wheat cultivars are widely observed in production practices. However, little is known about the composition and structure of the root-associated microbiota in different wheat cultivars, and it is not sure whether root-associated microbial communities are relevant in host nitrogen absorption. Therefore, there is an urgent need for systematic assessment of root-associated microbial communities and their association with host nitrogen absorption in field-grown wheat. Here, we investigated the root-associated microbial community composition, structure, and keystone taxa in wheat cultivars with different nitrogen absorption characteristics at different stages and their relationships with edaphic variables and host nitrogen uptake. Our results indicated that cultivar nitrogen absorption characteristics strongly interacted with bacterial and archaeal communities in the roots and edaphic physicochemical factors. The impact of host cultivar identity, developmental stage, and spatial niche on bacterial and archaeal community structure and network complexity increased progressively from rhizosphere soils to roots. The root microbial community had a significant direct effect on plant nitrogen absorption, while plant nitrogen absorption and soil temperature also significantly influenced root microbial community structure. The cultivar with higher nitrogen absorption at the jointing stage tended to cooperate with root microbial community to facilitate their own nitrogen absorption. Our work provides important information for further wheat microbiome manipulation to influence host nitrogen absorption. KEY POINTS: • Wheat cultivar and developmental stage affected microbiome structure and network. • The root microbial community strongly interacted with plant nitrogen absorption. • High nitrogen absorption cultivar tended to cooperate with root microbiome.
Collapse
Affiliation(s)
- Chenghang Du
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Runlai Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xuan Zhao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ying Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaohan Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wanqing Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaonan Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Naiyue Hu
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yinghua Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhencai Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Zhimin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
Swift JF, Migicovsky Z, Trello GE, Miller AJ. Grapevine bacterial communities display compartment-specific dynamics over space and time within the Central Valley of California. ENVIRONMENTAL MICROBIOME 2023; 18:84. [PMID: 37996903 PMCID: PMC10668525 DOI: 10.1186/s40793-023-00539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose 'terroir', the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity via genome-to-genome interactions. RESULTS To understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA amplicon sequencing to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflected rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time. CONCLUSIONS These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local soil microbiome in the Central Valley of California.
Collapse
Affiliation(s)
- Joel F Swift
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO, 63103, USA.
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA.
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA.
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
- Department of Biology, Acadia University, Wolfville, NS, B4P 2R6, Canada
| | - Grace E Trello
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO, 63103, USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO, 63103, USA.
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA.
| |
Collapse
|
43
|
Taniguchi T, Isobe K, Imada S, Eltayeb MM, Akaji Y, Nakayama M, Allen MF, Aronson EL. Root endophytic bacterial and fungal communities in a natural hot desert are differentially regulated in dry and wet seasons by stochastic processes and functional traits. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165524. [PMID: 37467971 DOI: 10.1016/j.scitotenv.2023.165524] [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: 02/12/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023]
Abstract
Dryland ecosystems experience seasonal cycles of severe drought and moderate precipitation. Desert plants may develop symbiotic relationships with root endophytic microbes to survive under the repeated wet and extremely dry conditions. Although community coalescence has been found in many systems, the colonization by functional microbes and its relationship to seasonal transitions in arid regions are not well understood. Here we examined root endophytic microbial taxa, and their traits in relation to their root colonization, during the dry and wet seasons in a hot desert of the southwestern United States. We used high-throughput DNA sequencing of 16S rRNA and internal transcribed spacer gene profiling of five desert shrubs, and analyzed the seasonal change in endophytic microbial lineages. Goodness of fit to the neutral community model in relationship to microbial traits was evaluated. In summer, Actinobacteria and Bacteroidia increased, although this was not genus-specific. For fungi, Glomeraceae selectively increased in summer. In winter, Gram-negative bacterial genera, including those capable of nitrogen fixation and plant growth promotion, increased. Neutral model analysis revealed a strong stochastic influence on endophytic bacteria but a weak effect for fungi, especially in summer. The taxa with higher frequency than that predicted by neutral model shared environmental adaptability and symbiotic traits, whereas the frequency of pathogenic fungi was at or under the predicted value. These results suggest that community assembly of bacteria and fungi is regulated differently. The bacterial community was affected by stochastic and deterministic processes via bacterial response to drought (response trait), beneficial effect on plants (effect trait), and likely stable mutualistic interactions with plants suggested by the frequency of nodule bacteria. For fungi, mycorrhizal fungi were selected by plants in summer. The regulation of beneficial microbes by plants in both dry and wet seasons suggests the presence of plant-soil positive feedback in this natural desert ecosystem.
Collapse
Affiliation(s)
- Takeshi Taniguchi
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan.
| | - Kazuo Isobe
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Shogo Imada
- Department of Radioecology, Institute for Environmental Sciences, Aomori 039-3212, Japan
| | - Mohamed M Eltayeb
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; Department of Food Science and Technology, Faculty of Agriculture, University of Khartoum, Shambat 13314, Sudan
| | - Yasuaki Akaji
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki 305-8506, Japan
| | - Masataka Nakayama
- Research Group for Environmental Science, Japan Atomic Energy Agency, Ibaraki 319-1195, Japan
| | - Michael F Allen
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
| | - Emma L Aronson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
| |
Collapse
|
44
|
Baker CR, Patel‐Tupper D, Cole BJ, Ching LG, Dautermann O, Kelikian AC, Allison C, Pedraza J, Sievert J, Bilbao A, Lee J, Kim Y, Kyle JE, Bloodsworth KJ, Paurus V, Hixson KK, Hutmacher R, Dahlberg J, Lemaux PG, Niyogi KK. Metabolomic, photoprotective, and photosynthetic acclimatory responses to post-flowering drought in sorghum. PLANT DIRECT 2023; 7:e545. [PMID: 37965197 PMCID: PMC10641490 DOI: 10.1002/pld3.545] [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: 07/03/2023] [Revised: 10/08/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023]
Abstract
Climate change is globally affecting rainfall patterns, necessitating the improvement of drought tolerance in crops. Sorghum bicolor is a relatively drought-tolerant cereal. Functional stay-green sorghum genotypes can maintain green leaf area and efficient grain filling during terminal post-flowering water deprivation, a period of ~10 weeks. To obtain molecular insights into these characteristics, two drought-tolerant genotypes, BTx642 and RTx430, were grown in replicated control and terminal post-flowering drought field plots in California's Central Valley. Photosynthetic, photoprotective, and water dynamics traits were quantified and correlated with metabolomic data collected from leaves, stems, and roots at multiple timepoints during control and drought conditions. Physiological and metabolomic data were then compared to longitudinal RNA sequencing data collected from these two genotypes. The unique metabolic and transcriptomic response to post-flowering drought in sorghum supports a role for the metabolite galactinol in controlling photosynthetic activity through regulating stomatal closure in post-flowering drought. Additionally, in the functional stay-green genotype BTx642, photoprotective responses were specifically induced in post-flowering drought, supporting a role for photoprotection in the molecular response associated with the functional stay-green trait. From these insights, new pathways are identified that can be targeted to maximize yields under growth conditions with limited water.
Collapse
Affiliation(s)
- Christopher R. Baker
- Howard Hughes Medical Institute, Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Dhruv Patel‐Tupper
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Benjamin J. Cole
- DOE‐Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Lindsey G. Ching
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Oliver Dautermann
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Armen C. Kelikian
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Cayci Allison
- UC‐ANR Kearney Agricultural Research and Extension (KARE) CenterParlierCaliforniaUSA
| | - Julie Pedraza
- UC‐ANR Kearney Agricultural Research and Extension (KARE) CenterParlierCaliforniaUSA
| | - Julie Sievert
- UC‐ANR Kearney Agricultural Research and Extension (KARE) CenterParlierCaliforniaUSA
| | - Aivett Bilbao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Joon‐Yong Lee
- Biological Sciences Division, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Young‐Mo Kim
- Biological Sciences Division, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Jennifer E. Kyle
- Biological Sciences Division, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Kent J. Bloodsworth
- Biological Sciences Division, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Vanessa Paurus
- Biological Sciences Division, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Kim K. Hixson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Robert Hutmacher
- Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | - Jeffery Dahlberg
- UC‐ANR Kearney Agricultural Research and Extension (KARE) CenterParlierCaliforniaUSA
| | - Peggy G. Lemaux
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Krishna K. Niyogi
- Howard Hughes Medical Institute, Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| |
Collapse
|
45
|
Santos-Medellín C, Blazewicz SJ, Pett-Ridge J, Firestone MK, Emerson JB. Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils. Nat Ecol Evol 2023; 7:1809-1822. [PMID: 37770548 DOI: 10.1038/s41559-023-02207-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 08/25/2023] [Indexed: 09/30/2023]
Abstract
As central members of soil trophic networks, viruses have the potential to drive substantial microbial mortality and nutrient turnover. Pinpointing viral contributions to terrestrial ecosystem processes remains a challenge, as temporal dynamics are difficult to unravel in the spatially and physicochemically heterogeneous soil environment. In Mediterranean grasslands, the first rainfall after seasonal drought provides an ecosystem reset, triggering microbial activity during a tractable window for capturing short-term dynamics. Here, we simulated precipitation in microcosms from four distinct dry grassland soils and generated 144 viromes, 84 metagenomes and 84 16S ribosomal RNA gene amplicon datasets to characterize viral, prokaryotic and relic DNA dynamics over 10 days. Vastly different viral communities in each soil followed remarkably similar successional trajectories. Wet-up triggered a significant increase in viral richness, followed by extensive compositional turnover. Temporal succession in prokaryotic communities was much less pronounced, perhaps suggesting differences in the scales of activity captured by viromes (representing recently produced, ephemeral viral particles) and total DNA. Still, differences in the relative abundances of Actinobacteria (enriched in dry soils) and Proteobacteria (enriched in wetted soils) matched those of their predicted phages, indicating viral predation of dominant bacterial taxa. Rewetting also rapidly depleted relic DNA, which subsequently reaccumulated, indicating substantial new microbial mortality in the days after wet-up, particularly of the taxa putatively under phage predation. Production of abundant, diverse viral particles via microbial host cell lysis appears to be a conserved feature of the early response to soil rewetting, and results suggest the potential for 'Cull-the-Winner' dynamics, whereby viruses infect and cull but do not decimate dominant host populations.
Collapse
Affiliation(s)
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California, Merced, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, USA.
| |
Collapse
|
46
|
Fang J, Shi G, Wei S, Ma J, Zhang X, Wang J, Chen L, Liu Y, Zhao X, Lu Z. Drought Sensitivity of Spring Wheat Cultivars Shapes Rhizosphere Microbial Community Patterns in Response to Drought. PLANTS (BASEL, SWITZERLAND) 2023; 12:3650. [PMID: 37896113 PMCID: PMC10609721 DOI: 10.3390/plants12203650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023]
Abstract
Drought is the most important natural disaster affecting crop growth and development. Crop rhizosphere microorganisms can affect crop growth and development, enhance the effective utilization of nutrients, and resist adversity and hazards. In this paper, six spring wheat varieties were used as research material in the dry farming area of the western foot of the Greater Khingan Mountains, and two kinds of water control treatments were carried out: dry shed rain prevention (DT) and regulated water replenishment (CK). Phenotypic traits, including physiological and biochemical indices, drought resistance gene expression, soil enzyme activity, soil nutrient content, and the responses of potential functional bacteria and fungi under drought stress, were systematically analyzed. The results showed that compared with the control (CK), the leaf wilting, drooping, and yellowing of six spring wheat varieties were enhanced under drought (DT) treatment. The plant height, fresh weight (FW), dry weight (DW), net photosynthetic rate (Pn) and stomatal conductance (Gs), soil total nitrogen (TN), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), microbial biomass phosphorus (MBP), organic carbon (SOC), and soil alkaline phosphatase (S-ALP) contents were significantly decreased, among which, FW, Gs and MBC decreased by more than 7.84%, 17.43% and 11.31%, respectively. By contrast, the soil total phosphorus (TP), total potassium (TK), and soil catalase (S-CAT) contents were significantly increased (p < 0.05). TaWdreb2 and TaBADHb genes were highly expressed in T.D40, T.L36, and T.L33 and were expressed at low levels in T.N2, T.B12, and T.F5. Among them, the relative expression of the TaWdreb2 gene in T.L36 was significantly increased by 2.683 times compared with CK. Soil TN and TP are the most sensitive to drought stress and can be used as the characteristic values of drought stress. Based on this, a drought-tolerant variety (T.L36) and a drought-sensitive variety (T.B12) were selected to further analyze the changes in rhizosphere microorganisms. Drought treatment and cultivar differences significantly affected the composition of the rhizosphere microbial community. Drought caused a decrease in the complexity of the rhizosphere microbial network, and the structure of bacteria was more complex than that of fungi. The Shannon index and network modular number of bacteria in these varieties (T.L36) increased, with rich small-world network properties. Actinobacteria, Chloroflexi, Firmicutes, Basidiomycota, and Ascomycota were the dominant bacteria under drought treatment. The beneficial bacteria Bacillus, Penicillium, and Blastococcus were enriched in the rhizosphere of T.L36. Brevibacillus and Glycomyce were enriched in the rhizosphere of T.B12. In general, drought can inhibit the growth and development of spring wheat, and spring wheat can resist drought hazards by regulating the expression of drought-related genes, regulating physiological metabolites, and enriching beneficial microorganisms.
Collapse
Affiliation(s)
- Jing Fang
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Gongfu Shi
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
| | - Shuli Wei
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Jie Ma
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Xiangqian Zhang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Jianguo Wang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Liyu Chen
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Ying Liu
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Xiaoqing Zhao
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| | - Zhanyuan Lu
- School of Life Science, Inner Mongolia University, Hohhot 010020, China; (J.F.); (G.S.); (S.W.); (J.M.); (Y.L.)
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (X.Z.); (J.W.); (L.C.)
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
| |
Collapse
|
47
|
Molinari S, Leonetti P. Resistance to Plant Parasites in Tomato Is Induced by Soil Enrichment with Specific Bacterial and Fungal Rhizosphere Microbiome. Int J Mol Sci 2023; 24:15416. [PMID: 37895095 PMCID: PMC10607013 DOI: 10.3390/ijms242015416] [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: 09/27/2023] [Revised: 10/10/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Commercial formulations of beneficial microbes have been used to enrich the rhizosphere microbiome of tomato plants grown in pots located in a glasshouse. These plants have been subjected to attacks by soil-borne parasites, such as root-knot nematodes (RKNs), and herbivores, such as the miner insect Tuta absoluta. The development of both parasites and the symptoms of their parasitism were restricted in these plants with respect to plants left untreated. A mixture, named in the text as Myco, containing plant growth-promoting rhizobacteria (PGPR), opportunistic biocontrol fungi (BCF), and arbuscular mycorrhizal fungi (AMF) was more effective in limiting pest damage than a formulation containing the sole AMF (Ozor). Therefore, Myco-treated plants inoculated with RKNs were taken as a model for further studies. The PGPR contained in Myco were not able to reduce nematode infection; rather, they worsened symptoms in plants compared with those observed in untreated plants. Therefore, it was argued that both BCF and AMF were the microorganisms that colonized roots and stimulated the plant immune system against RKNs. Beneficial fungi colonized the roots by lowering the activities of the defense supporting enzymes endochitinases and β-1,3-glucanase. However, as early as three days after nematode inoculation, these enzyme activities and the expression of the encoding pathogenesis-related genes (PR-2, PR-3) were found to be enhanced in roots with respect to non-inoculated plants, thus indicating that plants had been primed against RKNs. The addition of paclobutrazol, which reduces salicylic acid (SA) levels in cells, and diphenyliodonium chloride, which inhibits superoxide generation, completely abolished the repressive effect of Myco on nematode infection. Inhibitors of copper enzymes and the alternative cyanide-resistant respiration did not significantly alter resistance induction by Myco. When Myco-treated plants were subjected to moderate water stress and inoculated with nematodes, they retained numbers of developed individuals in the roots similar to those present in regularly watered plants, in contrast to what occurred in roots of untreated stressed plants that hosted very few individuals because of poor nutrient availability.
Collapse
Affiliation(s)
- Sergio Molinari
- Institute for Sustainable Plant Protection, IPSP-Bari Unit, Department of Biology, Agricultural and Food Sciences, DISBA, National Council of Research, CNR, 70126 Bari, Italy;
| | | |
Collapse
|
48
|
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.
Collapse
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.
| |
Collapse
|
49
|
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.
Collapse
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.
| |
Collapse
|
50
|
Guo B, Zhang H, Liu Y, Chen J, Li J. Drought-resistant trait of different crop genotypes determines assembly patterns of soil and phyllosphere microbial communities. Microbiol Spectr 2023; 11:e0006823. [PMID: 37754752 PMCID: PMC10581042 DOI: 10.1128/spectrum.00068-23] [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: 01/10/2023] [Accepted: 08/04/2023] [Indexed: 09/28/2023] Open
Abstract
Crop microbiomes are widely recognized to play a role in crop stress resistance, but the ecological processes that shape crop microbiomes under water stress are unclear. Therefore, we investigated the bacterial communities of two oat (Avena sativa) and two wheat (Triticum aestivum) genotypes under different water stress conditions. Our results show that the microbial assemblage was determined by the crop compartment niche. Host selection pressure on the bacterial community increased progressively from soil to epiphyte to endophyte pathways, leading to a decrease in bacterial community diversity and network complexity. Source tracing shows that soil is the primary source of crop microbial communities and that bulk soil is the main potential source of crop microbiota. It filters gradually through the different compartment niches of the crop. We found that the phyla Actinobacteria, Proteobacteria, Gemmatimonadota, and Myxococcota were significantly enriched in bacterial communities associated with crop-resistance enzyme activity. Crop genotype influenced the composition of the rhizosphere soil microbial community, and the composition of the phylloplane microbial community was affected by water stress. IMPORTANCE In this paper, we investigated the assembly of the plant microbiome in response to water stress. We found that the determinant of microbiome assembly under water stress was the host type and that microbial communities were progressively filtered and enriched as they moved from soil to epiphyte to endophyte communities, with the main potential source being bulk soil. We also screened for bacterial communities that were significantly associated with crop enzyme activity. Our research provides insights into the manipulation of microbes in response to crop resistance to water stress.
Collapse
Affiliation(s)
- Baobei Guo
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
- Pomology Institute, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Hong Zhang
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Yong Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Jianwen Chen
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Junjian Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| |
Collapse
|