1
|
Liu C, Li H, Dong J, He X, Zhang L, Qiu B. Structure and function of rhizosphere soil microbial communities associated with root rot of Knoxia roxburghii. Front Microbiol 2024; 15:1424633. [PMID: 39091303 PMCID: PMC11291326 DOI: 10.3389/fmicb.2024.1424633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 07/01/2024] [Indexed: 08/04/2024] Open
Abstract
The microbial communities in rhizosphere soil play important roles in plant health and crop productivity. However, the microbial community structure of rhizosphere soil still remains unclear. In this study, the composition, diversity and function of the microbial communities in the rhizosphere soil of healthy and diseased plants were compared using Illumina MiSeq high-throughput sequencing. The Sobs (richness) and Shannon (diversity) indices of the soil microbial communities were higher in the rhizospheres of 2- and 3-year-old susceptible plants than in those of the healthy plants. With the increase in planting time, the numbers of fungi tended to decrease, while those of the bacteria tended to increase. Fungal diversity could be used as a biological indicator to measure the health of Knoxia roxburghii. The microbial composition and differential analyses revealed that the rhizosphere soil infested with fungi had a higher relative abundance at the phylum level in Ascomycota and Basidiomycota, while the bacteria had a higher relative abundance of Chloroflexi and a lower relative abundance of Actinobacteriota. At the genus level, the rhizosphere soil infested with fungi had relatively more abundant unclassified_f__Didymellaceae and Solicoccozyma and relatively less abundant Saitozyma and Penicillium. The bacterial genus norank_f__Gemmatimonadaceae was the most abundant, while Arthrobacter was less abundant. In addition, the abundance of Fusarium in the fungal community varied (p = 0.001). It tended to increase in parallel with the planting years. Therefore, it was hypothesized that the change in the community composition of Fusarium may be the primary reason for the occurrence of root rot in K. roxburghii, and the change in the abundance of Fusarium OTU1450 may be an indication of the occurrence of root rot in this species. The community function and prediction analyses showed that the pathogenic fungi increased with the increase in planting years. In general, soil fungi can be roughly divided into three types, including pathotrophs, symbiotrophs, and saprotrophs. An analysis of the differences in the prediction of different rhizosphere functions showed that D and L were significantly different in the COG enrichment pathway of the K. roxburghii rhizosphere bacteria (p < 0.05). The soil physical and chemical properties, including the pH, AK, total potassium (TK), and catalase (S_CAT), had the most significant effect on the soil fungal community, and most of the soil physical and chemical properties significantly correlated with the bacterial community. This study demonstrated that the occurrence of root rot had an important effect on the diversity, structure and composition of microbial communities. In addition, the results will provide a theoretical basis to prevent and control root rot in K. roxburghii.
Collapse
Affiliation(s)
- Chunju Liu
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Heng Li
- R&D Center of Yunnan Yuntianhua Co., Ltd., Kunming, Yunnan, China
| | - Jiahong Dong
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Xiahong He
- School of Landscape Architecture and Horticulture Science, Southwest Forestry University, Kunming, Yunnan, China
| | - Lei Zhang
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Bin Qiu
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| |
Collapse
|
2
|
Galarde-López M, Velazquez-Meza ME, Godoy-Lozano EE, Carrillo-Quiroz BA, Cornejo-Juárez P, Sassoé-González A, Ponce-de-León A, Saturno-Hernández P, Alpuche-Aranda CM. Presence and Persistence of ESKAPEE Bacteria before and after Hospital Wastewater Treatment. Microorganisms 2024; 12:1231. [PMID: 38930614 PMCID: PMC11206169 DOI: 10.3390/microorganisms12061231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/02/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The metagenomic surveillance of antimicrobial resistance in wastewater has been suggested as a methodological tool to characterize the distribution, status, and trends of antibiotic-resistant bacteria. In this study, a cross-sectional collection of samples of hospital-associated raw and treated wastewater were obtained from February to March 2020. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize bacterial abundance and antimicrobial resistance gene analysis. The main bacterial phyla found in all the samples were as follows: Proteobacteria, Bacteroides, Firmicutes, and Actinobacteria. At the species level, ESKAPEE bacteria such as E. coli relative abundance decreased between raw and treated wastewater, but S. aureus, A. baumannii, and P. aeruginosa increased, as did the persistence of K. pneumoniae in both raw and treated wastewater. A total of 172 different ARGs were detected; blaOXA, blaVEB, blaKPC, blaGES, mphE, mef, erm, msrE, AAC(6'), ant(3″), aadS, lnu, PBP-2, dfrA, vanA-G, tet, and sul were found at the highest abundance and persistence. This study demonstrates the ability of ESKAPEE bacteria to survive tertiary treatment processes of hospital wastewater, as well as the persistence of clinically important antimicrobial resistance genes that are spreading in the environment.
Collapse
Affiliation(s)
- Miguel Galarde-López
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (M.G.-L.); (E.E.G.-L.); (B.A.C.-Q.)
| | - Maria Elena Velazquez-Meza
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (M.G.-L.); (E.E.G.-L.); (B.A.C.-Q.)
| | - Elizabeth Ernestina Godoy-Lozano
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (M.G.-L.); (E.E.G.-L.); (B.A.C.-Q.)
| | - Berta Alicia Carrillo-Quiroz
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (M.G.-L.); (E.E.G.-L.); (B.A.C.-Q.)
| | - Patricia Cornejo-Juárez
- Departamento de Infectología, Instituto Nacional de Cancerología, Tlalpan, Mexico City 14080, Mexico;
| | - Alejandro Sassoé-González
- Unidad de Inteligencia Epidemiológica, Hospital Regional de Alta Especialidad de Ixtapaluca, Ixtapaluca 56530, Mexico;
| | - Alfredo Ponce-de-León
- Laboratorio Nacional de Máxima Seguridad para el Estudio de Tuberculosis y Enfermedades Emergentes, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City 14080, Mexico;
| | - Pedro Saturno-Hernández
- Centro de Investigación en Evaluación de Encuestas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico;
| | - Celia Mercedes Alpuche-Aranda
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (M.G.-L.); (E.E.G.-L.); (B.A.C.-Q.)
| |
Collapse
|
3
|
Liu C, Zhang L, Li H, He X, Dong J, Qiu B. Assessing the biodiversity of rhizosphere and endophytic fungi in Knoxia valerianoides under continuous cropping conditions. BMC Microbiol 2024; 24:195. [PMID: 38849736 PMCID: PMC11157913 DOI: 10.1186/s12866-024-03357-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Rhizosphere and endophytic fungi play important roles in plant health and crop productivity. However, their community dynamics during the continuous cropping of Knoxia valerianoides have rarely been reported. K. valerianoides is a perennial herb of the family Rubiaceae and has been used in herbal medicines for ages. Here, we used high-throughput sequencing technology Illumina MiSeq to study the structural and functional dynamics of the rhizosphere and endophytic fungi of K. valerianoides. RESULTS The findings indicate that continuous planting has led to an increase in the richness and diversity of rhizosphere fungi, while concomitantly resulting in a decrease in the richness and diversity of root fungi. The diversity of endophytic fungal communities in roots was lower than that of the rhizosphere fungi. Ascomycota and Basidiomycota were the dominant phyla detected during the continuous cropping of K. valerianoides. In addition, we found that root rot directly affected the structure and diversity of fungal communities in the rhizosphere and the roots of K. valerianoides. Consequently, both the rhizosphere and endophyte fungal communities of root rot-infected plants showed higher richness than the healthy plants. The relative abundance of Fusarium in two and three years old root rot-infected plants was significantly higher than the control, indicating that continuous planting negatively affected the health of K. valerianoides plants. Decision Curve Analysis showed that soil pH, organic matter (OM), available K, total K, soil sucrase (S_SC), soil catalase (S_CAT), and soil cellulase (S_CL) were significantly related (p < 0.05) to the fungal community dynamics. CONCLUSIONS The diversity of fungal species in the rhizosphere and root of K. valerianoides was reported for the first time. The fungal diversity of rhizosphere soil was higher than that of root endophytic fungi. The fungal diversity of root rot plants was higher than that of healthy plants. Soil pH, OM, available K, total K, S_CAT, S_SC, and S_CL were significantly related to the fungal diversity. The occurrence of root rot had an effect on the community structure and diversity of rhizosphere and root endophytic fungi.
Collapse
Affiliation(s)
- Chunju Liu
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Lei Zhang
- Institute of Medicinal Plant Cultivation, School of Chinese Materia Medica, Academy of Southern Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Heng Li
- R&D center of Yunnan Yuntianhua Co., Ltd, Kunming, 650228, China
| | - Xiahong He
- Southwest Forestry University, Kunming, 650244, China.
| | - Jiahong Dong
- Institute of Medicinal Plant Cultivation, School of Chinese Materia Medica, Academy of Southern Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| | - Bin Qiu
- Institute of Medicinal Plant Cultivation, School of Chinese Materia Medica, Academy of Southern Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| |
Collapse
|
4
|
Huang Q, Zhang Y, Tan Y, Kong H, Cao Y, Wang J, Yin G, Guo A. Bt-Modified Transgenic Rice May Shift the Composition and Diversity of Rhizosphere Microbiota. PLANTS (BASEL, SWITZERLAND) 2024; 13:1300. [PMID: 38794371 PMCID: PMC11125220 DOI: 10.3390/plants13101300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/21/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
Plants significantly shape root-associated microbiota, making rhizosphere microbes useful environmental indicator organisms for safety assessment. Here, we report the pyrosequencing of the bacterial 16S ribosomal RNA in rhizosphere soil samples collected from transgenic cry1Ab/cry1Ac Bt rice Huahui No. 1 (GM crop) and its parental counterpart, Minghui63. We identified a total of 2579 quantifiable bacterial operational taxonomic units (OTUs). Many treatment-enriched microbial OTUs were identified, including 14 NonGM-enriched OTUs and 10 GM-enriched OTUs. OTUs belonging to the phyla Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, Nitrospirae, Chlorobi and GN04 were identified as statistically different in abundance between GM and the other two treatments. Compared with the different impacts of different rice varieties on microbiota, the impact of rice planting on microbiota is more obvious. Furthermore, Huahui No. 1 transgenic Bt rice had a greater impact on the rhizosphere bacterial communities than Minghui63. Early developmental stages of the transgenic Bt rice had a significant impact on many Bacillaceae communities. Soil chemical properties were not significantly altered by the presence of transgenic Bt rice. The peak concentration level of Bt protein products was detected during the seedling stage of transgenic Bt rice, which may be an intriguing factor for bacterial diversity variations. Based on these findings, we conclude that transgenic Bt rice has a significant impact on root-associated bacteria. This information may be leveraged in future environmental safety assessments of transgenic Bt rice varieties.
Collapse
Affiliation(s)
- Qixing Huang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
- National Plant Protection Observation and Experiment Station at Sanya, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China
| | - Yuliang Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
- National Plant Protection Observation and Experiment Station at Sanya, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China
| | - Yanhua Tan
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
- National Plant Protection Observation and Experiment Station at Sanya, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China
| | - Hua Kong
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
- National Plant Protection Observation and Experiment Station at Sanya, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China
| | - Yang Cao
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
- National Plant Protection Observation and Experiment Station at Sanya, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China
| | - Jungang Wang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
| | - Guohua Yin
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan 250200, China
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Anping Guo
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China; (Q.H.); (Y.Z.); (Y.C.); (J.W.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, China
- National Plant Protection Observation and Experiment Station at Sanya, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Sanya 572024, China
| |
Collapse
|
5
|
Nisha FA, Tagoe JNA, Pease AB, Horne SM, Ugrinov A, Geddes BA, Prüß BM. Plant seedlings of peas, tomatoes, and cucumbers exude compounds that are needed for growth and chemoattraction of Rhizobium leguminosarum bv. viciae 3841 and Azospirillum brasilense Sp7. Can J Microbiol 2024; 70:150-162. [PMID: 38427979 DOI: 10.1139/cjm-2023-0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
This study characterizes seedling exudates of peas, tomatoes, and cucumbers at the level of chemical composition and functionality. A plant experiment confirmed that Rhizobium leguminosarum bv. viciae 3841 enhanced growth of pea shoots, while Azospirillum brasilense Sp7 supported growth of pea, tomato, and cucumber roots. Chemical analysis of exudates after 1 day of seedling incubation in water yielded differences between the exudates of the three plants. Most remarkably, cucumber seedling exudate did not contain detectable sugars. All exudates contained amino acids, nucleobases/nucleosides, and organic acids, among other compounds. Cucumber seedling exudate contained reduced glutathione. Migration on semi solid agar plates containing individual exudate compounds as putative chemoattractants revealed that R. leguminosarum bv. viciae was more selective than A. brasilense, which migrated towards any of the compounds tested. Migration on semi solid agar plates containing 1:1 dilutions of seedling exudate was observed for each of the combinations of bacteria and exudates tested. Likewise, R. leguminosarum bv. viciae and A. brasilense grew on each of the three seedling exudates, though at varying growth rates. We conclude that the seedling exudates of peas, tomatoes, and cucumbers contain everything that is needed for their symbiotic bacteria to migrate and grow on.
Collapse
Affiliation(s)
- Fatema A Nisha
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Janice N A Tagoe
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Amanda B Pease
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Shelley M Horne
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Angel Ugrinov
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
| | - Barney A Geddes
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Birgit M Prüß
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| |
Collapse
|
6
|
Habteweld A, Kantor M, Kantor C, Handoo Z. Understanding the dynamic interactions of root-knot nematodes and their host: role of plant growth promoting bacteria and abiotic factors. FRONTIERS IN PLANT SCIENCE 2024; 15:1377453. [PMID: 38745927 PMCID: PMC11091308 DOI: 10.3389/fpls.2024.1377453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024]
Abstract
Root-knot nematodes (Meloidogyne spp., RKN) are among the most destructive endoparasitic nematodes worldwide, often leading to a reduction of crop growth and yield. Insights into the dynamics of host-RKN interactions, especially in varied biotic and abiotic environments, could be pivotal in devising novel RKN mitigation measures. Plant growth-promoting bacteria (PGPB) involves different plant growth-enhancing activities such as biofertilization, pathogen suppression, and induction of systemic resistance. We summarized the up-to-date knowledge on the role of PGPB and abiotic factors such as soil pH, texture, structure, moisture, etc. in modulating RKN-host interactions. RKN are directly or indirectly affected by different PGPB, abiotic factors interplay in the interactions, and host responses to RKN infection. We highlighted the tripartite (host-RKN-PGPB) phenomenon with respect to (i) PGPB direct and indirect effect on RKN-host interactions; (ii) host influence in the selection and enrichment of PGPB in the rhizosphere; (iii) how soil microbes enhance RKN parasitism; (iv) influence of host in RKN-PGPB interactions, and (v) the role of abiotic factors in modulating the tripartite interactions. Furthermore, we discussed how different agricultural practices alter the interactions. Finally, we emphasized the importance of incorporating the knowledge of tripartite interactions in the integrated RKN management strategies.
Collapse
Affiliation(s)
- Alemayehu Habteweld
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Northeast Area, Beltsville, MD, United States
| | - Mihail Kantor
- Plant Pathology and Environmental Microbiology Department, Pennsylvania State University, University Park, PA, United States
| | - Camelia Kantor
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, United States
| | - Zafar Handoo
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Northeast Area, Beltsville, MD, United States
| |
Collapse
|
7
|
Zhao J, Yu X, Zhang C, Hou L, Wu N, Zhang W, Wang Y, Yao B, Delaplace P, Tian J. Harnessing microbial interactions with rice: Strategies for abiotic stress alleviation in the face of environmental challenges and climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168847. [PMID: 38036127 DOI: 10.1016/j.scitotenv.2023.168847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
Rice, which feeds more than half of the world's population, confronts significant challenges due to environmental and climatic changes. Abiotic stressors such as extreme temperatures, drought, heavy metals, organic pollutants, and salinity disrupt its cellular balance, impair photosynthetic efficiency, and degrade grain quality. Beneficial microorganisms from rice and soil microbiomes have emerged as crucial in enhancing rice's tolerance to these stresses. This review delves into the multifaceted impacts of these abiotic stressors on rice growth, exploring the origins of the interacting microorganisms and the intricate dynamics between rice-associated and soil microbiomes. We highlight their synergistic roles in mitigating rice's abiotic stresses and outline rice's strategies for recruiting these microorganisms under various environmental conditions, including the development of techniques to maximize their benefits. Through an in-depth analysis, we shed light on the multifarious mechanisms through which microorganisms fortify rice resilience, such as modulation of antioxidant enzymes, enhanced nutrient uptake, plant hormone adjustments, exopolysaccharide secretion, and strategic gene expression regulation, emphasizing the objective of leveraging microorganisms to boost rice's stress tolerance. The review also recognizes the growing prominence of microbial inoculants in modern rice cultivation for their eco-friendliness and sustainability. We discuss ongoing efforts to optimize these inoculants, providing insights into the rigorous processes involved in their formulation and strategic deployment. In conclusion, this review emphasizes the importance of microbial interventions in bolstering rice agriculture and ensuring its resilience in the face of rising environmental challenges.
Collapse
Affiliation(s)
- Jintong Zhao
- Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, 5030 Gembloux, Belgium; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoxia Yu
- School of Water Resources & Environmental Engineering, East China University of Technology, Nanchang, Jiangxi 330000, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Sanya Institute, Hainan, Academy of Agricultural Sciences, Sanya 572000, China
| | - Ligang Hou
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin 136100, China
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Pierre Delaplace
- Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, 5030 Gembloux, Belgium
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| |
Collapse
|
8
|
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
|
9
|
Lanzavecchia G, Frascarelli G, Rocchetti L, Bellucci E, Bitocchi E, Di Vittori V, Sillo F, Ferraris I, Carta G, Delledonne M, Nanni L, Papa R. Genotype Combinations Drive Variability in the Microbiome Configuration of the Rhizosphere of Maize/Bean Intercropping System. Int J Mol Sci 2024; 25:1288. [PMID: 38279288 PMCID: PMC10815965 DOI: 10.3390/ijms25021288] [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: 10/30/2023] [Revised: 12/23/2023] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
In an intercropping system, the interplay between cereals and legumes, which is strongly driven by the complementarity of below-ground structures and their interactions with the soil microbiome, raises a fundamental query: Can different genotypes alter the configuration of the rhizosphere microbial communities? To address this issue, we conducted a field study, probing the effects of intercropping and diverse maize (Zea mays L.) and bean (Phaseolus vulgaris L., Phaseolus coccineus L.) genotype combinations. Through amplicon sequencing of bacterial 16S rRNA genes from rhizosphere samples, our results unveil that the intercropping condition alters the rhizosphere bacterial communities, but that the degree of this impact is substantially affected by specific genotype combinations. Overall, intercropping allows the recruitment of exclusive bacterial species and enhances community complexity. Nevertheless, combinations of maize and bean genotypes determine two distinct groups characterized by higher or lower bacterial community diversity and complexity, which are influenced by the specific bean line associated. Moreover, intercropped maize lines exhibit varying propensities in recruiting bacterial members with more responsive lines showing preferential interactions with specific microorganisms. Our study conclusively shows that genotype has an impact on the rhizosphere microbiome and that a careful selection of genotype combinations for both species involved is essential to achieve compatibility optimization in intercropping.
Collapse
Affiliation(s)
- Giovanna Lanzavecchia
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Giulia Frascarelli
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Lorenzo Rocchetti
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Valerio Di Vittori
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Fabiano Sillo
- National Research Council of Italy, Institute for Sustainable Plant, Strada delle Cacce 73, 10135 Torino, Italy;
| | - Irene Ferraris
- Department of Biotechnologies, Strada le Grazie 15, 37134 Verona, Italy; (I.F.); (G.C.); (M.D.)
| | - Giada Carta
- Department of Biotechnologies, Strada le Grazie 15, 37134 Verona, Italy; (I.F.); (G.C.); (M.D.)
| | - Massimo Delledonne
- Department of Biotechnologies, Strada le Grazie 15, 37134 Verona, Italy; (I.F.); (G.C.); (M.D.)
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| |
Collapse
|
10
|
Timofeeva AM, Galyamova MR, Sedykh SE. Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production. Microorganisms 2023; 11:2864. [PMID: 38138008 PMCID: PMC10745983 DOI: 10.3390/microorganisms11122864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia are believed to be the most promising form of these bacteria. However, designing and modeling bacterial consortia to achieve desired phenotypic outcomes in plants is challenging. This review aims to address this challenge by exploring key antimicrobial interactions. Special attention is given to approaches for developing soil plant growth-promoting bacteria consortia. Additionally, advanced omics-based methods are analyzed that allow soil microbiomes to be characterized, providing an understanding of the molecular and functional aspects of these microbial communities. A comprehensive discussion explores the utilization of bacterial preparations in biofertilizers for agricultural applications, focusing on the intricate design of synthetic bacterial consortia with these preparations. Overall, the review provides valuable insights and strategies for intentionally designing bacterial consortia to enhance plant growth and development.
Collapse
Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Maria R. Galyamova
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| |
Collapse
|
11
|
Fuller E, Germaine KJ, Rathore DS. The Good, the Bad, and the Useable Microbes within the Common Alder ( Alnus glutinosa) Microbiome-Potential Bio-Agents to Combat Alder Dieback. Microorganisms 2023; 11:2187. [PMID: 37764031 PMCID: PMC10535473 DOI: 10.3390/microorganisms11092187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Common Alder (Alnus glutinosa (L.) Gaertn.) is a tree species native to Ireland and Europe with high economic and ecological importance. The presence of Alder has many benefits including the ability to adapt to multiple climate types, as well as aiding in ecosystem restoration due to its colonization capabilities within disturbed soils. However, Alder is susceptible to infection of the root rot pathogen Phytophthora alni, amongst other pathogens associated with this tree species. P. alni has become an issue within the forestry sector as it continues to spread across Europe, infecting Alder plantations, thus affecting their growth and survival and altering ecosystem dynamics. Beneficial microbiota and biocontrol agents play a crucial role in maintaining the health and resilience of plants. Studies have shown that beneficial microbes promote plant growth as well as aid in the protection against pathogens and abiotic stress. Understanding the interactions between A. glutinosa and its microbiota, both beneficial and pathogenic, is essential for developing integrated management strategies to mitigate the impact of P. alni and maintain the health of Alder trees. This review is focused on collating the relevant literature associated with Alder, current threats to the species, what is known about its microbial composition, and Common Alder-microbe interactions that have been observed worldwide to date. It also summarizes the beneficial fungi, bacteria, and biocontrol agents, underpinning genetic mechanisms and secondary metabolites identified within the forestry sector in relation to the Alder tree species. In addition, biocontrol mechanisms and microbiome-assisted breeding as well as gaps within research that require further attention are discussed.
Collapse
Affiliation(s)
- Emma Fuller
- EnviroCore, Dargan Research Centre, Department of Applied Science, South East Technological University, Kilkenny Road, R93 V960 Carlow, Ireland; (E.F.); (K.J.G.)
- Teagasc, Forestry Development Department, Oak Park Research Centre, R93 XE12 Carlow, Ireland
| | - Kieran J. Germaine
- EnviroCore, Dargan Research Centre, Department of Applied Science, South East Technological University, Kilkenny Road, R93 V960 Carlow, Ireland; (E.F.); (K.J.G.)
| | - Dheeraj Singh Rathore
- Teagasc, Forestry Development Department, Oak Park Research Centre, R93 XE12 Carlow, Ireland
| |
Collapse
|
12
|
Nadarajah K, Abdul Rahman NSN. The Microbial Connection to Sustainable Agriculture. PLANTS (BASEL, SWITZERLAND) 2023; 12:2307. [PMID: 37375932 DOI: 10.3390/plants12122307] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
Abstract
Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants' growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant-soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome's diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant-soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.
Collapse
Affiliation(s)
- Kalaivani Nadarajah
- Department of Biological Sciences and Biotechnology, Faculty of Sciences and Technology, University Kebangsaan Malaysia, Bangi 43600, Malaysia
| | - Nur Sabrina Natasha Abdul Rahman
- Department of Biological Sciences and Biotechnology, Faculty of Sciences and Technology, University Kebangsaan Malaysia, Bangi 43600, Malaysia
| |
Collapse
|
13
|
Zhang F, Xu N, Zhang Z, Zhang Q, Yang Y, Yu Z, Sun L, Lu T, Qian H. Shaping effects of rice, wheat, maize, and soybean seedlings on their rhizosphere microbial community. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:35972-35984. [PMID: 36539666 DOI: 10.1007/s11356-022-24835-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
The rhizosphere microbiome plays critical roles in plant growth and is an important interface for resource exchange between plants and the soil environment. Crops at various growing stages, especially the seedling stage, have strong shaping effects on the rhizosphere microbial community, and such community reconstruction will positively feed back to the plant growth. In the present study, we analyzed the variations of bacterial and fungal communities in the rhizosphere of four crop species: rice, soybean, maize, and wheat during successive cultivations (three repeats for the seedling stages) using 16S rRNA gene and internal transcribed spacer (ITS) high-throughput sequencing. We found that the relative abundances of specific microorganisms decreased after different cultivation times, e.g., Sphingomonas, Pseudomonas, Rhodanobacter, and Caulobacter, which have been reported as plant-growth beneficial bacteria. The relative abundances of potential plant pathogenic fungi Myrothecium and Ascochyta increased with the successive cultivation times. The co-occurrence network analysis showed that the bacterial and fungal communities under maize were much more stable than those under rice, soybean, and wheat. The present study explored the characteristics of bacteria and fungi in crop seedling rhizosphere and indicated that the characteristics of indigenous soil flora might determine the plant growth status. Further study will focus on the use of the critical microorganisms to control the growth and yield of specific crops.
Collapse
Affiliation(s)
- Fan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yaohui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Zhitao Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| |
Collapse
|
14
|
Migration Rates on Swim Plates Vary between Escherichia coli Soil Isolates: Differences Are Associated with Variants in Metabolic Genes. Appl Environ Microbiol 2023; 89:e0172722. [PMID: 36695629 PMCID: PMC9972950 DOI: 10.1128/aem.01727-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This study investigates migration phenotypes of 265 Escherichia coli soil isolates from the Buffalo River basin in Minnesota, USA. Migration rates on semisolid tryptone swim plates ranged from nonmotile to 190% of the migration rate of a highly motile E. coli K-12 strain. The nonmotile isolate, LGE0550, had mutations in flagellar and chemotaxis genes, including two IS3 elements in the flagellin-encoding gene fliC. A genome-wide association study (GWAS), associating the migration rates with genetic variants in specific genes, yielded two metabolic variants (rygD-serA and metR-metE) with previous implications in chemotaxis. As a novel way of confirming GWAS results, we used minimal medium swim plates to confirm the associations. Other variants in metabolic genes and genes that are associated with biofilm were positively or negatively associated with migration rates. A determination of growth phenotypes on Biolog EcoPlates yielded differential growth for the 10 tested isolates on d-malic acid, putrescine, and d-xylose, all of which are important in the soil environment. IMPORTANCE E. coli is a Gram-negative, facultative anaerobic bacterium whose life cycle includes extra host environments in addition to human, animal, and plant hosts. The bacterium has the genomic capability of being motile. In this context, the significance of this study is severalfold: (i) the great diversity of migration phenotypes that we observed within our isolate collection supports previous (G. NandaKafle, A. A. Christie, S. Vilain, and V. S. Brözel, Front Microbiol 9:762, 2018, https://doi.org/10.3389/fmicb.2018.00762; Y. Somorin, F. Abram, F. Brennan, and C. O'Byrne, Appl Environ Microbiol 82:4628-4640, 2016, https://doi.org/10.1128/AEM.01175-16) ideas of soil promoting phenotypic heterogeneity, (ii) such heterogeneity may facilitate bacterial growth in the many different soil niches, and (iii) such heterogeneity may enable the bacteria to interact with human, animal, and plant hosts.
Collapse
|
15
|
Lu B, Qian J, Hu J, Huang Y, Wang P, Shen J, He Y, Tang S, Liu Y, Zhang Y. Plant rhizosphere defense system respond differently to emerging polyfluoroalkyl substances F-53B and PFOS stress. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130119. [PMID: 36265386 DOI: 10.1016/j.jhazmat.2022.130119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Chlorinated polyfluoroalkyl ether sulfonate (F-53B) and perfluorooctanesulfonate (PFOS) are used and emitted as fog inhibitors in the chromium plating industry, and they are widely detected worldwide. To study the effects of F-53B and PFOS on the rhizosphere defense system, they were added at two levels (0.1 and 50 mg L-1) to the soil where different plants (Lythrum salicaria and Phragmites communis) were grown. In bulk soils, high concentrations of F-53B/PFOS resulted in significant increases in soil pH, NH4+-N, and NO3--N (the effect of PFOS on NO3--N was not significant). Moreover, the extent of the effects of PFOS and F-53B on the physicochemical properties of bulk soils were different (e.g., PFOS caused an increase of NH4+-N by 8.94%-45.97% compared to 1.63%-25.20% for F-53B). Root exudates and PFASs together influenced the physicochemical properties of rhizosphere soils (e.g., TOC increased significantly in contaminated rhizosphere soils but did not change in non-bulk soils). Under the influence of F-53B/PFOS, the root exudates regulated by plants were changed and weakened the effect of F-53B/PFOS on microbial community of rhizosphere soil. The rhizosphere defense systems of different plants have both similarities and differences in response to different substances and concentrations.
Collapse
Affiliation(s)
- Bianhe Lu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Jin Qian
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China.
| | - Jing Hu
- Geosystems Research Institute, Mississippi State University, MS 39759, USA
| | | | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China.
| | - Junwei Shen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Yuxuan He
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Sijing Tang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Yin Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Yuhang Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| |
Collapse
|
16
|
Afridi MS, Javed MA, Ali S, De Medeiros FHV, Ali B, Salam A, Sumaira, Marc RA, Alkhalifah DHM, Selim S, Santoyo G. New opportunities in plant microbiome engineering for increasing agricultural sustainability under stressful conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:899464. [PMID: 36186071 PMCID: PMC9524194 DOI: 10.3389/fpls.2022.899464] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/08/2022] [Indexed: 07/30/2023]
Abstract
Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.
Collapse
Affiliation(s)
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Sher Ali
- Department of Food Engineering, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), São Paulo, Brazil
| | | | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Salam
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sumaira
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | - Dalal Hussien M. Alkhalifah
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| |
Collapse
|
17
|
Li Q, Li H, Yang Z, Cheng X, Zhao Y, Qin L, Bisseling T, Cao Q, Willemsen V. Plant growth-promoting rhizobacterium Pseudomonas sp. CM11 specifically induces lateral roots. THE NEW PHYTOLOGIST 2022; 235:1575-1588. [PMID: 35510807 PMCID: PMC9546010 DOI: 10.1111/nph.18199] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/28/2022] [Indexed: 06/10/2023]
Abstract
Plant growth-promoting rhizobacteria are involved in altering secondary root (SR) formation, but hitherto there has been no distinction between the different types of SRs upon induction of soil biota, and the genetic pathways involved. By using plate and soil systems, we studied the effects of the Pseudomonas strains CM11 and WCS417 on plant performance with a focus on root development. Through a combination of cellular, molecular and genetic analyses, we investigated the type of SRs induced upon CM11 and WCS417 root inoculation using genetic pathways associated with specific SR types. CM11 was shown to affect the root architecture differently from WCS417. CM11 inoculation leads to primary root arrest, whereas WCS417 reveals a longer primary root. Both CM11 and WCS417 activate the PLETHORA 3,5,7-controlled lateral root pathway, rather than the WUSCHEL-RELATED HOMEOBOX 11,12-controlled adventitious (lateral) root pathway. In addition, CM11 promotes plant growth in model and various crop species. It improves plant fitness traits, such as bigger shoots, faster bolting and higher yield in terms of seeds. Our results indicate that the root system architecture can be promoted by activation of PLETHORA 3,5,7 dependent primed lateral pre-branch sites upon inoculation with CM11, which creates great potential to gain a better understanding of root plasticity.
Collapse
Affiliation(s)
- Qian Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing University of AgricultureBeijing102206China
- Cluster of Plant Developmental BiologyLaboratory of Molecular BiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenthe Netherlands
- Beijing Bei Nong Enterprise Management Co. LtdBeijing102206China
| | - Huchen Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing University of AgricultureBeijing102206China
- Cluster of Plant Developmental BiologyLaboratory of Molecular BiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Zhuang Yang
- Cluster of Plant Developmental BiologyLaboratory of Molecular BiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Xu Cheng
- Cluster of Plant Developmental BiologyLaboratory of Molecular BiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Yaceng Zhao
- College of Plant Science and TechnologyBeijing Key Laboratory for Agricultural Application and New TechniqueBeijing University of AgricultureBeijing102206China
| | - Ling Qin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing University of AgricultureBeijing102206China
- College of Plant Science and TechnologyBeijing Key Laboratory for Agricultural Application and New TechniqueBeijing University of AgricultureBeijing102206China
| | - Ton Bisseling
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing University of AgricultureBeijing102206China
- Cluster of Plant Developmental BiologyLaboratory of Molecular BiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Qingqin Cao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing University of AgricultureBeijing102206China
- College of Plant Science and TechnologyBeijing Key Laboratory for Agricultural Application and New TechniqueBeijing University of AgricultureBeijing102206China
| | - Viola Willemsen
- Cluster of Plant Developmental BiologyLaboratory of Molecular BiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| |
Collapse
|
18
|
Culturable Screening of Plant Growth-Promoting and Biocontrol Bacteria in the Rhizosphere and Phyllosphere of Wild Rice. Microorganisms 2022; 10:microorganisms10071468. [PMID: 35889186 PMCID: PMC9324538 DOI: 10.3390/microorganisms10071468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/04/2022] [Accepted: 07/14/2022] [Indexed: 02/01/2023] Open
Abstract
Wild rice is an important improved resource for cultivated rice and its unique ability to resist biotic and abiotic stress has attracted the attention of many scholars. The microbial community structure in the rhizosphere and leaf area of different rice varieties is also different, which may be one of the reasons for the difference in stress resistance between wild rice and cultivated rice. Forty-six bacteria were screened from the rhizosphere and phyllospheric of four different wild rice varieties. The results of functions of the screened strains showed that 18 strains had a good inhibitory effect on rice blast, and 33 strains had the ability to dissolve phosphorus, potassium, or fix nitrogen. Through potted experiment, the three bacterial strains, 499G2 (Peribacillus simplex), 499G3 (Bacillus velezensis), and 499G4 (B. megaterium) have a positive effect on the growth of cultivated rice in addition to the resistance to rice blast. The contents of total nitrogen, total phosphorus, total potassium, indole acetic acid (IAA), and chlorophyll in plant leaves were increased. In addition, in the verification test of rice blast infection, the application of inoculants can significantly reduce the content of malondialdehyde (MDA), increase the content of soluble sugar, and increase the activity of plant antioxidant enzymes, which may thereby improve rice in resisting to rice blast.
Collapse
|
19
|
Marasco R, Alturkey H, Fusi M, Brandi M, Ghiglieno I, Valenti L, Daffonchio D. Rootstock-scion combination contributes to shape diversity and composition of microbial communities associated with grapevine root system. Environ Microbiol 2022; 24:3791-3808. [PMID: 35581159 PMCID: PMC9544687 DOI: 10.1111/1462-2920.16042] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/06/2022] [Indexed: 12/01/2022]
Abstract
To alleviate biotic and abiotic stresses and enhance fruit yield, many crops are cultivated in the form of grafted plants, in which the shoot (scion) and root (rootstock) systems of different species are joined together. Because (i) the plant species determines the microbial recruitment from the soil to the root and (ii) both scion and rootstock impact the physiology, morphology and biochemistry of the grafted plant, it can be expected that their different combinations should affect the recruitment and assembly of plant microbiome. To test our hypothesis, we investigated at a field scale the bacterial and fungal communities associated with the root system of seven grapevine rootstock–scion combinations cultivated across 10 different vineyards. Following the soil type, which resulted in the main determinant of the grapevine root microbial community diversity, the rootstock–scion combination resulted more important than the two components taken alone. Notably, the microbiome differences among the rootstock–scion combinations were mainly dictated by the changes in the relative abundance of microbiome members rather than by their presence/absence. These results reveal that the microbiome of grafted grapevine root systems is largely influenced by the combination of rootstock and scion, which affects the microbial diversity uptaken from soil.
Collapse
Affiliation(s)
- Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Hend Alturkey
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Marco Fusi
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Michele Brandi
- Marchesi Frescobaldi Società Agricola s.p.a. Fattoria Poggio a Remole, Sieci, Italy
| | - Isabella Ghiglieno
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Milan, Italy.,Department of Civil, Environmental, Architectural Engineering and Mathematics (DICATAM), University of Brescia, Agrofood Research Hub, Brescia, Italy
| | - Leonardo Valenti
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| |
Collapse
|
20
|
McCoy RM, Widhalm JR, McNickle GG. Allelopathy as an evolutionary game. PLANT DIRECT 2022; 6:e382. [PMID: 35169675 PMCID: PMC8832168 DOI: 10.1002/pld3.382] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/21/2021] [Accepted: 01/11/2022] [Indexed: 05/30/2023]
Abstract
In plants, most competition is resource competition, where one plant simply preempts the resources away from its neighbors. Interference competition, as the name implies, is a form of direct interference to prevent resource access. Interference competition is common among animals that can physically fight, but in plants, one of the main mechanisms of interference competition is allelopathy. Allelopathic plants release cytotoxic chemicals into the environment which can increase their ability to compete with surrounding organisms for limited resources. The circumstances and conditions favoring the development and maintenance of allelochemicals, however, are not well understood. Particularly, despite the obvious benefits of allelopathy, current data suggest it seems to have only rarely evolved. To gain insight into the cost and benefit of allelopathy, we have developed a 2 × 2 matrix game to model the interaction between plants that produce allelochemicals and plants that do not. Production of an allelochemical introduces novel cost associated with both synthesis and detoxifying a toxic chemical but may also convey a competitive advantage. A plant that does not produce an allelochemical will suffer the cost of encountering one. Our model predicts three cases in which the evolutionarily stable strategies are different. In the first, the nonallelopathic plant is a stronger competitor, and not producing allelochemicals is the evolutionarily stable strategy. In the second, the allelopathic plant is the better competitor, and production of allelochemicals is the more beneficial strategy. In the last case, neither is the evolutionarily stable strategy. Instead, there are alternating stable states, depending on whether the allelopathic or nonallelopathic plant arrived first. The generated model reveals circumstances leading to the evolution of allelochemicals and sheds light on utilizing allelochemicals as part of weed management strategies. In particular, the wide region of alternative stable states in most parameterizations, combined with the fact that the absence of allelopathy is likely the ancestral state, provides an elegant answer to the question of why allelopathy seems to rarely evolve despite its obvious benefits. Allelopathic plants can indeed outcompete nonallelopathic plants, but this benefit is simply not great enough to allow them to go to fixation and spread through the population. Thus, most populations would remain purely nonallelopathic.
Collapse
Affiliation(s)
- Rachel M. McCoy
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteINUSA
| | - Joshua R. Widhalm
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteINUSA
| | - Gordon G. McNickle
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteINUSA
| |
Collapse
|
21
|
Ma X, Chao L, Li J, Ding Z, Wang S, Li F, Bao Y. The Distribution and Turnover of Bacterial Communities in the Root Zone of Seven Stipa Species Across an Arid and Semi-arid Steppe. Front Microbiol 2022; 12:782621. [PMID: 35003012 PMCID: PMC8741278 DOI: 10.3389/fmicb.2021.782621] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/26/2021] [Indexed: 11/23/2022] Open
Abstract
The bacterial communities of the root-zone soil are capable of regulating vital biogeochemical cycles and the succession of plant growth. Stipa as grassland constructive species is restricted by the difference features of east–west humidity and north–south heat, which shows the population substituting distribution. The distribution, turnover, and potential driving factors and ecological significance of the root-zone bacterial community along broad spatial gradients of Stipa taxa transition remain unclear. This paper investigated seven Stipa species root-zone soils based on high-throughput sequencing combined with the measurements of multiple environmental parameters in arid and semi-arid steppe. The communities of soil bacteria in root zone had considerable turnover, and some regular variations in structure along the Stipa taxa transition are largely determined by climatic factors, vegetation coverage, and pH at a regional scale. Bacterial communities had a clear Stipa population specificity, but they were more strongly affected by the main annual precipitation, which resulted in a biogeographical distribution pattern along precipitation gradient, among which Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi were the phyla that were most abundant. During the transformation of Stipa taxa from east to west, the trend of diversity shown by bacterial community in the root zone decreased first, and then increased sharply at S. breviflora, which was followed by continuous decreasing toward northwest afterwards. However, the richness and evenness showed an opposite trend, and α diversity had close association with altitude and pH. There would be specific and different bacterial taxa interactions in different Stipa species, in which S. krylovii had the simplest and most stable interaction network with the strongest resistance to the environment and S. breviflora had most complex and erratic. Moreover, the bacterial community was mainly affected by dispersal limitation at a certain period. These results are conducive to the prediction of sustainable ecosystem services and protection of microbial resources in a semi-arid grassland ecosystem.
Collapse
Affiliation(s)
- Xiaodan Ma
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Lumeng Chao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Jingpeng Li
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Zhiying Ding
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Siyu Wang
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Fansheng Li
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Yuying Bao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| |
Collapse
|
22
|
Zhang X, Wang H, Que Y, Yu D, Wang H. The influence of rhizosphere soil fungal diversity and complex community structure on wheat root rot disease. PeerJ 2022; 9:e12601. [PMID: 34993020 PMCID: PMC8675258 DOI: 10.7717/peerj.12601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/15/2021] [Indexed: 11/20/2022] Open
Abstract
Wheat root rot disease due to soil-borne fungal pathogens leads to tremendous yield losses worth billions of dollars worldwide every year. It is very important to study the relationship between rhizosphere soil fungal diversity and wheat roots to understand the occurrence and development of wheat root rot disease. A significant difference in fungal diversity was observed in the rhizosphere soil of healthy and diseased wheat roots in the heading stage, but the trend was the opposite in the filling stage. The abundance of most genera with high richness decreased significantly from the heading to the filling stage in the diseased groups; the richness of approximately one-third of all genera remained unchanged, and only a few low-richness genera, such as Fusarium and Ceratobasidium, had a very significant increase from the heading to the filling stage. In the healthy groups, the abundance of most genera increased significantly from the heading to filling stage; the abundance of some genera did not change markedly, or the abundance of very few genera increased significantly. Physical and chemical soil indicators showed that low soil pH and density, increases in ammonium nitrogen, nitrate nitrogen and total nitrogen contributed to the occurrence of wheat root rot disease. Our results revealed that in the early stages of disease, highly diverse rhizosphere soil fungi and a complex community structure can easily cause wheat root rot disease. The existence of pathogenic fungi is a necessary condition for wheat root rot disease, but the richness of pathogenic fungi is not necessarily important. The increases in ammonium nitrogen, nitrate nitrogen and total nitrogen contributed to the occurrence of wheat root rot disease. Low soil pH and soil density are beneficial to the occurrence of wheat root rot disease.
Collapse
Affiliation(s)
- Xuejiang Zhang
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, Hubei Province, China.,Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, Hubei Province, China.,Institute of Plant Protection and Soil & Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Heyun Wang
- HuBei University of Technology, Wuhan, Hubei Province, China
| | - Yawei Que
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, Hubei Province, China.,Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, Hubei Province, China.,Institute of Plant Protection and Soil & Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Dazhao Yu
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, Hubei Province, China.,Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, Hubei Province, China.,Institute of Plant Protection and Soil & Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Hua Wang
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, Hubei Province, China.,Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, Hubei Province, China.,Institute of Plant Protection and Soil & Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| |
Collapse
|
23
|
Bhattacharjee A, Dubey S, Sharma S. Storage of soil microbiome for application in sustainable agriculture: prospects and challenges. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3171-3183. [PMID: 34718953 DOI: 10.1007/s11356-021-17164-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Soil microbiome is a dynamic micro-ecosystem driving and fine-tuning several biological processes in the global macro-ecosystems. Its tremendous potential towards mediating sustainability in the ecosystem necessitates the urgent need to store it optimally and efficiently as "next-generation biologicals" for future applications via soil transplantation. The challenge, therefore, is to devise a strategy for the storage of soil microbiome such that its "functionality" is preserved for later application. This review discusses the current endeavours made towards storage of the soil microbiome. The methods for assessing the integrity of soil microbiome by targeting the structural diversity and functional potential of the preserved microbiomes have also been discussed. Further, the success stories related to the storage of fecal microbiome for application in transplants have also been highlighted. This is done primarily with the objective of learning lessons, and parallel application of the knowledge gained, in bringing about improvement in the research domain of soil microbiome storage. Subsequently, the limitations of current techniques of preservation have also been delineated. Further, the open questions in the area have been critically discussed. In conclusion, possible alternatives for storage, comprehensive analyses of the composition of the stored microbiome and their potential have been presented.
Collapse
Affiliation(s)
- Annapurna Bhattacharjee
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shubham Dubey
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| |
Collapse
|
24
|
Rupawalla Z, Robinson N, Schmidt S, Li S, Carruthers S, Buisset E, Roles J, Hankamer B, Wolf J. Algae biofertilisers promote sustainable food production and a circular nutrient economy - An integrated empirical-modelling study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:148913. [PMID: 34328895 DOI: 10.1016/j.scitotenv.2021.148913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Agriculture has radically changed the global nitrogen (N) cycle and is heavily dependent on synthetic N-fertiliser. However, the N-use efficiency of synthetic fertilisers is often only 50% with N-losses from crop systems polluting the biosphere, hydrosphere and atmosphere. To address the large carbon and energy footprint of N-fertiliser synthesis and curb N-pollution, new technologies are required to deliver enhanced energy efficiency, decarbonisation and a circular nutrient economy. Algae fertilisers (AF) are an alternative to synthetic N-fertiliser (SF). Here microalgae were used as biofertiliser for spinach production. AF production was evaluated using life-cycle analyses. Over 4 weeks, AF released 63.5% of N as bioavailable ammonium and nitrate, and 25% of phosphorous (P) as phosphate to the growth substrate; SF released 100% N and 20% P. To maximise crop N-use and minimise N-leaching, we explored AF and SF dose-response-curves with spinach in glasshouse conditions. AF-grown spinach produced 36% less biomass than SF-grown plants due to AF's slower and linear N-release; SF exhibited 5-times higher N-leaching than AF. Optimised AF:SF blends yielded greater synchrony between N-release and crop-uptake, boosting crop yields and minimising N-loss. Additional benefits of AF included greener leaves, lower leaf nitrate concentration, and higher microbial diversity and water holding capacity of the growth substrate. An integrated techno-economic and life-cycle-analysis of scaled-up microalgae systems (+/- wastewater) normalised to the application dose showed that replacing the most effective SF-dose with AF lowered the annual carbon footprint of fertiliser production from 3.644 kg CO2 m-2 (C-producing) to -6.039 kg CO2 m-2 (C-assimilation). N-loss from growth substrate was lowered by 54%. Embodied energy for AF:SF blends could be reduced by 29% when cultivating microalgae on wastewater. Conclusions: (i) microalgae offer a sustainable alternative to synthetic N-fertiliser for spinach production and potentially other crop systems, (ii) microalgae biofertilisers support the circular-nutrient-economy and several UN-Sustainable-Development-Goals.
Collapse
Affiliation(s)
- Zeenat Rupawalla
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nicole Robinson
- School of Agriculture and Food Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Susanne Schmidt
- School of Agriculture and Food Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sijie Li
- School of Agriculture and Food Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Selina Carruthers
- School of Agriculture and Food Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Elodie Buisset
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - John Roles
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ben Hankamer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Juliane Wolf
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
| |
Collapse
|
25
|
Rebello S, Nathan VK, Sindhu R, Binod P, Awasthi MK, Pandey A. Bioengineered Microbes for Soil Health Restoration - Present Status and Future. Bioengineered 2021; 12:12839-12853. [PMID: 34775906 PMCID: PMC8810056 DOI: 10.1080/21655979.2021.2004645] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
According to the United Nations Environment Programme (UNEP), soil health is declining over the decades and it has an adverse impact on human health and food security. Hence, soil health restoration is a need of the hour. It is known that microorganisms play a vital role in remediation of soil pollutants like heavy metals, pesticides, hydrocarbons, etc. However, the indigenous microbes have a limited capacity to degrade these pollutants and it will be a slow process. Genetically modified organisms (GMOs) can catalyze the degradation process as their altered metabolic pathways lead to hypersecretions of various biomolecules that favor the bioremediation process. This review provides an overview on the application of bioengineered microorganisms for the restoration of soil health by degradation of various pollutants. It also sheds light on the challenges of using GMOs in environmental application as their introduction may affect the normal microbial community in soil. Since soil health also refers to the potential of native organisms to survive, the possible changes in the native microbial community with the introduction of GMOs are also discussed. Finally, the future prospects of using bioengineered microorganisms in environmental engineering applications to make the soil fertile and healthy have been deciphered. With the alarming rates of soil health loss, the treatment of soil and soil health restoration need to be fastened to a greater pace and the combinatorial efforts unifying GMOs, plant growth-promoting rhizobacteria, and other soil amendments will provide an effective solution to soil heath restoration ten years ahead.
Collapse
Affiliation(s)
| | - Vinod Kumar Nathan
- School of Chemical and Biotechnology, Sastra University, Thanjavur, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum - 695 019, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum - 695 019, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, North West A & F University, Yangling, Shaanxi - 712 100, China
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR- Indian Institute for Toxicology Research, Lucknow - 226 001, India.,Centre for Energy and Environmental Sustainability, Lucknow-226 029, Uttar Pradesh, India
| |
Collapse
|
26
|
Rhizospheric microbiome: Bio-based emerging strategies for sustainable agriculture development and future perspectives. Microbiol Res 2021; 254:126901. [PMID: 34700186 DOI: 10.1016/j.micres.2021.126901] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 10/16/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022]
Abstract
In the light of intensification of cropping practices and changing climatic conditions, nourishing a growing global population requires optimizing environmental sustainability and reducing ecosystem impacts of food production. The use of microbiological systems to ameliorate the agricultural production in a sustainable and eco-friendly way is widespread accepted as a future key-technology. However, the multitude of interaction possibilities between the numerous beneficial microbes and plants in their habitat calls for systematic analysis and management of the rhizospheric microbiome. This review exploits present and future strategies for rhizospheric microbiome management with the aim to generate a comprehensive understanding of the known tools and techniques. Significant information on the structure and dynamics of rhizospheric microbiota of isolated microbial communities is now available. These microbial communities have beneficial effects including increased plant growth, essential nutrient acquisition, pathogens tolerance, and increased abiotic as well as biotic stress tolerance such as drought, temperature, salinity and antagonistic activities against the phyto-pathogens. A better and comprehensive understanding of the various effects and microbial interactions can be gained by application of molecular approaches as extraction of DNA/RNA and other biochemical markers to analyze microbial soil diversity. Novel techniques like interactome network analysis and split-ubiquitin system framework will enable to gain more insight into communication and interactions between the proteins from microbes and plants. The aim of the analysis tasks leads to the novel approach of Rhizosphere microbiome engineering. The capability of forming the rhizospheric microbiome in a defined way will allow combining several microbes (e.g. bacteria and fungi) for a given environment (soil type and climatic zone) in order to exert beneficial influences on specific plants. This integration will require a large-scale effort among academic researchers, industry researchers and farmers to understand and manage interactions of plant-microbiomes within modern farming systems, and is clearly a multi-domain approach and can be mastered only jointly by microbiology, mathematics and information technology. These innovations will open up a new avenue for designing and implementing intensive farming microbiome management approaches to maximize resource productivity and stress tolerance of agro-ecosystems, which in return will create value to the increasing worldwide population, for both food production and consumption.
Collapse
|
27
|
Lee SI, Choi J, Hong H, Nam JH, Strik B, Davis A, Cho Y, Ha SD, Park SH. Investigation of soil microbiome under the influence of different mulching treatments in northern highbush blueberry. AMB Express 2021; 11:134. [PMID: 34581888 PMCID: PMC8479055 DOI: 10.1186/s13568-021-01294-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial communities on soil are fundamental for the long-term sustainability of agriculture ecosystems. Microbiota in soil would impact the yield and quality of blueberries since microbial communities in soil can interact with the rhizosphere of plant. This study was conducted to determine how different mulching treatments induce changes in soil microbial composition, diversity, and functional properties. A total of 150 soil samples were collected from 5 different mulch treatments (sawdust, green weed mat, sawdust topped with green weed mat, black weed mat, and sawdust topped with black weed mat) at 3 different depths (bottom, middle, and top region of 20 cm soil depth) from 2 different months (June and July 2018). A total of 8,583,839 sequencing reads and 480 operational taxonomic units (OTUs) of bacteria were identified at genus level. Eight different plant growth promoting rhizobacteria (PGPR) were detected, and the relative abundances of Bradyrhizobium, Bacillus, and Paenibacillus were more than 0.1% among all soil samples. Sampling depth and month of soil samples impacted the amount of PGPR, while there were no significant differences based on mulch type. Functional properties of bacteria were identified through PICRUSt2, which found that there is no significant difference between mulch treatment, depth, and month. The results indicated that sampling month and depth of soil impacted the relative abundance of PGPR in soil samples, but there were no significant differences of functional properties and beneficial microbial communities based on mulch type.
Collapse
|
28
|
Nadarajah K, Abdul Rahman NSN. Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad. Int J Mol Sci 2021; 22:ijms221910388. [PMID: 34638728 PMCID: PMC8508622 DOI: 10.3390/ijms221910388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023] Open
Abstract
Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.
Collapse
|
29
|
Matus-Acuña V, Caballero-Flores G, Martínez-Romero E. The influence of maize genotype on the rhizosphere eukaryotic community. FEMS Microbiol Ecol 2021; 97:6261178. [PMID: 33930111 DOI: 10.1093/femsec/fiab066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 04/28/2021] [Indexed: 01/04/2023] Open
Abstract
The microbiota colonizing the rhizosphere contributes to plant growth, productivity, carbon sequestration and phytoremediation. Several studies address plant-associated bacteria; however, few studies analyze the effect of plant genotype on the eukaryotic community. Here, we analyzed the eukaryotic composition of maize rhizosphere from three different plant landraces and one inbred line grown in the same soil (common garden approach). This experimental design, coupled with 18S rDNA gene amplicon sequencing, allowed us to test the influence of maize and its genotype on the rhizosphere's eukaryotic community. We found that plant growth modified the eukaryotic community in soil, as diversity comparisons between maize rhizosphere and unplanted soil revealed significantly different eukaryotic composition. Various genera of nematodes and fungi, predominantly bacterial feeding nematodes and mycorrhizal fungi among other taxa, were increased in the rhizosphere samples. We also observed that maize genotype differentially shaped the relative abundance of the following fungal families in the rhizosphere: Acaulosporaceae, Aspergillaceae, Chaetomiaceae, Claroideoglomeraceae, Corticiaceae, Mortierellaceae, Trichocomaceae and Trichomeriaceae. Thus, plant genotype has a selective influence on establishing fungal communities in the rhizosphere. This study emphasizes the importance of an integrated consideration of plant genetics for future agricultural applications of microbes to crops.
Collapse
Affiliation(s)
- Violeta Matus-Acuña
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Gustavo Caballero-Flores
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Esperanza Martínez-Romero
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| |
Collapse
|
30
|
Above and below-ground involvement in cyclic energy transformation that helps in the establishment of rhizosphere microbial communities. Symbiosis 2021. [DOI: 10.1007/s13199-021-00791-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
31
|
Zhu L, Yan H, Zhou GS, Jiang CH, Liu P, Yu G, Guo S, Wu QN, Duan JA. Insights into the mechanism of the effects of rhizosphere microorganisms on the quality of authentic Angelica sinensis under different soil microenvironments. BMC PLANT BIOLOGY 2021; 21:285. [PMID: 34157988 PMCID: PMC8220839 DOI: 10.1186/s12870-021-03047-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/11/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND Angelica sinensis (Oliv.) Diels (A. sinensis) is a Chinese herb grown in different geographical locations. It contains numerous active components with therapeutic value. Rhizosphere microbiomes affect various aspects of plant performance, such as nutrient acquisition, growth and development and plant diseases resistance. So far, few studies have investigated how the microbiome effects level of active components of A. sinensis. This study investigated whether changes in rhizosphere microbial communities and metabolites of A. sinensis vary with the soil microenvironment. Soils from the two main A. sinensis-producing areas, Gansu and Yunnan Province, were used to conduct pot experiments. The soil samples were divided into two parts, one part was sterilized and the other was unsterilized planting with the seedling variety of Gansu danggui 90-01. All seedlings were allowed to grow for 180 days. At the end of the experiment, radix A. sinensis were collected and used to characterize growth targets and chemical compositions. Rhizosphere soils were subjected to microbial analyses. RESULTS Changes in metabolic profiles and rhizosphere microbial communities of A. sinensis grown under different soil microenvironments were similar. The GN (Gansu non-sterilized), YN (Yunnan non-sterilized), GS (Gansu sterilized), and YS (Yunnan sterilized) groups were significantly separated. Notably, antagonistic bacteria such as Sphingomonas, Pseudomonas, Lysobacter, Pseudoxanthomonas, etc. were significantly (p < 0.05) enriched in Gansu soil compared with Yunnan soil. Moreover, senkyunolide I and ligustilide dimers which were enriched in GS group were strongly positively correlated with Pseudomonas parafulva; organic acids (including chlorogenic acid, dicaffeoylquinic acid and 5-feruloylquinic acid) and their ester coniferyl ferulate which were enriched in YS Group were positively associated with Gemmatimonadetes bacterium WY71 and Mucilaginibater sp., respectively. CONCLUSIONS The soil microenvironment influences growth and level/type of active components in A. sinensis. Further studies should explore the functional features of quality-related bacteria, identify the key response genes and clarify the interactions between genes and soil environments. This will reveal the mechanisms that determine the quality formation of genuine A. sinensis.
Collapse
Affiliation(s)
- Lei Zhu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hui Yan
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Gui-Sheng Zhou
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chun-Hao Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Pei Liu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Guang Yu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Sheng Guo
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qi-Nan Wu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jin-Ao Duan
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China.
| |
Collapse
|
32
|
Wang J, Wu H, Wu L, Liu Y, Letuma P, Qin X, Chen T, Rensing C, Lin S, Lin W. Revealing Microbiome Structure and Assembly Process in Three Rhizocompartments of Achyranthes bidentata Under Continuous Monoculture Regimes. Front Microbiol 2021; 12:677654. [PMID: 34194412 PMCID: PMC8236951 DOI: 10.3389/fmicb.2021.677654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
The complex composition and interaction of root-associated microbes are critical to plant health and performance. In this study, we presented a detailed characterization of three rhizocompartment (rhizosphere, rhizoplane, and root) microbiomes of Achyranthes bidentata under different years of consecutive monoculture by deep sequencing in order to determine keystone microorganisms via co-occurrence network analysis. The network analysis showed that multiple consecutive monoculture (MCM, represented 5Y and 10Y) soils generated some distinct beneficial bacterial taxa such as Bacillus, Fictibacillus, Bradyrhizobium, Shinella, and Herbaspirillum. For fungi, Mortierella substituted for Fusarium in occupying an important position in different rhizocompartments under A. bidentate monoculture. Quantitative PCR analysis confirmed a significant increase in Bacillus, Pseudomonas, and Burkholderia spp. The results of the inoculation assay showed that addition of beneficial bacteria Bacillus subtilis 74 and Bacillus halodurans 75 significantly increased the root length and fresh weight of A. bidentata. Furthermore, three types of phytosterones, as the main allochemicals, were identified both in the rhizosphere soil and in culture medium under sterile conditions by LC-MS/MS. When looking at in vitro interactions, it was found that phytosterones displayed a positive interaction with dominant beneficial species (Bacillus amyloliquefaciens 4 and B. halodurans 75) and had a negative effect on the presence of the pathogenic fungi Fusarium solani and Fusarium oxysporum. Overall, this study demonstrated that consecutive monoculture of A. bidentata can alter the bacterial and fungal community by secreting root exudates, leading to recruitment of beneficial microbes and replacement of plant-specific pathogenic fungi with plant beneficial fungi.
Collapse
Affiliation(s)
- Juanying Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hongmiao Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Linkun Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Liu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Puleng Letuma
- Department of Crop Science, National University of Lesotho, Maseru, Lesotho
| | - Xianjin Qin
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ting Chen
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
33
|
Pivato B, Semblat A, Guégan T, Jacquiod S, Martin J, Deau F, Moutier N, Lecomte C, Burstin J, Lemanceau P. Rhizosphere Bacterial Networks, but Not Diversity, Are Impacted by Pea-Wheat Intercropping. Front Microbiol 2021; 12:674556. [PMID: 34127925 PMCID: PMC8195745 DOI: 10.3389/fmicb.2021.674556] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022] Open
Abstract
Plant-plant associations, notably cereal-legume intercropping, have been proposed in agroecology to better value resources and thus reduce the use of chemical inputs in agriculture. Wheat-pea intercropping allows to decreasing the use of nitrogen fertilization through ecological processes such as niche complementarity and facilitation. Rhizosphere microbial communities may account for these processes, since they play a major role in biogeochemical cycles and impact plant nutrition. Still, knowledge on the effect of intecropping on the rhizosphere microbiota remains scarce. Especially, it is an open question whether rhizosphere microbial communities in cereal-legume intercropping are the sum or not of the microbiota of each plant species cultivated in sole cropping. In the present study, we assessed the impact of wheat and pea in IC on the diversity and structure of their respective rhizosphere microbiota. For this purpose, several cultivars of wheat and pea were cultivated in sole and intercropping. Roots of wheat and pea were collected separately in intercropping for microbiota analyses to allow deciphering the effect of IC on the bacterial community of each plant species/cultivar tested. Our data confirmed the well-known specificity of the rhizosphere effect and further stress the differentiation of bacterial communities between pea genotypes (Hr and hr). As regards the intercropping effect, diversity and structure of the rhizosphere microbiota were comparable to sole cropping. However, a specific co-occurrence pattern in each crop rhizosphere due to intercropping was revealed through network analysis. Bacterial co-occurrence network of wheat rhizosphere in IC was dominated by OTUs belonging to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. We also evidenced a common network found in both rhizosphere under IC, indicating the interaction between the plant species; this common network was dominated by Acidobacteria, Alphaproteobacteria, and Bacteroidetes, with three OTUs belonging to Acidobacteria, Betaproteobacteria and Chloroflexi that were identified as keystone taxa. These findings indicate more complex rhizosphere bacterial networks in intercropping. Possible implications of these conclusions are discussed in relation with the functioning of rhizosphere microbiota in intercropping accounting for its beneficial effects.
Collapse
Affiliation(s)
- Barbara Pivato
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | - Amélie Semblat
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | - Thibault Guégan
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | - Samuel Jacquiod
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | | | - Florence Deau
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | - Nathalie Moutier
- IGEPP, INRAE, Institut Agro Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Christophe Lecomte
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | - Judith Burstin
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | - Philippe Lemanceau
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| |
Collapse
|
34
|
Sohn SI, Ahn JH, Pandian S, Oh YJ, Shin EK, Kang HJ, Cho WS, Cho YS, Shin KS. Dynamics of Bacterial Community Structure in the Rhizosphere and Root Nodule of Soybean: Impacts of Growth Stages and Varieties. Int J Mol Sci 2021; 22:5577. [PMID: 34070397 PMCID: PMC8197538 DOI: 10.3390/ijms22115577] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/20/2021] [Accepted: 05/22/2021] [Indexed: 11/17/2022] Open
Abstract
Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max (L.) Merr.). In this report, we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology, respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina sequencing analysis, the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria, and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.
Collapse
Affiliation(s)
- Soo-In Sohn
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (S.P.); (E.-K.S.); (H.-J.K.); (W.-S.C.); (Y.-S.C.)
| | - Jae-Hyung Ahn
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Jeonju 55365, Korea;
| | - Subramani Pandian
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (S.P.); (E.-K.S.); (H.-J.K.); (W.-S.C.); (Y.-S.C.)
| | - Young-Ju Oh
- Institute for Future Environmental Ecology Co., Ltd., Jeonju 54883, Korea;
| | - Eun-Kyoung Shin
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (S.P.); (E.-K.S.); (H.-J.K.); (W.-S.C.); (Y.-S.C.)
| | - Hyeon-Jung Kang
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (S.P.); (E.-K.S.); (H.-J.K.); (W.-S.C.); (Y.-S.C.)
| | - Woo-Suk Cho
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (S.P.); (E.-K.S.); (H.-J.K.); (W.-S.C.); (Y.-S.C.)
| | - Youn-Sung Cho
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (S.P.); (E.-K.S.); (H.-J.K.); (W.-S.C.); (Y.-S.C.)
| | - Kong-Sik Shin
- Audit and Inspection Office, Rural Development of Administration, Jeonju 54875, Korea;
| |
Collapse
|
35
|
The microbial community from the early-plant colonizer (Baccharis linearis) is required for plant establishment on copper mine tailings. Sci Rep 2021; 11:10448. [PMID: 34001948 PMCID: PMC8129112 DOI: 10.1038/s41598-021-89769-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/29/2021] [Indexed: 11/17/2022] Open
Abstract
Plants must deal with harsh environmental conditions when colonizing abandoned copper mine tailings. We hypothesized that the presence of a native microbial community can improve the colonization of the pioneer plant, Baccharis linearis, in soils from copper mining tailings. Plant growth and microbial community compositions and dynamics were determined in cultivation pots containing material from two abandoned copper mining tailings (Huana and Tambillos) and compared with pots containing fresh tailings or surrounding agricultural soil. Controls without plants or using irradiated microbe-free substrates, were also performed. Results indicated that bacteria (Actinobacteria, Gammaproteobacteria, and Firmicutes groups) and fungi (Glomus genus) are associated with B. linearis and may support plant acclimation, since growth parameters decreased in both irradiated (transiently without microbial community) and fresh tailing substrates (with a significantly different microbial community). Consistently, the composition of the bacterial community from abandoned copper mining tailings was more impacted by plant establishment than by differences in the physicochemical properties of the substrates. Bacteria located at B. linearis rhizoplane were clearly the most distinct bacterial community compared with those of fresh tailings, surrounding soil and non-rhizosphere abandoned tailings substrates. Beta diversity analyses showed that the rhizoplane bacterial community changed mainly through species replacement (turnover) than species loss (nestedness). In contrast, location/geographical conditions were more relevant than interaction with the plants, to explain fungal community differences.
Collapse
|
36
|
Fadiji AE, Kanu JO, Babalola OO. Impact of cropping systems on the functional diversity of rhizosphere microbial communities associated with maize plant: a shotgun approach. Arch Microbiol 2021; 203:3605-3613. [PMID: 33973044 DOI: 10.1007/s00203-021-02354-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 01/03/2023]
Abstract
Understanding the functions carried out by rhizosphere microbiomes will further explore their importance in biotechnological improvement and agricultural sustainability. This study presents one of the foremost attempts to understand the functional diversity of the rhizosphere microbiome in mono-cropping and crop rotation farming sites using shotgun metagenomic techniques. We hypothesized that the functional diversity would vary in the cropping sites and more abundant in the rotational cropping site. Hence, we carried out complete DNA extraction from the bulk and rhizospheric soils associated with maize plant cultivated on the mono-cropping farm (LT and LTc) and the crop rotation farm (VD and VDc), respectively, and sequenced employing shotgun approach. Using the SEED subsystem, our result revealed that a total of 24 functional categories dominated the rotational cropping site, while four functional categories dominated the mono-cropping sites. Alpha diversity assessment showed that no significant difference (p > 0.05) was observed across the cropping sites, while beta diversity assessment revealed a significant difference. Going by the high abundance of functional groups observed in the samples from the crop rotational site, it is evident that cropping systems influenced the functions of soil microbiomes. Worthy of note is the high abundance of unknown functions associated with these maize rhizosphere microbiomes. This is an indication that there are still some under-investigated functional genes associated with the maize rhizosphere microbiome. It is, therefore, imperative that further studies explore these functional genes for their agricultural and biotechnological potentials.
Collapse
Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa
| | - Jerry Onyemaechi Kanu
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa.
| |
Collapse
|
37
|
Shahrtash M, Brown SP. A Path Forward: Promoting Microbial-Based Methods in the Control of Invasive Plant Species. PLANTS (BASEL, SWITZERLAND) 2021; 10:943. [PMID: 34065068 PMCID: PMC8151036 DOI: 10.3390/plants10050943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 01/18/2023]
Abstract
In this review, we discuss the unrealized potential of incorporating plant-microbe and microbe-microbe interactions into invasive plant management strategies. While the development of this as a viable strategy is in its infancy, we argue that incorporation of microbial components into management plans should be a priority and has great potential for diversifying sustainable control options. We advocate for increased research into microbial-mediated phytochemical production, microbial controls to reduce the competitiveness of invasive plants, microbial-mediated increases of herbicidal tolerance of native plants, and to facilitate increased pathogenicity of plant pathogens of invasive plants.
Collapse
Affiliation(s)
| | - Shawn P. Brown
- Department of Biological Sciences, The University of Memphis, Memphis, TN 38152, USA;
| |
Collapse
|
38
|
Pankievicz VCS, do Amaral FP, Ané JM, Stacey G. Diazotrophic Bacteria and Their Mechanisms to Interact and Benefit Cereals. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:491-498. [PMID: 33543986 DOI: 10.1094/mpmi-11-20-0316-fi] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plant-growth-promoting bacteria (PGPB) stimulate plant growth through diverse mechanisms. In addition to biological nitrogen fixation, diazotrophic PGPB can improve nutrient uptake efficiency from the soil, produce and release phytohormones to the host, and confer resistance against pathogens. The genetic determinants that drive the success of biological nitrogen fixation in nonlegume plants are understudied. These determinants include recognition and signaling pathways, bacterial colonization, and genotype specificity between host and bacteria. This review presents recent discoveries of how nitrogen-fixing PGPB interact with cereals and promote plant growth. We suggest adopting an experimental model system, such as the Setaria-diazotrophic bacteria association, as a reliable way to better understand the associated mechanisms and, ultimately, increase the use of PGPB inoculants for sustainable agriculture.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
| | - Fernanda Plucani do Amaral
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, U.S.A
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, U.S.A
| |
Collapse
|
39
|
Chouhan GK, Verma JP, Jaiswal DK, Mukherjee A, Singh S, de Araujo Pereira AP, Liu H, Abd Allah EF, Singh BK. Phytomicrobiome for promoting sustainable agriculture and food security: Opportunities, challenges, and solutions. Microbiol Res 2021; 248:126763. [PMID: 33892241 DOI: 10.1016/j.micres.2021.126763] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/24/2021] [Accepted: 03/31/2021] [Indexed: 12/29/2022]
Abstract
Ensuring food security in an environmentally sustainable way is a global challenge. To achieve this agriculture productivity requires increasing by 70 % under increasingly harsh climatic conditions without further damaging the environmental quality (e.g. reduced use of agrochemicals). Most governmental and inter-governmental agencies have highlighted the need for alternative approaches that harness natural resource to address this. Use of beneficial phytomicrobiome, (i.e. microbes intimately associated with plant tissues) is considered as one of the viable solutions to meet the twin challenges of food security and environmental sustainability. A diverse number of important microbes are found in various parts of the plant, i.e. root, shoot, leaf, seed, and flower, which play significant roles in plant health, development and productivity, and could contribute directly to improving the quality and quantity of food production. The phytomicrobiome can also increase productivity via increased resource use efficiency and resilience to biotic and abiotic stresses. In this article, we explore the role of phytomicrobiome in plant health and how functional properties of microbiome can be harnessed to increase agricultural productivity in environmental-friendly approaches. However, significant technical and translation challenges remain such as inconsistency in efficacy of microbial products in field conditions and a lack of tools to manipulate microbiome in situ. We propose pathways that require a system-based approach to realize the potential to phytomicrobiome in contributing towards food security. We suggest if these technical and translation constraints could be systematically addressed, phytomicrobiome can significantly contribute towards the sustainable increase in agriculture productivity and food security.
Collapse
Affiliation(s)
- Gowardhan Kumar Chouhan
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Jay Prakash Verma
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India.
| | - Durgesh Kumar Jaiswal
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Arpan Mukherjee
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Saurabh Singh
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | | | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Locked Bag 1797, Penrith, NSW, 2750, Sydney, Australia
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box. 2460, Riyadh, 11451, Saudi Arabia
| | - Brajesh Kumar Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Locked Bag 1797, Penrith, NSW, 2750, Sydney, Australia; Global Centre for Land-Based Innovation, Western Sydney University, Hawkesbury Campus, Locked Bag 1797, Penrith, NSW, 2750, Sydney, Australia
| |
Collapse
|
40
|
Hernández-Terán A, Navarro-Díaz M, Benítez M, Lira R, Wegier A, Escalante AE. Host genotype explains rhizospheric microbial community composition: the case of wild cotton metapopulations (Gossypium hirsutum L.) in Mexico. FEMS Microbiol Ecol 2021; 96:5850751. [PMID: 32490512 DOI: 10.1093/femsec/fiaa109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 06/01/2020] [Indexed: 01/04/2023] Open
Abstract
The rhizosphere provides several benefits to the plant host being a strong determinant for its health, growth and productivity. Nonetheless, the factors behind the assembly of the microbial communities associated with the rhizosphere such as the role of plant genotypes are not completely understood. In this study, we tested the role that intraspecific genetic variation has in rhizospheric microbial community assemblages, using genetically distinct wild cotton populations as a model of study. We followed a common garden experiment including five wild cotton populations, controlling for plant genotypes, environmental conditions and soil microbial community inoculum, to test for microbial differences associated with genetic variation of the plant hosts. Microbial communities of the treatments were characterized by culture-independent 16S rRNA gene amplicon sequencing with Illumina MiSeq platform. We analyzed microbial community diversity (alpha and beta), and diversity structure of such communities, determined by co-occurrence networks. Results show that different plant genotypes select for different and specific microbial communities from a common inoculum. Although we found common amplicon sequence variants (ASVs) to all plant populations (235), we also found unique ASVs for different populations that could be related to potential functional role of such ASVs in the rhizosphere.
Collapse
Affiliation(s)
- Alejandra Hernández-Terán
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Marcelo Navarro-Díaz
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Rafael Lira
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, 54090, Mexico City, Mexico
| | - Ana Wegier
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Ana E Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| |
Collapse
|
41
|
Song J, Min L, Wu J, He Q, Chen F, Wang Y. Response of the microbial community to phosphate-solubilizing bacterial inoculants on Ulmus chenmoui Cheng in Eastern China. PLoS One 2021; 16:e0247309. [PMID: 33630914 PMCID: PMC7906385 DOI: 10.1371/journal.pone.0247309] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/04/2021] [Indexed: 11/24/2022] Open
Abstract
Phosphate-solubilizing bacteria (PSB) have beneficial effects on plant health and soil composition. To date, studies of PSB in soil have largely been performed under field or greenhouse conditions. However, less is known about the impact of introducing indigenous PSB in the field, including their effects on the local microbial community. In this study, we conducted greenhouse and field experiments to explore the effects of the addition of indigenous PSB on the growth of Chenmou elm (Ulmus chenmoui) and on the diversity and composition of the bacterial community in the soil. We obtained four bacterial isolates with the highest phosphate-solubilizing activity: UC_1 (Pseudomonas sp.), UC_M (Klebsiella sp.), UC_J (Burkholderia sp.), and UC_3 (Chryseobacterium sp.). Sequencing on the Illumina MiSeq platform showed that the inoculated PSB did not become the dominant strains in the U. chenmoui rhizosphere. However, the soil bacterial community structure was altered by the addition of these PSB. The relative abundance of Chloroflexi decreased significantly in response to PSB application in all treatment groups, whereas the populations of several bacteria, including Proteobacteria and Bacteroidetes, increased. Network analysis indicated that Chloroflexi was the most strongly negatively correlated with Proteobacteria, whereas Proteobacteria was strongly positively correlated with Bacteroidetes. Our findings indicate that inoculation with PSB (UC_1, UC_M, UC_J, and UC_3) can improve the growth of U. chenmoui and regulate its rhizosphere microbial community. Therefore, inoculation with these bacterial strains could promote the efficient cultivation and production of high-quality plant materials.
Collapse
Affiliation(s)
- Juan Song
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Institute of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - LiJing Min
- College of Life Science, Huzhou University, Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou, Zhejiang, China
| | - JunRong Wu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Institute of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Qingfang He
- Department of Biology, University of Arkansas at Little Rock, Little Rock, Arkansas, United States of America
| | - FengMao Chen
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Institute of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yang Wang
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Institute of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
42
|
Avitia M, Barrón-Sandoval A, Hernández-Terán A, Benítez M, A Barron-Gafford G, Dontsova K, A Pavao-Zuckerman M, E Escalante A. Soil microbial composition and carbon mineralization are associated with vegetation type and temperature regime in mesocosms of a semiarid ecosystem. FEMS Microbiol Lett 2021; 368:6129800. [PMID: 33547887 DOI: 10.1093/femsle/fnab012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 02/03/2021] [Indexed: 12/21/2022] Open
Abstract
Transition from historic grasslands to woody plants in semiarid regions has led to questions about impacts on soil functioning, where microorganisms play a primary role. Understanding the relationship between microbes, plant diversity and soil functioning is relevant to assess such impacts. We evaluate the effect that plant type change in semiarid ecosystems has for microbial diversity and composition, and how this is related to carbon mineralization (CMIN) as a proxy for soil functioning. We followed a mesocosm experiment during 2 years within the Biosphere 2 facility in Oracle, AZ, USA. Two temperature regimes were established with two types of plants (grass or mesquite). Soil samples were analyzed for physicochemical and functional parameters, as well as microbial community composition using 16S rRNA amplicon metagenomics (Illumina MiSeq). Our results show the combined role of plant type and temperature regime in CMIN, where CMIN in grass has lower values at elevated temperatures compared with the opposite trend in mesquite. We also found a strong correlation of microbial composition with plant type but not with temperature regime. Overall, we provide evidence of the major effect of plant type in the specific composition of microbial communities as a potential result of the shrub encroachment.
Collapse
Affiliation(s)
- Morena Avitia
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Alberto Barrón-Sandoval
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.,Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Alejandra Hernández-Terán
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.,C3, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | | | - Katerina Dontsova
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Mitchell A Pavao-Zuckerman
- Department of Environmental Science and Technology, University of Maryland, College Park, College Park, MD, 20742, USA
| | - Ana E Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| |
Collapse
|
43
|
Wang Y, Liu Y, Li X, Han X, Zhang Z, Ma X, Li J. Potentilla anserina L. developmental changes affect the rhizosphere prokaryotic community. Sci Rep 2021; 11:2838. [PMID: 33531629 PMCID: PMC7854623 DOI: 10.1038/s41598-021-82610-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/22/2021] [Indexed: 11/23/2022] Open
Abstract
Plant roots and soil prokaryotes primarily interact with each other in the rhizosphere. Changes in the rhizosphere prokaryotic structure are influenced by several factors. In this study, the community structure of the Potentilla anserina L. rhizosphere prokaryotes was identified and evaluated by high-throughput sequencing technology in different continuous cropping fields and developmental stages of the plant. In total, 2 archaeal (Euryarchaeota and Thaumarchaeota) and 26 bacterial phyla were identified in the P. anserina rhizosphere. The bacterial community was mainly composed of Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria, and Verrucomicrobia. Moreover, the prokaryotic community structure of the rhizosphere varied significantly during plant development. Our results provide new insights into the dynamics of the P. anserina rhizosphere prokaryotic community and may provide useful information for enhancing the growth and development of P. anserina through artificial control of the soil prokaryotes.
Collapse
Affiliation(s)
- Yaqiong Wang
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China. .,Qinghai Provincial Key Laboratory of High-Value Utilization of Characteristic Economic Plants, Xining, 810007, China. .,Qinghai Provincial Biotechnology and Analytical Test Key Laboratory, Tibetan Plateau Juema Research Centre, Xining, 810007, China.
| | - Yuxi Liu
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China
| | - Xue Li
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China
| | - Xiaoyan Han
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China
| | - Zhen Zhang
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China
| | - Xiaoling Ma
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China
| | - Junqiao Li
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China. .,Qinghai Provincial Key Laboratory of High-Value Utilization of Characteristic Economic Plants, Xining, 810007, China. .,Qinghai Provincial Biotechnology and Analytical Test Key Laboratory, Tibetan Plateau Juema Research Centre, Xining, 810007, China.
| |
Collapse
|
44
|
García-Cabrerizo R, Carbia C, O Riordan KJ, Schellekens H, Cryan JF. Microbiota-gut-brain axis as a regulator of reward processes. J Neurochem 2021; 157:1495-1524. [PMID: 33368280 DOI: 10.1111/jnc.15284] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/08/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022]
Abstract
Our gut harbours trillions of microorganisms essential for the maintenance of homeostasis and host physiology in health and disease. In the last decade, there has been a growing interest in understanding the bidirectional pathway of communication between our microbiota and the central nervous system. With regard to reward processes there is accumulating evidence from both animal and human studies that this axis may be a key factor in gating reward valence. Focusing on the mesocorticolimbic pathway, we will discuss how the intestinal microbiota is involved in regulating brain reward functions, both in natural (i.e. eating, social or sexual behaviours) and non-natural reinforcers (drug addiction behaviours including those relevant to alcohol, psychostimulants, opioids and cannabinoids). We will integrate preclinical and clinical evidence suggesting that the microbiota-gut-brain axis could be implicated in the development of disorders associated with alterations in the reward system and how it may be targeted as a promising therapeutic strategy. Cover Image for this issue: https://doi.org/10.1111/jnc.15065.
Collapse
Affiliation(s)
| | - Carina Carbia
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Harriet Schellekens
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| |
Collapse
|
45
|
Weigh KV, Batista BD, Dennis PG. A Bait-Trap Assay to Characterize Soil Microbes that Exhibit Chemotaxis to Root Exudates. Methods Mol Biol 2021; 2232:283-289. [PMID: 33161554 DOI: 10.1007/978-1-0716-1040-4_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Here, we describe a novel "bait-trap" assay, which facilitates capture of soil microorganisms that exhibit chemotaxis to chemical attractants, such as root exudates. These multi-population assemblages represent potential guilds and can be characterized using a wide-range of culture-dependent and culture-independent methods. While in this example, we use root exudates as bait, any water-soluble compound(s) could be used. Hence, the potential applications for the assay are diverse.
Collapse
Affiliation(s)
- Katherine V Weigh
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Bruna D Batista
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia.
| |
Collapse
|
46
|
Vishwakarma K, Kumar N, Shandilya C, Mohapatra S, Bhayana S, Varma A. Revisiting Plant-Microbe Interactions and Microbial Consortia Application for Enhancing Sustainable Agriculture: A Review. Front Microbiol 2020; 11:560406. [PMID: 33408698 PMCID: PMC7779480 DOI: 10.3389/fmicb.2020.560406] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
The present scenario of agricultural sector is dependent hugely on the use of chemical-based fertilizers and pesticides that impact the nutritional quality, health status, and productivity of the crops. Moreover, continuous release of these chemical inputs causes toxic compounds such as metals to accumulate in the soil and move to the plants with prolonged exposure, which ultimately impact the human health. Hence, it becomes necessary to bring out the alternatives to chemical pesticides/fertilizers for improvement of agricultural outputs. The rhizosphere of plant is an important niche with abundant microorganisms residing in it. They possess the properties of plant growth promotion, disease suppression, removal of toxic compounds, and assimilating nutrients to plants. Utilizing such beneficial microbes for crop productivity presents an efficient way to modulate the crop yield and productivity by maintaining healthy status and quality of the plants through bioformulations. To understand these microbial formulation compositions, it becomes essential to understand the processes going on in the rhizosphere as well as their concrete identification for better utilization of the microbial diversity such as plant growth–promoting bacteria and arbuscular mycorrhizal fungi. Hence, with this background, the present review article highlights the plant microbiome aboveground and belowground, importance of microbial inoculants in various plant species, and their subsequent interactive mechanisms for sustainable agriculture.
Collapse
Affiliation(s)
| | - Nitin Kumar
- Department of Biotechnology, Periyar Maniammai Institute of Science and Technology, Thanjavur, India
| | | | - Swati Mohapatra
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Sahil Bhayana
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University, Noida, India
| |
Collapse
|
47
|
Ray P, Lakshmanan V, Labbé JL, Craven KD. Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture. Front Microbiol 2020; 11:622926. [PMID: 33408712 PMCID: PMC7779556 DOI: 10.3389/fmicb.2020.622926] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022] Open
Abstract
Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.
Collapse
Affiliation(s)
- Prasun Ray
- Noble Research Institute, LLC, Ardmore, OK, United States
| | | | - Jessy L. Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | |
Collapse
|
48
|
Chen M, Tong H, Qiao J, Lv Y, Jiang Q, Gao Y, Liu C. Microbial community response to the toxic effect of pentachlorophenol in paddy soil amended with an electron donor and shuttle. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 205:111328. [PMID: 32950805 DOI: 10.1016/j.ecoenv.2020.111328] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/21/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
Understanding the degradation of pentachlorophenol (PCP) by indigenous microorganisms stimulated by an electron donor and shuttle in paddy soil, and the influences of PCP/electron donor/shuttle on the native microbial community are important for biodegradation and ecological and environmental safety. Previous studies focused on the kinetics and the microbial actions of PCP degradation, however, the effects of toxic and antimicrobial PCP and electron donor/shuttle on the microbial community diversity and composition in paddy soil are poorly understood. In this study, the effects of PCP, an electron donor (lactate), and the electron shuttle (anthraquinone-2, 6-disulfonate, AQDS) on the microbial community in paddy soil were investigated. The results showed that the presence of PCP reduced the microbial diversity compared to the control during PCP degradation, while increased the microbial diversity was observed in response to lactate and AQDS. The addition of PCP stimulated the microorganisms involved in PCP dechlorination, including Clostridium, Desulfitobacterium, Pandoraea, and unclassified Veillonellaceae, which were dormant in raw soil without PCP stress. In all of the treatments with PCP, the addition of lactate or AQDS enhanced PCP dechlorination by stimulating the growth of functional groups involved in PCP dechlorination and by changing the microbial community during dechlorination process. The microbial community tended to be uniform after complete PCP degradation (28 days). However, when lactate and AQDS were present simultaneously in PCP-contaminated soil, lactate acted as a carbon source or electron donor to promote the activities of microbial community, and AQDS changed the redox potential because of the production of reduced AQDS. These findings enhance our understanding of the effect of PCP and a biostimulation method for PCP biodegradation in soil ecosystems at the microbial community level, and suggest the appropriate selection of an electron donor/shuttle for accelerating the bioremediation of PCP-contaminated soils.
Collapse
Affiliation(s)
- Manjia Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Science, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China
| | - Hui Tong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Science, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China
| | - Jiangtao Qiao
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Science, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China
| | - Yahui Lv
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Science, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China
| | - Qi Jiang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Science, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China
| | - Yuanxue Gao
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Science, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China
| | - Chengshuai Liu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Science, Guangzhou, 510650, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, 510650, China; State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China.
| |
Collapse
|
49
|
Acharya B, Ingram TW, Oh Y, Adhikari TB, Dean RA, Louws FJ. Opportunities and Challenges in Studies of Host-Pathogen Interactions and Management of Verticillium dahliae in Tomatoes. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1622. [PMID: 33266395 PMCID: PMC7700276 DOI: 10.3390/plants9111622] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/14/2022]
Abstract
Tomatoes (Solanum lycopersicum L.) are a valuable horticultural crop that are grown and consumed worldwide. Optimal production is hindered by several factors, among which Verticillium dahliae, the cause of Verticillium wilt, is considered a major biological constraint in temperate production regions. V. dahliae is difficult to mitigate because it is a vascular pathogen, has a broad host range and worldwide distribution, and can persist in soil for years. Understanding pathogen virulence and genetic diversity, host resistance, and plant-pathogen interactions could ultimately inform the development of integrated strategies to manage the disease. In recent years, considerable research has focused on providing new insights into these processes, as well as the development and integration of environment-friendly management approaches. Here, we discuss the current knowledge on the race and population structure of V. dahliae, including pathogenicity factors, host genes, proteins, enzymes involved in defense, and the emergent management strategies and future research directions for managing Verticillium wilt in tomatoes.
Collapse
Affiliation(s)
- Bhupendra Acharya
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - Thomas W. Ingram
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - YeonYee Oh
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - Ralph A. Dean
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - Frank J. Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| |
Collapse
|
50
|
Rossmann M, Pérez-Jaramillo JE, Kavamura VN, Chiaramonte JB, Dumack K, Fiore-Donno AM, Mendes LW, Ferreira MMC, Bonkowski M, Raaijmakers JM, Mauchline TH, Mendes R. Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists. FEMS Microbiol Ecol 2020; 96:5775476. [PMID: 32124916 DOI: 10.1093/femsec/fiaa032] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/28/2020] [Indexed: 11/14/2022] Open
Abstract
Plants modulate the soil microbiota by root exudation assembling a complex rhizosphere microbiome with organisms spanning different trophic levels. Here, we assessed the diversity of bacterial, fungal and cercozoan communities in landraces and modern varieties of wheat. The dominant taxa within each group were the bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria; the fungi phyla Ascomycota, Chytridiomycota and Basidiomycota; and the Cercozoa classes Sarcomonadea, Thecofilosea and Imbricatea. We showed that microbial networks of the wheat landraces formed a more intricate network topology than that of modern wheat cultivars, suggesting that breeding selection resulted in a reduced ability to recruit specific microbes in the rhizosphere. The high connectedness of certain cercozoan taxa to bacteria and fungi indicated trophic network hierarchies where certain predators gain predominance over others. Positive correlations between protists and bacteria in landraces were preserved as a subset in cultivars as was the case for the Sarcomonadea class with Actinobacteria. The correlations between the microbiome structure and plant genotype observed in our results suggest the importance of top-down control by organisms of higher trophic levels as a key factor for understanding the drivers of microbiome community assembly in the rhizosphere.
Collapse
Affiliation(s)
- Maike Rossmann
- Laboratory of Environmental Microbiology, Embrapa Environment, Rodovia SP 340 km 125.5, 13918-110, Jaguariúna SP, Brazil
| | - Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW); Institute of Biology, Leiden University, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Vanessa N Kavamura
- Sustainable Agriculture Sciences, West Common, AL5 2JQ, Harpenden, Rothamsted Research, UK
| | - Josiane B Chiaramonte
- Laboratory of Environmental Microbiology, Embrapa Environment, Rodovia SP 340 km 125.5, 13918-110, Jaguariúna SP, Brazil
| | - Kenneth Dumack
- Institute of Zoology & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Anna Maria Fiore-Donno
- Institute of Zoology & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Lucas W Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo, Av. Centenário, 303, 13416-000, Piracicaba SP, Brazil
| | - Márcia M C Ferreira
- Laboratory of Theoretical and Applied Chemometrics, Department of Chemistry, State University of Campinas (UNICAMP), Rua Josué de Castro, s/n, 13083-970, Campinas SP, Brazil
| | - Michael Bonkowski
- Institute of Zoology & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW); Institute of Biology, Leiden University, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Tim H Mauchline
- Sustainable Agriculture Sciences, West Common, AL5 2JQ, Harpenden, Rothamsted Research, UK
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Rodovia SP 340 km 125.5, 13918-110, Jaguariúna SP, Brazil
| |
Collapse
|