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Baker NR, Zhalnina K, Yuan M, Herman D, Ceja-Navarro JA, Sasse J, Jordan JS, Bowen BP, Wu L, Fossum C, Chew A, Fu Y, Saha M, Zhou J, Pett-Ridge J, Northen TR, Firestone MK. Nutrient and moisture limitations reveal keystone metabolites linking rhizosphere metabolomes and microbiomes. Proc Natl Acad Sci U S A 2024; 121:e2303439121. [PMID: 39093948 PMCID: PMC11317588 DOI: 10.1073/pnas.2303439121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/03/2024] [Indexed: 08/04/2024] Open
Abstract
Plants release a wealth of metabolites into the rhizosphere that can shape the composition and activity of microbial communities in response to environmental stress. The connection between rhizodeposition and rhizosphere microbiome succession has been suggested, particularly under environmental stress conditions, yet definitive evidence is scarce. In this study, we investigated the relationship between rhizosphere chemistry, microbiome dynamics, and abiotic stress in the bioenergy crop switchgrass grown in a marginal soil under nutrient-limited, moisture-limited, and nitrogen (N)-replete, phosphorus (P)-replete, and NP-replete conditions. We combined 16S rRNA amplicon sequencing and LC-MS/MS-based metabolomics to link rhizosphere microbial communities and metabolites. We identified significant changes in rhizosphere metabolite profiles in response to abiotic stress and linked them to changes in microbial communities using network analysis. N-limitation amplified the abundance of aromatic acids, pentoses, and their derivatives in the rhizosphere, and their enhanced availability was linked to the abundance of bacterial lineages from Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. Conversely, N-amended conditions increased the availability of N-rich rhizosphere compounds, which coincided with proliferation of Actinobacteria. Treatments with contrasting N availability differed greatly in the abundance of potential keystone metabolites; serotonin and ectoine were particularly abundant in N-replete soils, while chlorogenic, cinnamic, and glucuronic acids were enriched in N-limited soils. Serotonin, the keystone metabolite we identified with the largest number of links to microbial taxa, significantly affected root architecture and growth of rhizosphere microorganisms, highlighting its potential to shape microbial community and mediate rhizosphere plant-microbe interactions.
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Affiliation(s)
- Nameer R. Baker
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA94720
| | - Kateryna Zhalnina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Mengting Yuan
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA94720
| | - Don Herman
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA94720
| | - Javier A. Ceja-Navarro
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ86011
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Joelle Sasse
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Institute for Plant and Microbial Biology, University of Zurich, CH-8008Zurich, Switzerland
| | - Jacob S. Jordan
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Department of Chemistry, University of California, Berkeley, CA94720
| | - Benjamin P. Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK73019
| | - Christina Fossum
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA94720
| | - Aaron Chew
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA94720
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA94550
| | - Ying Fu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK73019
| | - Malay Saha
- Noble Research Institute, Ardmore, OK73401
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK73019
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA94550
- Life and Environmental Sciences Department, University of California Merced, Merced, CA95343
| | - Trent R. Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Mary K. Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA94720
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Pal G, Saxena S, Kumar K, Verma A, Kumar D, Shukla P, Pandey A, White J, Verma SK. Seed endophytic bacterium Lysinibacillus sp. (ZM1) from maize (Zea mays L.) shapes its root architecture through modulation of auxin biosynthesis and nitrogen metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108731. [PMID: 38761545 DOI: 10.1016/j.plaphy.2024.108731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/25/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Seed endophytic bacteria have been shown to promote the growth and development of numerous plants. However, the underlying mechanism still needs to be better understood. The present study aims to investigate the role of a seed endophytic bacterium Lysinibacillus sp. (ZM1) in promoting plant growth and shaping the root architecture of maize seedlings. The study explores how bacteria-mediated auxin biosynthesis and nitrogen metabolism affect plant growth promotion and shape the root architecture of maize seedlings. The results demonstrate that ZM1 inoculation significantly enhances root length, root biomass, and the number of seminal roots in maize seedlings. Additionally, the treated seedlings exhibit increased shoot biomass and higher levels of photosynthetic pigments. Confocal laser scanning microscopy (CLSM) analysis revealed extensive colonization of ZM1 on root hairs, as well as in the cortical and stellar regions of the root. Furthermore, LC-MS analysis demonstrated elevated auxin content in the roots of the ZM1 treated maize seedlings compared to the uninoculated control. Inoculation with ZM1 significantly increased the levels of endogenous ammonium content, GS, and GOGAT enzyme activities in the roots of treated maize seedlings compared to the control, indicating enhanced nitrogen metabolism. Furthermore, inoculation of bacteria under nitrogen-deficient conditions enhanced plant growth, as evidenced by increased root shoot length, fresh and dry weights, average number of seminal roots, and content of photosynthetic pigments. Transcript analysis indicated upregulation of auxin biosynthetic genes, along with genes involved in nitrogen metabolism at different time points in roots of ZM1-treated maize seedlings. Collectively, our findings highlight the positive impact of Lysinibacillus sp. ZM1 inoculation on maize seeds by improving root architecture through modulation of auxin biosynthesis and affecting various nitrogen metabolism related parameters. These findings provide valuable insights into the potential utilization of seed endophytic bacteria as biofertilizers to enhance plant growth and yield in nutrient deficient soils.
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Affiliation(s)
- Gaurav Pal
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 276957612, USA.
| | - Samiksha Saxena
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kanchan Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Anand Verma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Deepak Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Pooja Shukla
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - James White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA
| | - Satish K Verma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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3
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Chi Z, Li Y, Zhang J, Hu M, Wu Y, Fan X, Li Z, Miao Q, Li W. Effects of nitrogen application on ammonium assimilation and microenvironment in the rhizosphere of drip-irrigated sunflower under plastic mulch. Front Microbiol 2024; 15:1390331. [PMID: 38841064 PMCID: PMC11150556 DOI: 10.3389/fmicb.2024.1390331] [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: 02/23/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
This study investigated the effect of nitrogen application on the rhizosphere soil microenvironment of sunflower and clarified the relationship between ammonium assimilation and the microenvironment. In a field experiment high (HN, 190 kg/hm2), medium (MN, 120 kg/hm2) and low nitrogen (CK, 50 kg/hm2) treatments were made to replicate plots of sunflowers using drip irrigation. Metagenomic sequencing was used to analyze the community structure and functional genes involved in the ammonium assimilation pathway in rhizosphere soil. The findings indicated that glnA and gltB played a crucial role in the ammonium assimilation pathway in sunflower rhizosphere soil, with Actinobacteria and Proteobacteria being the primary contributors. Compared with CK treatment, the relative abundance of Actinobacteria increased by 15.57% under MN treatment, while the relative abundance decreased at flowering and maturation stages. Conversely, the relative abundance of Proteobacteria was 28.57 and 61.26% higher in the MN treatment during anthesis and maturation period, respectively, compared with the CK. Furthermore, during the bud stage and anthesis, the abundance of Actinobacteria, Proteobacteria, and their dominant species were influenced mainly by rhizosphere soil EC, ammonium nitrogen (NH 4 + -N), and nitrate nitrogen (NO 3 - -N), whereas, at maturity, soil pH and NO 3 - -N played a more significant role in shaping the community of ammonium-assimilating microorganisms. The MN treatment increased the root length density, surface area density, and root volume density of sunflower at the bud, flowering, and maturity stages compared to the CK. Moreover, root exudates such as oxalate and malate were positively correlated with the dominant species of Actinobacteria and Proteobacteria during anthesis and the maturation period. Under drip irrigation, applying 120 kg/hm2 of nitrogen to sunflowers effectively promoted the community structure of ammonium-assimilating microorganisms in rhizosphere soil and had a positive influence on the rhizosphere soil microenvironment and sunflower root growth.
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Affiliation(s)
- Zhaonan Chi
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuxin Li
- Inner Mongolia Key Lab of Molecular Biology, Inner Mongolia Medical University, Hohhot, China
| | - Jiapeng Zhang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Min Hu
- Vocational and Technical College of Inner Mongolia Agricultural University, Baotou, China
| | - Yixuan Wu
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Xueqin Fan
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhen Li
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Qingfeng Miao
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Weiping Li
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, China
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Tong J, Wu H, Jiang X, Wang J, Pang J, Zhang H, Xin Z, Shi J. The colonization of Penicillium oxalicum SL2 on rice root surface increased Pb interception capacity of iron plaque and decreased Pb uptake by roots. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 925:171770. [PMID: 38499093 DOI: 10.1016/j.scitotenv.2024.171770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/21/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
The exploration of microbial resources to reduce Pb accumulation in rice attracted great attention. In this study, we found Penicillium oxalicum SL2, a Pb-tolerant strain with good capability of dissolving phosphorus and stabilizing Pb in soil, was able to colonize on the root surface of rice seedlings without additional carbon sources, and promoted the secretion of metabolites related to amino acid metabolism, organic acid metabolism, signal transduction and other pathways in rhizosphere exudates, in which the secretion of oxalate increased by 47.7 %. However, P. oxalicum SL2 increased Fe(II) proportion and Fe availability on the root surface, resulting in iron plaque content decrease. Moreover, by converting root surface Pb from Pb-Fe state to PbC2O4 and Pb-P compounds, P. oxalicum SL2 increased Pb intercept capacity of iron plaque by 118.0 %. Furthermore, P. oxalicum SL2 regulated element distribution on the root surface, and reduced the relative content of Pb on the maturation zone of root tip, which was conducive to reducing Pb uptake by apoplastic pathway and the risk of Pb accumulation in root system. Our findings further revealed the interaction between P. oxalicum SL2 and rice root, providing a theoretical basis for the development and application of microbial agents in Pb-contaminated farmland.
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Affiliation(s)
- Jianhao Tong
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hanxin Wu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaohan Jiang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jing Wang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jingli Pang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Haonan Zhang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ziming Xin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiyan Shi
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Jin T, Ren J, Bai B, Wu W, Cao Y, Meng J, Zhang L. Effects of Klebsiella michiganensis LDS17 on Codonopsis pilosula growth, rhizosphere soil enzyme activities, and microflora, and genome-wide analysis of plant growth-promoting genes. Microbiol Spectr 2024; 12:e0405623. [PMID: 38563743 PMCID: PMC11064500 DOI: 10.1128/spectrum.04056-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Codonopsis pilosula is a perennial herbaceous liana with medicinal value. It is critical to promote Codonopsis pilosula growth through effective and sustainable methods, and the use of plant growth-promoting bacteria (PGPB) is a promising candidate. In this study, we isolated a PGPB, Klebsiella michiganensis LDS17, that produced a highly active 1-aminocyclopropane-1-carboxylate deaminase from the Codonopsis pilosula rhizosphere. The strain exhibited multiple plant growth-promoting properties. The antagonistic activity of strain LDS17 against eight phytopathogenic fungi was investigated, and the results showed that strain LDS17 had obvious antagonistic effects on Rhizoctonia solani, Colletotrichum camelliae, Cytospora chrysosperma, and Phomopsis macrospore with growth inhibition rates of 54.22%, 49.41%, 48.89%, and 41.11%, respectively. Inoculation of strain LDS17 not only significantly increased the growth of Codonopsis pilosula seedlings but also increased the invertase and urease activities, the number of culturable bacteria, actinomycetes, and fungi, as well as the functional diversity of microbial communities in the rhizosphere soil of the seedlings. Heavy metal (HM) resistance tests showed that LDS17 is resistant to copper, zinc, and nickel. Whole-genome analysis of strain LDS17 revealed the genes involved in IAA production, siderophore synthesis, nitrogen fixation, P solubilization, and HM resistance. We further identified a gene (koyR) encoding a plant-responsive LuxR solo in the LDS17 genome. Klebsiella michiganensis LDS17 may therefore be useful in microbial fertilizers for Codonopsis pilosula. The identification of genes related to plant growth and HM resistance provides an important foundation for future analyses of the molecular mechanisms underlying the plant growth promotion and HM resistance of LDS17. IMPORTANCE We comprehensively evaluated the plant growth-promoting characteristics and heavy metal (HM) resistance ability of the LDS17 strain, as well as the effects of strain LDS17 inoculation on the Codonopsis pilosula seedling growth and the soil qualities in the Codonopsis pilosula rhizosphere. We conducted whole-genome analysis and identified lots of genes and gene clusters contributing to plant-beneficial functions and HM resistance, which is critical for further elucidating the plant growth-promoting mechanism of strain LDS17 and expanding its application in the development of plant growth-promoting agents used in the environment under HM stress.
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Affiliation(s)
- Tingting Jin
- Department of Life Sciences, Changzhi University, Changzhi, China
| | - Jiahong Ren
- Department of Life Sciences, Changzhi University, Changzhi, China
| | - Bianxia Bai
- Department of Life Sciences, Changzhi University, Changzhi, China
| | - Wei Wu
- Department of Life Sciences, Changzhi University, Changzhi, China
| | - Yongqing Cao
- Department of Life Sciences, Changzhi University, Changzhi, China
| | - Jing Meng
- Department of Life Sciences, Changzhi University, Changzhi, China
| | - Lihui Zhang
- Department of Life Sciences, Changzhi University, Changzhi, China
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Zouagui R, Zouagui H, Aurag J, Ibrahimi A, Sbabou L. Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere. BMC Genomics 2024; 25:289. [PMID: 38500021 PMCID: PMC10946135 DOI: 10.1186/s12864-024-10088-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/03/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted. RESULTS Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera. CONCLUSIONS The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.
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Affiliation(s)
- Rahma Zouagui
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Houda Zouagui
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Jamal Aurag
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Laila Sbabou
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
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Blanco-Romero E, Garrido-Sanz D, Durán D, Rybtke M, Tolker-Nielsen T, Redondo-Nieto M, Rivilla R, Martín M. Role of extracellular matrix components in biofilm formation and adaptation of Pseudomonas ogarae F113 to the rhizosphere environment. Front Microbiol 2024; 15:1341728. [PMID: 38333580 PMCID: PMC10850567 DOI: 10.3389/fmicb.2024.1341728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/11/2024] [Indexed: 02/10/2024] Open
Abstract
Regulating the transition of bacteria from motile to sessile lifestyles is crucial for their ability to compete effectively in the rhizosphere environment. Pseudomonas are known to rely on extracellular matrix (ECM) components for microcolony and biofilm formation, allowing them to adapt to a sessile lifestyle. Pseudomonas ogarae F113 possesses eight gene clusters responsible for the production of ECM components. These gene clusters are tightly regulated by AmrZ, a major transcriptional regulator that influences the cellular levels of c-di-GMP. The AmrZ-mediated transcriptional regulation of ECM components is primarily mediated by the signaling molecule c-di-GMP and the flagella master regulator FleQ. To investigate the functional role of these ECM components in P. ogarae F113, we performed phenotypic analyses using mutants in genes encoding these ECM components. These analyses included assessments of colony morphology, dye-staining, static attachment to abiotic surfaces, dynamic biofilm formation on abiotic surfaces, swimming motility, and competitive colonization assays of the rhizosphere. Our results revealed that alginate and PNAG polysaccharides, along with PsmE and the fimbrial low molecular weight protein/tight adherence (Flp/Tad) pilus, are the major ECM components contributing to biofilm formation. Additionally, we found that the majority of these components and MapA are needed for a competitive colonization of the rhizosphere in P. ogarae F113.
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Affiliation(s)
- Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - David Durán
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Morten Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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Guo Z, Qin Y, Lv J, Wang X, Ye T, Dong X, Du N, Zhang T, Piao F, Dong H, Shen S. High red/far-red ratio promotes root colonization of Serratia plymuthica A21-4 in tomato by root exudates-stimulated chemotaxis and biofilm formation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108245. [PMID: 38064903 DOI: 10.1016/j.plaphy.2023.108245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/08/2023] [Accepted: 11/27/2023] [Indexed: 02/15/2024]
Abstract
Effective colonization on plant roots is a prerequisite for plant growth promoting rhizobacterias (PGPR) to exert beneficial activities. Light is essential for plant growth, development and stress response. However, how light modulates root colonization of PGPR remains unclear. Here, we found that high red/far red (R/FR) light promoted and low R/FR light inhibited the colonization and growth enhancement of Serratia plymuthica A21-4 (S. plymuthica A21-4) on tomato, respectively. Non-targeted metabolomic analysis of root exudates collected from different R/FR ratio treated tomato seedlings with or without S. plymuthica A21-4 inoculation by UPLC-MS/MS showed that 64 primary metabolites in high R/FR light-grown plants significantly increased compared with those determined for low R/FR light-grown plants. Among them, 7 amino acids, 1 organic acid and 1 sugar obviously induced the chemotaxis and biofilm formation of S. plymuthica A21-4 compared to the control. Furthermore, exogenous addition of five artificial root exudate compontents (leucine, methionine, glutamine, 6-aminocaproic acid and melezitose) regained and further increased the colonization ability and growth promoting ability of S. plymuthica A21-4 on tomato under low R/FR light and high R/FR light, respectively, indicating their involvement in high R/FR light-regulated the interaction of tomato root and S. plymuthica A21-4. Taken together, our results, for the first time, clearly demonstrate that high R/FR light-induced root exudates play a key role in chemotaxis, biofilm formation and root colonization of S. plymuthica A21-4. This study can help promote the combined application of light supplementation and PGPR to facilitate crop growth and health in green agricultural production.
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Affiliation(s)
- Zhixin Guo
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China; International Joint Laboratory of Henan Horticultural Crop Biology, Henan Provincial Facility Horticulture Engineering Technology Research Center, Zhengzhou, 450046, PR China
| | - Yanping Qin
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Jingli Lv
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Xiaojie Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Ting Ye
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Xiaoxing Dong
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Nanshan Du
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Tao Zhang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Fengzhi Piao
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Han Dong
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China; International Joint Laboratory of Henan Horticultural Crop Biology, Henan Provincial Facility Horticulture Engineering Technology Research Center, Zhengzhou, 450046, PR China.
| | - Shunshan Shen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450046, PR China.
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Tienda S, Gutiérrez-Barranquero JA, Padilla-Roji I, Arrebola E, de Vicente A, Cazorla FM. Polyhydroxyalkanoate production by the plant beneficial rhizobacterium Pseudomonas chlororaphis PCL1606 influences survival and rhizospheric performance. Microbiol Res 2024; 278:127527. [PMID: 37863020 DOI: 10.1016/j.micres.2023.127527] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/22/2023]
Abstract
Pseudomonas chlororaphis PCL1606 (PcPCL1606) is a model rhizobacterium used to study beneficial bacterial interactions with the plant rhizosphere. Many of its beneficial phenotypes depend on the production of the antifungal compound 2-hexyl, 5-propyl resorcinol (HPR). Transcriptomic analysis of PcPCL1606 and the deletional mutant in HPR production ΔdarB strain, assigned an additional regulatory role to HPR, and allowed the detection of differentially expressed genes during the bacterial interaction with the avocado rhizosphere. Interestingly, the putative genes phaG (PCL1606_46820) and phaI (PCL1606_56560), with a predicted role in polyhydroxyalkanoate biosynthesis, were detected to be under HPR control. Both putative genes were expressed in the HPR-producing wild-type strain, but strongly repressed in the derivative mutant ΔdarB, impaired in HPR production. Thus, a derivative mutant impaired in the phaG gene was constructed, characterized and compared with the wild-type strain PcPCL1606 and with the derivative mutant ΔdarB. The phaG mutant had strongly reduced PHA production by PcPCL1606, and displayed altered phenotypes involved in bacterial survival on the plant roots, such as tolerance to high temperature and hydrogen peroxide, and decreased root survival, in a similar way that the ΔdarB mutant. On the other hand, the phaG mutant does not have altered resistance to desiccation, motility, biofilm formation or adhesion phenotypes, as displayed by the HPR-defective ΔdarB mutant have. Interestingly, the mutant defective in PHA production also lacked a biocontrol phenotype against the soilborne pathogenic fungus Rosellinia necatrix, even when the derivative mutant still produced the antifungal HPR compound, demonstrating that the final biocontrol phenotype of PcPCL1606 first requires bacterial survival and adaptation traits to the soil and rhizosphere environment.
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Affiliation(s)
- Sandra Tienda
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, 29071 Málaga, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, 29010 Málaga, Spain
| | - José Antonio Gutiérrez-Barranquero
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, 29071 Málaga, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, 29010 Málaga, Spain
| | - Isabel Padilla-Roji
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, 29071 Málaga, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, 29010 Málaga, Spain
| | - Eva Arrebola
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, 29071 Málaga, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, 29010 Málaga, Spain
| | - Antonio de Vicente
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, 29071 Málaga, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, 29010 Málaga, Spain
| | - Francisco M Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, 29071 Málaga, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, 29010 Málaga, Spain.
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Webster G, Mullins AJ, Petrova YD, Mahenthiralingam E. Polyyne-producing Burkholderia suppress Globisporangium ultimum damping-off disease of Pisum sativum (pea). Front Microbiol 2023; 14:1240206. [PMID: 37692405 PMCID: PMC10485841 DOI: 10.3389/fmicb.2023.1240206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
Extensive crop losses are caused by oomycete and fungal damping-off diseases. Agriculture relies heavily on chemical pesticides to control disease, but due to safety concerns multiple agents have been withdrawn. Burkholderia were successfully used as commercial biopesticides because of their fungicidal activity and plant protective traits. However, their potential for opportunistic pathogenicity led to a moratorium on their registration as biopesticides. Subsequently, Burkholderia were shown to produce multiple specialised metabolites including potent antimicrobial polyynes. Cepacin A, a polyyne produced by Burkholderia ambifaria biopesticide strains was shown to be an important metabolite for the protection of germinating peas against Globisporangium ultimum (formerly Pythium) damping-off disease. Recently, there has been an expansion in bacterial polyyne discovery, with the metabolites and their biosynthetic gene pathways found in several bacterial genera including Burkholderia, Collimonas, Trinickia, and Pseudomonas. To define the efficacy of these bacterial polyyne producers as biopesticidal agents, we systematically evaluated metabolite production, in vitro microbial antagonism, and G. ultimum biocontrol across a panel of 30 strains representing four bacterial genera. In vitro polyyne production and antimicrobial activity was demonstrated for most strains, but only Burkholderia polyyne producers were protective within the in vivo G. ultimum damping-off pea protection model. B. ambifaria was the most effective cepacin-expressing biopesticide, and despite their known potential for plant pathogenicity Burkholderia gladioli and Burkholderia plantarii were uniquely shown to be protective as caryoynencin-producing biopesticides. In summary, Burkholderia are effective biopesticides due to their suite of antimicrobials, but the ability to deploy polyyne metabolites, caryoynencin and cepacin, is strain and species dependent. Graphical Abstract.
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Liu Y, Shu X, Chen L, Zhang H, Feng H, Sun X, Xiong Q, Li G, Xun W, Xu Z, Zhang N, Pieterse CMJ, Shen Q, Zhang R. Plant commensal type VII secretion system causes iron leakage from roots to promote colonization. Nat Microbiol 2023; 8:1434-1449. [PMID: 37248429 DOI: 10.1038/s41564-023-01402-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 05/04/2023] [Indexed: 05/31/2023]
Abstract
Competition for iron is an important factor for microbial niche establishment in the rhizosphere. Pathogenic and beneficial symbiotic bacteria use various secretion systems to interact with their hosts and acquire limited resources from the environment. Bacillus spp. are important plant commensals that encode a type VII secretion system (T7SS). However, the function of this secretion system in rhizobacteria-plant interactions is unclear. Here we use the beneficial rhizobacterium Bacillus velezensis SQR9 to show that the T7SS and the major secreted protein YukE are critical for root colonization. In planta experiments and liposome-based experiments demonstrate that secreted YukE inserts into the plant plasma membrane and causes root iron leakage in the early stage of inoculation. The increased availability of iron promotes root colonization by SQR9. Overall, our work reveals a previously undescribed role of the T7SS in a beneficial rhizobacterium to promote colonization and thus plant-microbe interactions.
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Affiliation(s)
- Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China (the Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xia Shu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China (the Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, P.R. China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lin Chen
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, P. R. China
| | - Huihui Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Haichao Feng
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Xiting Sun
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China (the Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qin Xiong
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China (the Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guangqi Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China (the Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weibing Xun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Ruifu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China (the Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, P.R. China.
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Bhattacharyya A, Mavrodi O, Bhowmik N, Weller D, Thomashow L, Mavrodi D. Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions. METHODS IN MICROBIOLOGY 2023; 53:3-48. [PMID: 38415193 PMCID: PMC10898258 DOI: 10.1016/bs.mim.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Affiliation(s)
- Ankita Bhattacharyya
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Olga Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Niladri Bhowmik
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - David Weller
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda Thomashow
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Dmitri Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
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Blanco-Romero E, Durán D, Garrido-Sanz D, Redondo-Nieto M, Martín M, Rivilla R. Adaption of Pseudomonas ogarae F113 to the Rhizosphere Environment-The AmrZ-FleQ Hub. Microorganisms 2023; 11:microorganisms11041037. [PMID: 37110460 PMCID: PMC10146422 DOI: 10.3390/microorganisms11041037] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Motility and biofilm formation are two crucial traits in the process of rhizosphere colonization by pseudomonads. The regulation of both traits requires a complex signaling network that is coordinated by the AmrZ-FleQ hub. In this review, we describe the role of this hub in the adaption to the rhizosphere. The study of the direct regulon of AmrZ and the phenotypic analyses of an amrZ mutant in Pseudomonas ogarae F113 has shown that this protein plays a crucial role in the regulation of several cellular functions, including motility, biofilm formation, iron homeostasis, and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) turnover, controlling the synthesis of extracellular matrix components. On the other hand, FleQ is the master regulator of flagellar synthesis in P. ogarae F113 and other pseudomonads, but its implication in the regulation of multiple traits related with environmental adaption has been shown. Genomic scale studies (ChIP-Seq and RNA-Seq) have shown that in P. ogarae F113, AmrZ and FleQ are general transcription factors that regulate multiple traits. It has also been shown that there is a common regulon shared by the two transcription factors. Moreover, these studies have shown that AmrZ and FleQ form a regulatory hub that inversely regulate traits such as motility, extracellular matrix component production, and iron homeostasis. The messenger molecule c-di-GMP plays an essential role in this hub since its production is regulated by AmrZ and it is sensed by FleQ and required for its regulatory role. This regulatory hub is functional both in culture and in the rhizosphere, indicating that the AmrZ-FleQ hub is a main player of P. ogarae F113 adaption to the rhizosphere environment.
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Affiliation(s)
- Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - David Durán
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Marta Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
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14
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Siddharthan N, Balagurunathan R, Venkatesan S, Hemalatha N. Bio-efficacy of Geobacillus thermodenitrificans PS41 against larvicidal, fungicidal, and plant growth-promoting activities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:42596-42607. [PMID: 35670947 DOI: 10.1007/s11356-022-20455-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
The microbial interactions with plant hosts were known to establish plant growth and beneficial productivity. Some bacteria, fungi, actinomycetes, yeast, and algae have proven as potential effective microbes in agricultural field. In this study, the insecticidal effect of Geobacillus thermodenitrificans PS41 secondary metabolites was tested against third instar larvae of Spodoptera litura, with mortality rate 60.26 ± 1.5% which might influence the agropest management. The test bacterial metabolites were subjected to GC-MS analysis. Totally, 17 different compounds were identified from the ethyl acetate extract metabolites of PS41 strain. The highest peak was obtained with behenic alcohol compound followed by 1-octadecene and penta erythrityl tetrachloride. The Geobacillus thermodenitrificans PS41 secondary metabolites showed potential antifungal activity against plant pathogenic fungi. The highest inhibit was attained against Cladosporium sp., (25 mm) followed by Rhizoctonia solani and Alternaria brassicola (23 mm). However, no toxic effect was exerted upon earthworm (Perionyx excavatus) when treated with PS41 bacterial metabolites. The potential PS41 strain was also found supporting the plant growth. The potential bacterial strain PS41 did not show antagonistic activity against soil bacteria such as Rhizobium sp., Azotobacter sp., Azospirullum brasilense, Pseudomonas fluorescens and Bacillus megaterium. The potential test organism, Geobacillus thermodenitrificans PS41, possessing biopesticide and biofertilizer properties can be a suitable ecofriendly organic applicant in agricultural field for enhancing crop production.
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Affiliation(s)
- Nagarajan Siddharthan
- Department of Microbiology, Periyar University, Periyar Palkalai Nagar, Salem, Tamil Nadu, 11, India
| | - Ramasamy Balagurunathan
- Department of Microbiology, Periyar University, Periyar Palkalai Nagar, Salem, Tamil Nadu, 11, India
| | - Srinivasan Venkatesan
- Department of Environmental Science, Periyar University, Periyar Palkalai Nagar, Salem, Tamil Nadu, 11, India
| | - Natarajan Hemalatha
- Department of Microbiology, Periyar University, Periyar Palkalai Nagar, Salem, Tamil Nadu, 11, India.
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Orozco-Mosqueda MDC, Kumar A, Fadiji AE, Babalola OO, Puopolo G, Santoyo G. Agroecological Management of the Grey Mould Fungus Botrytis cinerea by Plant Growth-Promoting Bacteria. PLANTS (BASEL, SWITZERLAND) 2023; 12:637. [PMID: 36771719 PMCID: PMC9919678 DOI: 10.3390/plants12030637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/21/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Botrytis cinerea is the causal agent of grey mould and one of the most important plant pathogens in the world because of the damage it causes to fruits and vegetables. Although the application of botrycides is one of the most common plant protection strategies used in the world, the application of plant-beneficial bacteria might replace botrycides facilitating agroecological production practices. Based on this, we reviewed the different stages of B. cinerea infection in plants and the biocontrol mechanisms exerted by plant-beneficial bacteria, including the well-known plant growth-promoting bacteria (PGPB). Some PGPB mechanisms to control grey mould disease include antibiosis, space occupation, nutrient uptake, ethylene modulation, and the induction of plant defence mechanisms. In addition, recent studies on the action of anti-Botrytis compounds produced by PGPB and how they damage the conidial and mycelial structures of the pathogen are reviewed. Likewise, the advantages of individual inoculations of PGPB versus those that require the joint action of antagonist agents (microbial consortia) are discussed. Finally, it should be emphasised that PGPB are an excellent option to prevent grey mould in different crops and their use should be expanded for environmentally friendly agricultural practices.
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Affiliation(s)
| | - Ajay Kumar
- Centre of Advanced study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Gerardo Puopolo
- Center Agriculture Food Environment (C3A), University of Trento, Via Edmund Mach 1, 38098 San Michele all’Adige, Italy
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mich, Mexico
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Naz B, Liu Z, Malard LA, Ali I, Song H, Wang Y, Li X, Usman M, Ali I, Liu K, An L, Xiao S, Chen S. Dominant plant species play an important role in regulating bacterial antagonism in terrestrial Antarctica. Front Microbiol 2023; 14:1130321. [PMID: 37032907 PMCID: PMC10076557 DOI: 10.3389/fmicb.2023.1130321] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
In Antarctic terrestrial ecosystems, dominant plant species (grasses and mosses) and soil physicochemical properties have a significant influence on soil microbial communities. However, the effects of dominant plants on bacterial antagonistic interactions in Antarctica remain unclear. We hypothesized that dominant plant species can affect bacterial antagonistic interactions directly and indirectly by inducing alterations in soil physicochemical properties and bacterial abundance. We collected soil samples from two typical dominant plant species; the Antarctic grass Deschampsia antarctica and the Antarctic moss Sanionia uncinata, as well as bulk soil sample, devoid of vegetation. We evaluated bacterial antagonistic interactions, focusing on species from the genera Actinomyces, Bacillus, and Pseudomonas. We also measured soil physicochemical properties and evaluated bacterial abundance and diversity using high-throughput sequencing. Our results suggested that Antarctic dominant plants significantly influenced bacterial antagonistic interactions compared to bulk soils. Using structural equation modelling (SEM), we compared and analyzed the direct effect of grasses and mosses on bacterial antagonistic interactions and the indirect effects through changes in edaphic properties and bacterial abundance. SEMs showed that (1) grasses and mosses had a significant direct influence on bacterial antagonistic interactions; (2) grasses had a strong influence on soil water content, pH, and abundances of Actinomyces and Pseudomonas and (3) mosses influenced bacterial antagonistic interactions by impacting abundances of Actinomyces, Bacillus, and Pseudomonas. This study highlights the role of dominant plants in modulating bacterial antagonistic interactions in Antarctic terrestrial ecosystems.
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Affiliation(s)
- Beenish Naz
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Ziyang Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Lucie A. Malard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Izhar Ali
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Hongxian Song
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Yajun Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Xin Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Muhammad Usman
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ikram Ali
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Kun Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Sa Xiao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Shuyan Chen
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
- *Correspondence: Shuyan Chen,
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Dhuldhaj UP, Singh R, Singh VK. Pesticide contamination in agro-ecosystems: toxicity, impacts, and bio-based management strategies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:9243-9270. [PMID: 36456675 DOI: 10.1007/s11356-022-24381-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
Continuous rise in application of pesticides in the agro-ecosystems in order to ensure food supply to the ever-growing population is of greater concern to the human health and the environment. Once entered into the agro-ecosystem, the fate and transport of pesticides is determined largely by the nature of pesticides and the soil attributes, in addition to the soil-inhabiting microbes, fauna, and flora. Changes in the soil microbiological actions, soil properties, and enzymatic activities resulting from pesticide applications are the important factors substantially affecting the soil productivity. Disturbances in the microbial community composition may lead to the considerable perturbations in cycling of major nutrients, metals, and subsequent uptake by plants. Indiscriminate applications are linked with the accumulation of pesticides in plant-based foods, feeds, and animal products. Furthermore, rapid increase in the application of pesticides having long half-life has also been reported to contaminate the nearby aquatic environments and accumulation in the plants, animals, and microbes surviving there. To circumvent the negative consequences of pesticide application, multitude of techniques falling in physical, chemical, and biological categories are presented by different investigators. In the present study, important findings pertaining to the pesticide contamination in cultivated agricultural soils; toxicity on soil microbes, plants, invertebrates, and vertebrates; effects on soil characteristics; and alleviation of toxicity by bio-based management approaches have been thoroughly reviewed. With the help of bibliometric analysis, thematic evolution and research trends on the bioremediation of pesticides in the agro-ecosystems have also been highlighted.
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Affiliation(s)
- Umesh Pravin Dhuldhaj
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, 431606, India
| | - Rishikesh Singh
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Vipin Kumar Singh
- Department of Botany, K. S. Saket P. G. College, (Affiliated to Dr. Ram Manohar Lohia Avadh University), Ayodhya, 224123, India.
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Bhatt K, Suyal DC, Kumar S, Singh K, Goswami P. New insights into engineered plant-microbe interactions for pesticide removal. CHEMOSPHERE 2022; 309:136635. [PMID: 36183882 DOI: 10.1016/j.chemosphere.2022.136635] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/21/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Over the past decades, rapid industrialization along with the overutilization of organic pollutants/pesticides has altered the environmental circumstances. Moreover, various anthropogenic, xenobiotics and natural activities also affected plants, soil, and human health, in both direct and indirect ways. To counter this, several conventional methods are currently practiced, but are uneconomical, noxious, and is yet inefficient for large-scale application. Plant-microbe interactions are mediated naturally in an ecosystem and are practiced in several areas. Plant growth promoting rhizobacteria (PGPR) possess certain attributes affecting plant and soil consequently performing decontamination activity via a direct and indirect mechanism. PGPR also harbors indispensable genes stimulating the mineralization of several organic and inorganic compounds. This makes microbes potential candidates for contributing to sustainably remediating the harmful pesticide contaminants. There is a limited piece of information about the plant-microbe interaction pertaining predict and understand the overall interaction concerning a sustainable environment. Therefore, this review focuses on the plant-microbe interaction in the rhizosphere and inside the plant's tissues, along with the utilization augmenting the crop productivity, reduction in plant stress along with decontamination of pesticides/organic pollutants in soil for sustainable environmental management.
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Affiliation(s)
- Kalpana Bhatt
- Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA.
| | - Deep Chandra Suyal
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India.
| | - Saurabh Kumar
- ICAR-Research Complex for Eastern Region, Patna, 800014, Bihar, India
| | - Kuldeep Singh
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125004, India
| | - Priya Goswami
- Department of Biotechnology, Mangalayatan University, Uttar Pradesh, India
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Lv F, Zhan Y, Lu W, Ke X, Shao Y, Ma Y, Zheng J, Yang Z, Jiang S, Shang L, Ma Y, Cheng L, Elmerich C, Yan Y, Lin M. Regulation of hierarchical carbon substrate utilization, nitrogen fixation, and root colonization by the Hfq/Crc/CrcZY genes in Pseudomonas stutzeri. iScience 2022; 25:105663. [PMID: 36505936 PMCID: PMC9730152 DOI: 10.1016/j.isci.2022.105663] [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: 05/27/2022] [Revised: 09/08/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Bacteria of the genus Pseudomonas consume preferred carbon substrates in nearly reverse order to that of enterobacteria, and this process is controlled by RNA-binding translational repressors and regulatory ncRNA antagonists. However, their roles in microbe-plant interactions and the underlying mechanisms remain uncertain. Here we show that root-associated diazotrophic Pseudomonas stutzeri A1501 preferentially catabolizes succinate, followed by the less favorable substrate citrate, and ultimately glucose. Furthermore, the Hfq/Crc/CrcZY regulatory system orchestrates this preference and contributes to optimal nitrogenase activity and efficient root colonization. Hfq has a central role in this regulatory network through different mechanisms of action, including repressing the translation of substrate-specific catabolic genes, activating the nitrogenase gene nifH posttranscriptionally, and exerting a positive effect on the transcription of an exopolysaccharide gene cluster. Our results illustrate an Hfq-mediated mechanism linking carbon metabolism to nitrogen fixation and root colonization, which may confer rhizobacteria competitive advantages in rhizosphere environments.
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Affiliation(s)
- Fanyang Lv
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuhua Zhan
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Lu
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiubin Ke
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yahui Shao
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yiyuan Ma
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Zheng
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhimin Yang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanshan Jiang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liguo Shang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yao Ma
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | | | - Yongliang Yan
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China,Corresponding author
| | - Min Lin
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China,Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China,Corresponding author
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20
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Kong X, Guo Z, Yao Y, Xia L, Liu R, Song H, Zhang S. Acetic acid alters rhizosphere microbes and metabolic composition to improve willows drought resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:157132. [PMID: 35798115 DOI: 10.1016/j.scitotenv.2022.157132] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/16/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
The adverse effects of drought on plants are gradually exacerbated with global climatic change. Amelioration of the drought stress that is induced by low doses of acetic acid (AA) has been caused great interest in plants. However, whether AA can change soil microbial composition is still unknown. Here, we investigated how exogenous AA regulates the physiology, rhizosphere soil microorganisms and metabolic composition on Salix myrtillacea under drought stress. The physiological results showed that AA could improve the drought tolerance of S. myrtillacea. Azotobacter and Pseudomonas were enriched in the rhizosphere by AA irrigation. AA significantly increased the relative contents of amino acid metabolites (e.g., glycyl-L-tyrosine, l-glutamine and seryl-tryptophan) and decreased the relative contents of phenylpropane metabolites (e.g., fraxetin and sinapyl aldehyde) in soils. The enrichments of Azotobacter and Pseudomonas were significantly correlated with glycyl-L-tyrosine, l-glutamine, seryl-tryptophan, fraxetin and sinapyl aldehyde, which could increase the stress resistance by promoting nitrogen (N) uptake for willows. Furthermore, inoculation with Azotobacter chroococcum and Pseudomonas fluorescens could significantly improve willows drought tolerance. Therefore, our results reveal that the changes of plant physiology, rhizosphere soil microorganisms and metabolic composition induced by AA can improve willows drought resistance by enhancing N uptake.
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Affiliation(s)
- Xiangge Kong
- Key Laboratory for Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zian Guo
- Key Laboratory for Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuan Yao
- Key Laboratory for Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Linchao Xia
- Key Laboratory for Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ruixuan Liu
- Key Laboratory for Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Haifeng Song
- Key Laboratory for Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Sheng Zhang
- Key Laboratory for Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
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21
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Wen T, Yu GH, Hong WD, Yuan J, Niu GQ, Xie PH, Sun FS, Guo LD, Kuzyakov Y, Shen QR. Root exudate chemistry affects soil carbon mobilization via microbial community reassembly. FUNDAMENTAL RESEARCH 2022; 2:697-707. [PMID: 38933120 PMCID: PMC11197519 DOI: 10.1016/j.fmre.2021.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 11/20/2022] Open
Abstract
Plant roots are one of the major mediators that allocate carbon captured from the atmosphere to soils as rhizodeposits, including root exudates. Although rhizodeposition regulates both microbial activity and the biogeochemical cycling of nutrients, the effects of particular exudate species on soil carbon fluxes and key rhizosphere microorganisms remain unclear. By combining high-throughput sequencing, q-PCR, and NanoSIMS analyses, we characterized the bacterial community structure, quantified total bacteria depending on root exudate chemistry, and analyzed the consequences on the mobility of mineral-protected carbon. Using well-controlled incubation experiments, we showed that the three most abundant groups of root exudates (amino acids, carboxylic acids, and sugars) have contrasting effects on the release of dissolved organic carbon (DOC) and bioavailable Fe in an Ultisol through the disruption of organo-mineral associations and the alteration of bacterial communities, thus priming organic matter decomposition in the rhizosphere. High resolution (down to 50 nm) NanoSIMS images of mineral particles indicated that iron and silicon co-localized significantly more organic carbon following amino acid inputs than treatments without exudates or with carboxylic acids. The application of sugar strongly reduced microbial diversity without impacting soil carbon mobilization. Carboxylic acids increased the prevalence of Actinobacteria and facilitated carbon mobilization, whereas amino acid addition increased the abundances of Proteobacteria that prevented DOC release. In summary, root exudate functions are defined by their chemical composition that regulates bacterial community composition and, consequently, the biogeochemical cycling of carbon in the rhizosphere.
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Affiliation(s)
- Tao Wen
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Guang-Hui Yu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin 300072, China
| | - Wen-Dan Hong
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Yuan
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Guo-Qing Niu
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng-Hao Xie
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Fu-Sheng Sun
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin 300072, China
| | - Lao-Dong Guo
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Ave., Milwaukee, WI 53204, United States
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Göttingen 37073, Germany
- Agro-Technological Institute, Peoples Friendship University of Russia (RUDN University), Moscow 117198, Russia
| | - Qi-Rong Shen
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
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22
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Abid L, Smiri M, Federici E, Lievens B, Manai M, Yan Y, Sadfi-Zouaoui N. Diversity of rhizospheric and endophytic bacteria isolated from dried fruit of Ficus carica. Saudi J Biol Sci 2022; 29:103398. [PMID: 35942165 PMCID: PMC9356298 DOI: 10.1016/j.sjbs.2022.103398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/30/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Abstract
There is currently an increasing demand for the characterization of endophytic bacteria isolated from different parts of plants (rhizosphere, roots, fruit, leaf) in order to improve the organic agriculture practices. The current research was performed to identify both rhizospheric bacteria isolated from the rhizosphere of Ficus carica in three different sites in the north of Tunisia and endophytic bacteria isolated from dried figs. We then characterized them for a diversity of plant growth-promoting (PGP) activities. A collection of 120 isolates from rhizospheric soil and 9 isolates from dried figs was obtained and purified. 16SrDNA gene amplification of rhizospheric bacteria revealed significant diversity and allowed for the assigning of the isolates to 6 phyla: Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Representative strains of the collection (90 strains) were tested for numerous PGP activities and resistance to abiotic stresses. The most common PGP trait for all bacteria from the three regions was siderophore production (62%), followed by cellulase (38%), then protease activity (37%), then by lipases activity (17%) and lastly by solubilization of phosphates (9%). Twenty -three strains that showed most PGP traits were selected, 8 strains presented 12 or more, and 15 strains displayed between 7 and 11 of 17 PGP activities. The majority of the isolates manifested a possible adaptation to abiotic stress and unfavorable environments. PCR-DGGE analysis of soil rhizosphere of the three sites allowed also for the acquisition of a Cluster analysis of rhizospheric bacterial communities. Our current study identified and characterized for the first time in Tunisia rhizospheric and endophytic bacteria from dried fruit of Ficus carica.
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Affiliation(s)
- Lamis Abid
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Faculté des Sciences de Tunis Université de Tunis El Manar, 2092 Tunis, Tunisia
- Corresponding author.
| | - Marwa Smiri
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Faculté des Sciences de Tunis Université de Tunis El Manar, 2092 Tunis, Tunisia
| | - Ermanno Federici
- Laboratory of Microbiology, Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems, KU Leuven, Campus De Nayer, B-2860, Sint-Katelijne-Waver, Belgium
| | - Mohamed Manai
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Faculté des Sciences de Tunis Université de Tunis El Manar, 2092 Tunis, Tunisia
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Najla Sadfi-Zouaoui
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Faculté des Sciences de Tunis Université de Tunis El Manar, 2092 Tunis, Tunisia
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23
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Bonaterra A, Badosa E, Daranas N, Francés J, Roselló G, Montesinos E. Bacteria as Biological Control Agents of Plant Diseases. Microorganisms 2022; 10:microorganisms10091759. [PMID: 36144361 PMCID: PMC9502092 DOI: 10.3390/microorganisms10091759] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 12/04/2022] Open
Abstract
Biological control is an effective and sustainable alternative or complement to conventional pesticides for fungal and bacterial plant disease management. Some of the most intensively studied biological control agents are bacteria that can use multiple mechanisms implicated in the limitation of plant disease development, and several bacterial-based products have been already registered and marketed as biopesticides. However, efforts are still required to increase the commercially available microbial biopesticides. The inconsistency in the performance of bacterial biocontrol agents in the biological control has limited their extensive use in commercial agriculture. Pathosystem factors and environmental conditions have been shown to be key factors involved in the final levels of disease control achieved by bacteria. Several biotic and abiotic factors can influence the performance of the biocontrol agents, affecting their mechanisms of action or the multitrophic interaction between the plant, the pathogen, and the bacteria. This review shows some relevant examples of known bacterial biocontrol agents, with especial emphasis on research carried out by Spanish groups. In addition, the importance of the screening process and of the key steps in the development of bacterial biocontrol agents is highlighted. Besides, some improvement approaches and future trends are considered.
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24
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Ai W, Guo T, Lay KD, Ou K, Cai K, Ding Y, Liu J, Cao Y. Isolation of soybean-specific plant growth-promoting rhizobacteria using soybean agglutin and evaluation of their effects to improve soybean growth, yield, and soil nutritional status. Microbiol Res 2022; 261:127076. [PMID: 35636091 DOI: 10.1016/j.micres.2022.127076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/06/2022] [Accepted: 05/16/2022] [Indexed: 11/26/2022]
Abstract
The basic requirements of plant growth-promoting rhizobacteria (PGPR) for field applications are that they have an affinity for the host plant and that they can colonize the rhizosphere. Here, a new technique was established using soybean agglutin (SBA) as a tool to isolate soybean-specific PGPR. Thirty-three PGPR strains with an affinity for soybean were obtained via the screening method with SBA. All 33 isolates were able to produce indole acetic acid and solubilize inorganic phosphate and potassium. Most isolates (93.94%) were able to solubilize organic phosphate and almost half (45.45%) were able to produce siderophores. More than 40% of the isolates exhibited all five plant growth-promoting traits. The isolate Enterobacter sp. strain DN9 was selected for further analyses of its rhizosphere colonization and soybean growth-promoting effects because of its excellent activity in phosphate and potassium solubilization. The luciferase luxAB gene was electrotransformed into DN9, and the labelled DN9 (DN9-L) was able to survive in the soybean rhizosphere and colonize new spaces as the soybean roots elongated. This strain positively affected root system development and soybean seedling growth. In pot and field experiments, the isolates DN9, DW1, and DW13 significantly increased the nutrient contents in rhizosphere soil and soybean leaves. On average, the seed number per plant and the seed weight per plant were increased by 20% and 24% respectively, in plants inoculated with these PGPR strains in the pot experiment. In a field experiment, compared with uninoculated plants, those inoculated with DW1 showed 46.78% higher pod number per plant and 5.23% higher seed oil content; those inoculated with DW13 showed 79.82% higher seed number per plant and 65.10% higher seed weight per plant; and those inoculated with DN9 showed 9.13% higher 100-seed weight. These results show that SBA can be used as a tool to isolate efficient PGPR to enhance soybean production.
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Affiliation(s)
- Wenfeng Ai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Tingting Guo
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Khien Duc Lay
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Kangmiao Ou
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Ke Cai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yue Ding
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Jia Liu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yuanyuan Cao
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China.
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25
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Santos RMD, Desoignies N, Rigobelo EC. The bacterial world inside the plant. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.830198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sustainable agriculture requires the recruitment of bacterial agents to reduce the demand for mineral fertilizers and pesticides such as bacterial endophytes. Bacterial endophytes represent a potential alternative to the widespread use of synthetic fertilizers and pesticides in conventional agriculture practices. Endophytes are formed by complex microbial communities and microorganisms that colonize the plant interior for at least part of their life. Their functions range from mutualism to pathogenicity. Bacterial endophytes colonize plant tissues, and their composition and diversity depend on many factors, including the plant organ, physiological conditions, plant growth stage, and environmental conditions. The presence of endophytes influences several vital activities of the host plant. They can promote plant growth, elicit a defense response against pathogen attack, and lessen abiotic stress. Despite their potential, especially with regard to crop production and environmental sustainability, research remains sparse. This review provides an overview of the current research, including the concept of endophytes, endophytes in plant organs, endophyte colonization, nutrient efficiency use, endophytes and crop nutrition, inoculation with synergistic bacteria, the effect of inoculum concentration on plant root microbiota and synthetic communities. It also examines the practical opportunities and challenges when utilizing endophytes in the field of sustainable agriculture. Finally, it explores the importance of these associations with regard to the future of agriculture and the environment.
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26
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Recreating in vitro tripartite mycorrhizal associations through functional bacterial biofilms. Appl Microbiol Biotechnol 2022; 106:4237-4250. [DOI: 10.1007/s00253-022-11996-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 12/19/2022]
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27
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Lankau RA, George I, Miao M. Crop performance is predicted by soil microbial diversity across phylogenetic scales. Ecosphere 2022. [DOI: 10.1002/ecs2.4029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Richard A. Lankau
- Department of Plant Pathology University of Wisconsin‐Madison Madison Wisconsin USA
| | - Isabelle George
- Department of Plant Pathology University of Wisconsin‐Madison Madison Wisconsin USA
| | - Max Miao
- Department of Plant Pathology University of Wisconsin‐Madison Madison Wisconsin USA
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28
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Jiang Q, Lu W, Zhang L, Jin Y, Wang Y, Chen J, Ye Z, Xiao M. Promotion mechanism of self-transmissible degradative plasmid transfer in maize rhizosphere and its application in naphthalene degradation in soil. J Environ Sci (China) 2022; 115:240-252. [PMID: 34969451 DOI: 10.1016/j.jes.2021.07.014] [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: 04/03/2021] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 06/14/2023]
Abstract
Rhizospheres can promote self-transmissible plasmid transfer, however, the corresponding mechanism has not received much attention. Plant-microbe remediation is an effective way to promote pollutant biodegradation; however, some pollutants, such as naphthalene, are harmful to plants and result in inefficient plant-microbe remediation. In this study, transfer of a TOL-like plasmid, a self-transmissible plasmid loaded with genetic determinants for pollutant degradation, among different bacteria was examined in bulk and rhizosphere soils as well as addition of maize root exudate and its artificial root exudate (ARE). The results showed that the numbers of transconjugants and recipients as well as bacterial metabolic activities, such as xylE mRNA expression levels and catechol 2,3-dioxygenase (C23O) activities of bacteria, remained high in rhizosphere soils, when compared with bulk soils. The number of transconjugants and bacterial metabolic activities increased with the increasing exudate and ARE concentrations, whereas the populations of donor and recipient bacteria were substantially unaltered at all concentrations. All the experiments consistently showed that a certain number of bacteria is required for self-transmissible plasmid transfer, and that the increased plasmid transfer might predominantly be owing to bacterial metabolic activity stimulated by root exudates and ARE. Furthermore, ARE addition increased naphthalene degradation by transconjugants in both culture medium and soil. Thus, the combined action of a wide variety of components in ARE might contribute to the increased plasmid transfer and naphthalene degradation. These findings suggest that ARE could be an effectively alternative for plant-microbe remediation of pollutants in environments where plants cannot survive.
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Affiliation(s)
- Qiuyan Jiang
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wenwei Lu
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; Department of Food Science, Shanghai Business School, Shanghai 200235, China
| | - Lei Zhang
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yeqing Jin
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yujing Wang
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jun Chen
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ziyi Ye
- Shanghai Landscape Architecture Construction Co., Ltd., Shanghai 200235, China
| | - Ming Xiao
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture, Shanghai 200240, China.
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29
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Emmeline D, Alexandra L, Hervé C, Pierre G, Jean-Yves C, Thierry L. Effect of Pseudomonas putida-producing pyoverdine on copper uptake by Helianthus annuus cultivated on vineyard soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:152113. [PMID: 34875330 DOI: 10.1016/j.scitotenv.2021.152113] [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: 08/04/2021] [Revised: 11/27/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
Bioaugmentation-assisted phytoextraction was used to reduce the Cu load in vineyard soils. While performance is usually the endpoint of such studies, here we identified some mechanisms underlying Cu soil to plant transfer, particularly the role of siderophores in the extraction of Cu from the soil-bearing phases and its phytoavailability. Carbonated vs. non‑carbonated vineyard soils were cultivated with sunflower in rhizoboxes bioaugmented with Pseudomonas putida. gfp-Tagged P. putida was monitored in the soil and pyoverdine (Pvd), Cu, Fe, Mn, and Zn were measured in the soil solution. Trace elements (TE) were analysed in the roots and shoots. Plant growth and nutritional status were also measured. With bioaugmentation, the concentration of total Cu (vs. Cu2+) in the soil solution increased (decreased) by a factor of 1.6 to 2.6 (7 to 13) depending on the soil. The almost 1:1 relationship between the excess of Fe + Cu mobilized from the solid phase and the amount of Pvd in the soil solution in bioaugmented treatments suggests that Pvd mobilized Fe and Cu mainly by ligand-controlled dissolution via a 1:1 metal-Pvd complex. Bioaugmentation increased the Cu concentration by 17% in the shoots and by 93% in the roots, and by 30% to 60% the sunflower shoot biomass leading to an increase in the amount of Cu phytoextracted by up to 87%. The amount of Fe, Mn, Zn, and P also increased in the roots and shoots. Contrary to what was expected, carbonated soil did not increase the mobilization of TE. Our results showed that bioaugmentation increased phytoextraction, and its performance can be further improved by promoting the dissociation of Pvd-Cu complex in the solution at the soil-root interface.
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Affiliation(s)
- D'Incau Emmeline
- LPG, UMR 6112 CNRS-Université de Nantes, BP 92208, 44322 Nantes cedex 3, France
| | - Lépinay Alexandra
- OSUNA, UMS 3281 CNRS-Université de Nantes, BP 92208, 44322 Nantes cedex 3, France
| | - Capiaux Hervé
- LPG, UMR 6112 CNRS-Université de Nantes, BP 92208, 44322 Nantes cedex 3, France; OSUNA, UMS 3281 CNRS-Université de Nantes, BP 92208, 44322 Nantes cedex 3, France
| | - Gaudin Pierre
- LPG, UMR 6112 CNRS-Université de Nantes, BP 92208, 44322 Nantes cedex 3, France; OSUNA, UMS 3281 CNRS-Université de Nantes, BP 92208, 44322 Nantes cedex 3, France
| | - Cornu Jean-Yves
- ISPA, Bordeaux Sciences Agro, INRA, 33140 Villenave d'Ornon, France
| | - Lebeau Thierry
- LPG, UMR 6112 CNRS-Université de Nantes, BP 92208, 44322 Nantes cedex 3, France; OSUNA, UMS 3281 CNRS-Université de Nantes, BP 92208, 44322 Nantes cedex 3, France.
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Bacteria isolated from Triticum monococcum ssp. monococcum roots can improve wheat hologenome in agriculture. Mol Biol Rep 2022; 49:5389-5395. [PMID: 35182319 DOI: 10.1007/s11033-022-07118-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Triticum monococcum ssp. monococcum is an ancestral wheat species originated from Karacadağ Mountain of Turkey more than ten thousand years ago. Because of environmental and anthropogenic effects, food supply and demand are not balanced. Agricultural activities such as breeding, and fertilization are important to sustain the balance. Conventional breeding and fertilization applications usually neglect contribution of plant related hologenomes in agricultural yield. The disruption of plant growth promoting microorganisms results in intensive usage of chemical fertilizers. The harmony between plant and plant-associated microorganisms is important for sustainability. In this study, isolation, biochemical characterization, and impact on plant growth parameters of natural bacteria associated with Triticum monococcum ssp. monococcum hologenome were aimed. METHODS AND RESULTS The collection of root samples and isolations of the root-associated bacterial species were carried out from local wheat lands. According to interpretation of three identification methods (MALDI-TOF, 16S rDNA, 16S-23S rDNA) eight isolates are Arthrobacter spp. ESU164, Arthrobacter spp. ESU193, Pseudomonas spp. ESU131, Pseudomonas spp. ESU141, Pseudomonas poae strain ESU182, Pseudomonas thivervalensis strain ESU192, Pseudomonas spp. ESU1531, Bacillus subtilis strain ESU181. For each isolate we investigated biochemical properties especially nitrogen fixation, phosphate solubilization, and indole-3-acetic acid production abilities. The results show that all isolates are nitrogen fixers and the best phosphate solubilizer have been reported as Pseudomonas spp. ESU131 with 2.805 ± 0.439. CONCLUSIONS All isolates are indole-3-acetic acid productors. 2 isolates affected the coleoptile lengths, 7 bacterial isolates showed statistically positive effect on root number, and 5 isolates promote the root lengths and the root fresh weights.
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Genome-wide identification of bacterial colonization and fitness determinants on the floating macrophyte, duckweed. Commun Biol 2022; 5:68. [PMID: 35046504 PMCID: PMC8770550 DOI: 10.1038/s42003-022-03014-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/23/2021] [Indexed: 11/08/2022] Open
Abstract
AbstractBacterial communities associated with aquatic macrophytes largely influence host primary production and nutrient cycling in freshwater environments; however, little is known about how specific bacteria migrate to and proliferate at this unique habitat. Here, we separately identified bacterial genes involved in the initial colonization and overall fitness on plant surface, using the genome-wide transposon sequencing (Tn-seq) of Aquitalea magnusonii H3, a plant growth-promoting bacterium of the floating macrophyte, duckweed. Functional annotation of identified genes indicated that initial colonization efficiency might be simply explained by motility and cell surface structure, while overall fitness was associated with diverse metabolic and regulatory functions. Genes involved in lipopolysaccharides and type-IV pili biosynthesis showed different contributions to colonization and fitness, reflecting their metabolic cost and profound roles in host association. These results provide a comprehensive genetic perspective on aquatic-plant-bacterial interactions, and highlight the potential trade-off between bacterial colonization and proliferation abilities on plant surface.
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Shi P, Zhang J, Li X, Zhou L, Luo H, Wang L, Zhang Y, Chou M, Wei G. Multiple Metabolic Phenotypes as Screening Criteria Are Correlated With the Plant Growth-Promoting Ability of Rhizobacterial Isolates. Front Microbiol 2022; 12:747982. [PMID: 35069464 PMCID: PMC8767003 DOI: 10.3389/fmicb.2021.747982] [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: 07/27/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
Efficient screening method is the prerequisite for getting plant growth-promoting (PGP) rhizobacteria (PGPR) which may play an important role in sustainable agriculture from the natural environment. Many current traditional preliminary screening criteria based on knowledge of PGP mechanisms do not always work well due to complex plant-microbe interactions and may lead to the low screening efficiency. More new screening criteria should be evaluated to establish a more effective screening system. However, the studies focused on this issue were not enough, and few new screening criteria had been proposed. The aim of this study was to analyze the correlation between the metabolic phenotypes of rhizobacterial isolates and their PGP ability. The feasibility of using these phenotypes as preliminary screening criteria for PGPR was also evaluated. Twenty-one rhizobacterial isolates were screened for their PGP ability, traditional PGP traits, and multiple metabolic phenotypes that are not directly related to PGP mechanisms, but are possibly related to rhizosphere colonization. Correlations between the PGP traits or metabolic phenotypes and increases in plant agronomic parameters were analyzed to find the indicators that are most closely related to PGP ability. The utilization of 11 nutrient substrates commonly found in root exudates, such as D-salicin, β-methyl-D-glucoside, and D-cellobiose, was significantly positively correlated with the PGP ability of the rhizobacterial isolates. The utilization of one amino acid and two organic acids, namely L-aspartic acid, α-keto-glutaric acid, and formic acid, was negatively correlated with PGP ability. There were no significant correlations between four PGP traits tested in this study and the PGP ability. The ability of rhizobacterial isolates to metabolize nutrient substrates that are identical or similar to root exudate components may act as better criteria than PGP traits for the primary screening of PGPR, because rhizosphere colonization is a prerequisite for PGPR to affect plants.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
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Riesco R, Ortúzar M, Fernández-Ábalos JM, Trujillo ME. Deciphering Genomes: Genetic Signatures of Plant-Associated Micromonospora. FRONTIERS IN PLANT SCIENCE 2022; 13:872356. [PMID: 35401599 PMCID: PMC8990736 DOI: 10.3389/fpls.2022.872356] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/28/2022] [Indexed: 05/13/2023]
Abstract
Understanding plant-microbe interactions with the possibility to modulate the plant's microbiome is essential to design new strategies for a more productive and sustainable agriculture and to maintain natural ecosystems. Therefore, a key question is how to design bacterial consortia that will yield the desired host phenotype. This work was designed to identify the potential genomic features involved in the interaction between Micromonospora and known host plants. Seventy-four Micromonospora genomes representing diverse environments were used to generate a database of all potentially plant-related genes using a novel bioinformatic pipeline that combined screening for microbial-plant related features and comparison with available plant host proteomes. The strains were recovered in three clusters, highly correlated with several environments: plant-associated, soil/rhizosphere, and marine/mangrove. Irrespective of their isolation source, most strains shared genes coding for commonly screened plant growth promotion features, while differences in plant colonization related traits were observed. When Arabidopsis thaliana plants were inoculated with representative Micromonospora strains selected from the three environments, significant differences were in found in the corresponding plant phenotypes. Our results indicate that the identified genomic signatures help select those strains with the highest probability to successfully colonize the plant and contribute to its wellbeing. These results also suggest that plant growth promotion markers alone are not good indicators for the selection of beneficial bacteria to improve crop production and the recovery of ecosystems.
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Usyskin-Tonne A, Hadar Y, Minz D. Spike Formation Is a Turning Point Determining Wheat Root Microbiome Abundance, Structures and Functions. Int J Mol Sci 2021; 22:11948. [PMID: 34769377 PMCID: PMC8585012 DOI: 10.3390/ijms222111948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/24/2021] [Accepted: 10/29/2021] [Indexed: 11/17/2022] Open
Abstract
Root selection of their associated microbiome composition and activities is determined by the plant's developmental stage and distance from the root. Total gene abundance, structure and functions of root-associated and rhizospheric microbiomes were studied throughout wheat growth season under field conditions. On the root surface, abundance of the well-known wheat colonizers Proteobacteria and Actinobacteria decreased and increased, respectively, during spike formation, whereas abundance of Bacteroidetes was independent of spike formation. Metagenomic analysis combined with functional co-occurrence networks revealed a significant impact of plant developmental stage on its microbiome during the transition from vegetative growth to spike formation. For example, gene functions related to biofilm and sensorial movement, antibiotic production and resistance and carbons and amino acids and their transporters. Genes associated with these functions were also in higher abundance in root vs. the rhizosphere microbiome. We propose that abundance of transporter-encoding genes related to carbon and amino acid, may mirror the availability and utilization of root exudates. Genes related to antibiotic resistance mechanisms were abundant during vegetative growth, while after spike formation, genes related to the biosynthesis of various antibiotics were enriched. This observation suggests that during root colonization and biofilm formation, bacteria cope with competitor's antibiotics, whereas in the mature biofilm stage, they invest in inhibiting new colonizers. Additionally, there is higher abundance of genes related to denitrification in rhizosphere compared to root-associated microbiome during wheat growth, possibly due to competition with the plant over nitrogen in the root vicinity. We demonstrated functional and phylogenetic division in wheat root zone microbiome in both time and space: pre- and post-spike formation, and root-associated vs. rhizospheric niches. These findings shed light on the dynamics of plant-microbe and microbe-microbe interactions in the developing root zone.
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Affiliation(s)
- Alla Usyskin-Tonne
- Soil, Water and Environmental Sciences, Volcani Research Center, Rishon LeZion 7505101, Israel;
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel;
| | - Yitzhak Hadar
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel;
| | - Dror Minz
- Soil, Water and Environmental Sciences, Volcani Research Center, Rishon LeZion 7505101, Israel;
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Liu TY, Ye N, Wang X, Das D, Tan Y, You X, Long M, Hu T, Dai L, Zhang J, Chen MX. Drought stress and plant ecotype drive microbiome recruitment in switchgrass rhizosheath. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1753-1774. [PMID: 34288433 DOI: 10.1111/jipb.13154] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/18/2021] [Indexed: 05/27/2023]
Abstract
The rhizosheath, a layer of soil grains that adheres firmly to roots, is beneficial for plant growth and adaptation to drought environments. Switchgrass is a perennial C4 grass which can form contact rhizosheath under drought conditions. In this study, we characterized the microbiomes of four different rhizocompartments of two switchgrass ecotypes (Alamo and Kanlow) grown under drought or well-watered conditions via 16S ribosomal RNA amplicon sequencing. These four rhizocompartments, the bulk soil, rhizosheath soil, rhizoplane, and root endosphere, harbored both distinct and overlapping microbial communities. The root compartments (rhizoplane and root endosphere) displayed low-complexity communities dominated by Proteobacteria and Firmicutes. Compared to bulk soil, Cyanobacteria and Bacteroidetes were selectively enriched, while Proteobacteria and Firmicutes were selectively depleted, in rhizosheath soil. Taxa from Proteobacteria or Firmicutes were specifically selected in Alamo or Kanlow rhizosheath soil. Following drought stress, Citrobacter and Acinetobacter were further enriched in rhizosheath soil, suggesting that rhizosheath microbiome assembly is driven by drought stress. Additionally, the ecotype-specific recruitment of rhizosheath microbiome reveals their differences in drought stress responses. Collectively, these results shed light on rhizosheath microbiome recruitment in switchgrass and lay the foundation for the improvement of drought tolerance in switchgrass by regulating the rhizosheath microbiome.
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Affiliation(s)
- Tie-Yuan Liu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, 999077, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Xinyu Wang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Debatosh Das
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, 999077, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China
| | - Yuxiang Tan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiangkai You
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Mingxiu Long
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jianhua Zhang
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, 999077, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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Saeed Q, Xiukang W, Haider FU, Kučerik J, Mumtaz MZ, Holatko J, Naseem M, Kintl A, Ejaz M, Naveed M, Brtnicky M, Mustafa A. Rhizosphere Bacteria in Plant Growth Promotion, Biocontrol, and Bioremediation of Contaminated Sites: A Comprehensive Review of Effects and Mechanisms. Int J Mol Sci 2021; 22:10529. [PMID: 34638870 PMCID: PMC8509026 DOI: 10.3390/ijms221910529] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 01/23/2023] Open
Abstract
Agriculture in the 21st century is facing multiple challenges, such as those related to soil fertility, climatic fluctuations, environmental degradation, urbanization, and the increase in food demand for the increasing world population. In the meanwhile, the scientific community is facing key challenges in increasing crop production from the existing land base. In this regard, traditional farming has witnessed enhanced per acre crop yields due to irregular and injudicious use of agrochemicals, including pesticides and synthetic fertilizers, but at a substantial environmental cost. Another major concern in modern agriculture is that crop pests are developing pesticide resistance. Therefore, the future of sustainable crop production requires the use of alternative strategies that can enhance crop yields in an environmentally sound manner. The application of rhizobacteria, specifically, plant growth-promoting rhizobacteria (PGPR), as an alternative to chemical pesticides has gained much attention from the scientific community. These rhizobacteria harbor a number of mechanisms through which they promote plant growth, control plant pests, and induce resistance to various abiotic stresses. This review presents a comprehensive overview of the mechanisms of rhizobacteria involved in plant growth promotion, biocontrol of pests, and bioremediation of contaminated soils. It also focuses on the effects of PGPR inoculation on plant growth survival under environmental stress. Furthermore, the pros and cons of rhizobacterial application along with future directions for the sustainable use of rhizobacteria in agriculture are discussed in depth.
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Affiliation(s)
- Qudsia Saeed
- College of Natural Resources and Environment, Northwest Agriculture and Forestry University, Yangling 712100, China;
| | - Wang Xiukang
- College of Life Sciences, Yan’an University, Yan’an 716000, China
| | - Fasih Ullah Haider
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China;
| | - Jiří Kučerik
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; (J.K.); (M.B.)
| | - Muhammad Zahid Mumtaz
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Defense Road, Lahore 54000, Pakistan;
| | - Jiri Holatko
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; (J.H.); (A.K.)
| | - Munaza Naseem
- Institute of Soil and Environmental Science, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (M.N.); (M.N.)
| | - Antonin Kintl
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; (J.H.); (A.K.)
- Agricultural Research, Ltd., Zahradni 400/1, 664 41 Troubsko, Czech Republic
| | - Mukkaram Ejaz
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China;
| | - Muhammad Naveed
- Institute of Soil and Environmental Science, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (M.N.); (M.N.)
| | - Martin Brtnicky
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; (J.K.); (M.B.)
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; (J.H.); (A.K.)
| | - Adnan Mustafa
- Biology Center CAS, SoWa RI, Na Sadkach 7, 370 05 České Budějovice, Czech Republic
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Phale PS, Mohapatra B, Malhotra H, Shah BA. Eco-physiological portrait of a novel Pseudomonas sp. CSV86: an ideal host/candidate for metabolic engineering and bioremediation. Environ Microbiol 2021; 24:2797-2816. [PMID: 34347343 DOI: 10.1111/1462-2920.15694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/30/2022]
Abstract
Pseudomonas sp. CSV86, an Indian soil isolate, degrades wide range of aromatic compounds like naphthalene, benzoate and phenylpropanoids, amongst others. Isolate displays the unique and novel property of preferential utilization of aromatics over glucose and co-metabolizes them with organic acids. Interestingly, as compared to other Pseudomonads, strain CSV86 harbours only high-affinity glucokinase pathway (and absence of low-affinity oxidative route) for glucose metabolism. Such lack of gluconate loop might be responsible for the novel phenotype of preferential utilization of aromatics. The genome analysis and comparative functional mining indicated a large genome (6.79 Mb) with significant enrichment of regulators, transporters as well as presence of various secondary metabolite production clusters, suggesting its eco-physiological and metabolic versatility. Strain harbours various integrative conjugative elements (ICEs) and genomic islands, probably acquired through horizontal gene transfer events, leading to genome mosaicity and plasticity. Naphthalene degradation genes are arranged as regulonic clusters and found to be part of ICECSV86nah . Various eco-physiological properties and absence of major pathogenicity and virulence factors (risk group-1) in CSV86 suggest it to be an ideal candidate for bioremediation. Further, strain can serve as an ideal chassis for metabolic engineering to degrade various xenobiotics preferentially over simple carbon sources for efficient remediation.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
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Phytase-Producing Rahnella aquatilis JZ-GX1 Promotes Seed Germination and Growth in Corn ( Zea mays L.). Microorganisms 2021; 9:microorganisms9081647. [PMID: 34442724 PMCID: PMC8400716 DOI: 10.3390/microorganisms9081647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 11/30/2022] Open
Abstract
Phytase plays an important role in crop seed germination and plant growth. In order to fully understand the plant growth-promoting mechanism by Rahnella aquatilis JZ-GX1, the effect of this strain on germination of maize seeds was determined in vitro, and the colonization of maize root by R. aquatilis JZ-GX1 was observed by scanning electron microscope. Different inoculum concentrations and Phytate-related soil properties were applied to investigate the effect of R. aquatilis JZ-GX1 on the growth of maize seedlings. The results showed that R. aquatilis JZ-GX1 could effectively secrete indole acetic acid and had significantly promoted seed germination and root length of maize. A large number of R. aquatilis JZ-GX1 cells colonized on the root surface, root hair and the root interior of maize. When the inoculation concentration was 107 cfu/mL and the insoluble organophosphorus compound phytate existed in the soil, the net photosynthetic rate, chlorophyll content, phytase activity secreted by roots, total phosphorus concentration and biomass accumulation of maize seedlings were the highest. In contrast, no significant effect of inoculation was found when the total P content was low or when inorganic P was sufficient in the soil. R. aquatilis JZ-GX1 promotes the growth of maize directly by secreting IAA and indirectly by secreting phytase. This work provides beneficial information for the development and application of R. aquatilis JZ-GX1 as a microbial fertilizer in the future.
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Huang M, Bulut A, Shrestha B, Matera C, Grundler FMW, Schleker ASS. Bacillus firmus I-1582 promotes plant growth and impairs infection and development of the cyst nematode Heterodera schachtii over two generations. Sci Rep 2021; 11:14114. [PMID: 34239009 PMCID: PMC8266893 DOI: 10.1038/s41598-021-93567-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/25/2021] [Indexed: 11/09/2022] Open
Abstract
Plant-parasitic nematodes wreak havoc on crops by root parasitism worldwide. An approach to combat nematode root parasitism is the application of antagonistic microbes like the rhizobacterium Bacillus firmus I-1582 which is promoted as biological control agent. Although B. firmus is a known nematode antagonist in general, the underlying mechanisms about its interaction with nematodes and plants have not yet been elucidated. Therefore, we explored the influence of B. firmus I-1582 as well as its extracellular and secreted molecules on plant–nematode interaction utilizing the plant–pathogen system Arabidopsis thaliana–Heterodera schachtii. We demonstrated that B. firmus I-1582 is attracted by A. thaliana root exudates, particularly by those of young plants. The bacterium colonized the root and showed a strictly pH-dependent development and plant growth promotion effect. Our results revealed that root colonization by B. firmus I-1582 significantly protected A. thaliana from infestation by the beet cyst nematode whereas dead bacterial cells or the culture supernatant were not effective. The bacterium also negatively affected nematode reproduction as well as pathogenicity and development of next generation nematodes. The obtained results highlight B. firmus I-1582 as a promising biocontrol agent that is well suited as an element of integrated control management strategies in sustainable agriculture.
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Affiliation(s)
- Mengmeng Huang
- INRES-Department of Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, 53115, Bonn, Germany
| | - Aylin Bulut
- INRES-Department of Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, 53115, Bonn, Germany
| | - Bidhya Shrestha
- INRES-Department of Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, 53115, Bonn, Germany
| | - Christiane Matera
- INRES-Department of Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, 53115, Bonn, Germany
| | - Florian M W Grundler
- INRES-Department of Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, 53115, Bonn, Germany
| | - A Sylvia S Schleker
- INRES-Department of Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, 53115, Bonn, Germany.
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Li E, Zhang H, Jiang H, Pieterse CMJ, Jousset A, Bakker PAHM, de Jonge R. Experimental-Evolution-Driven Identification of Arabidopsis Rhizosphere Competence Genes in Pseudomonas protegens. mBio 2021; 12:e0092721. [PMID: 34101491 PMCID: PMC8262913 DOI: 10.1128/mbio.00927-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/30/2021] [Indexed: 11/20/2022] Open
Abstract
Beneficial plant root-associated microorganisms carry out a range of functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming several challenges, including competition with neighboring microorganisms and host immunity. Forward and reverse genetics have led to the identification of mechanisms that are used by beneficial microorganisms to overcome these challenges, such as the production of iron-chelating compounds, the formation of strong biofilms, or the concealment of characteristic microbial molecular patterns that trigger the host immune system. However, how such mechanisms arose from an evolutionary perspective is much less understood. To study bacterial adaptation in the rhizosphere, we employed experimental evolution to track the physiological and genetic dynamics of root-dwelling Pseudomonas protegens in the Arabidopsis thaliana rhizosphere under axenic conditions. This simplified binary one plant/one bacterium system allows for the amplification of key adaptive mechanisms for bacterial rhizosphere colonization. We identified 35 mutations, including single-nucleotide polymorphisms, insertions, and deletions, distributed over 28 genes. We found that mutations in genes encoding global regulators and in genes for siderophore production, cell surface decoration, attachment, and motility accumulated in parallel, underlining the finding that bacterial adaptation to the rhizosphere follows multiple strategies. Notably, we observed that motility increased in parallel across multiple independent evolutionary lines. All together, these results underscore the strength of experimental evolution in identifying key genes, pathways, and processes for bacterial rhizosphere colonization and a methodology for the development of elite beneficial microorganisms with enhanced root-colonizing capacities that can support sustainable agriculture in the future. IMPORTANCE Beneficial root-associated microorganisms carry out many functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming many challenges. Previously, diverse mechanisms that are used by beneficial microorganisms to overcome these challenges were identified. However, how such mechanisms have developed from an evolutionary perspective is much less understood. Here, we employed experimental evolution to track the evolutionary dynamics of a root-dwelling pseudomonad on the root of Arabidopsis. We found that mutations in global regulators, as well as in genes for siderophore production, cell surface decoration, attachment, and motility, accumulate in parallel, emphasizing these strategies for bacterial adaptation to the rhizosphere. We identified 35 mutations distributed over 28 genes. All together, our results demonstrate the power of experimental evolution in identifying key pathways for rhizosphere colonization and a methodology for the development of elite beneficial microorganisms that can support sustainable agriculture.
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Affiliation(s)
- Erqin Li
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Hao Zhang
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Henan Jiang
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Corné M. J. Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Alexandre Jousset
- Ecology and Biodiversity, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Peter A. H. M. Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
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Santoyo G, Urtis-Flores CA, Loeza-Lara PD, Orozco-Mosqueda MDC, Glick BR. Rhizosphere Colonization Determinants by Plant Growth-Promoting Rhizobacteria (PGPR). BIOLOGY 2021; 10:biology10060475. [PMID: 34072072 PMCID: PMC8229920 DOI: 10.3390/biology10060475] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/15/2022]
Abstract
Simple Summary Plant growth-promoting rhizobacteria (PGPR) are an eco-friendly alternative to the use of chemicals in agricultural production and crop protection. However, the efficacy of PGPR as bioinoculants can be diminished by a low capacity to colonize spaces in the rhizosphere. In this work, we review pioneering and recent developments on several important functions that rhizobacteria exhibit in order to compete, colonize, and establish themselves in the plant rhizosphere. Therefore, the use of highly competitive strains in open field trials should be a priority, in order to have consistent and better results in agricultural production activities. Abstract The application of plant growth-promoting rhizobacteria (PGPR) in the field has been hampered by a number of gaps in the knowledge of the mechanisms that improve plant growth, health, and production. These gaps include (i) the ability of PGPR to colonize the rhizosphere of plants and (ii) the ability of bacterial strains to thrive under different environmental conditions. In this review, different strategies of PGPR to colonize the rhizosphere of host plants are summarized and the advantages of having highly competitive strains are discussed. Some mechanisms exhibited by PGPR to colonize the rhizosphere include recognition of chemical signals and nutrients from root exudates, antioxidant activities, biofilm production, bacterial motility, as well as efficient evasion and suppression of the plant immune system. Moreover, many PGPR contain secretion systems and produce antimicrobial compounds, such as antibiotics, volatile organic compounds, and lytic enzymes that enable them to restrict the growth of potentially phytopathogenic microorganisms. Finally, the ability of PGPR to compete and successfully colonize the rhizosphere should be considered in the development and application of bioinoculants.
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Affiliation(s)
- Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico;
- Correspondence:
| | - Carlos Alberto Urtis-Flores
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico;
| | - Pedro Damián Loeza-Lara
- Licenciatura en Genómica Alimentaria, Universidad de La Ciénega del Estado de Michoacán de Ocampo, Sahuayo 59103, Mexico;
| | - Ma. del Carmen Orozco-Mosqueda
- Facultad de Agrobiología “Presidente Juárez”, Universidad Michoacana de San Nicolás de Hidalgo, Melchor Ocampo, Uruapan 60170, Mexico;
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
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Nordstedt NP, Jones ML. Genomic Analysis of Serratia plymuthica MBSA-MJ1: A Plant Growth Promoting Rhizobacteria That Improves Water Stress Tolerance in Greenhouse Ornamentals. Front Microbiol 2021; 12:653556. [PMID: 34046022 PMCID: PMC8144289 DOI: 10.3389/fmicb.2021.653556] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/14/2021] [Indexed: 12/26/2022] Open
Abstract
Water stress decreases the health and quality of horticulture crops by inhibiting photosynthesis, transpiration, and nutrient uptake. Application of plant growth promoting rhizobacteria (PGPR) can increase the growth, stress tolerance, and overall quality of field and greenhouse grown crops subjected to water stress. Here, we evaluated Serratia plymuthica MBSA-MJ1 for its ability to increase plant growth and quality of Petunia × hybrida (petunia), Impatiens walleriana (impatiens), and Viola × wittrockiana (pansy) plants recovering from severe water stress. Plants were treated weekly with inoculum of MBSA-MJ1, and plant growth and quality were evaluated 2 weeks after recovery from water stress. Application of S. plymuthica MBSA-MJ1 increased the visual quality and shoot biomass of petunia and impatiens and increased the flower number of petunia after recovery from water stress. In addition, in vitro characterizations showed that MBSA-MJ1 is a motile bacterium with moderate levels of antibiotic resistance that can withstand osmotic stress. Further, comprehensive genomic analyses identified genes putatively involved in bacterial osmotic and oxidative stress responses and the synthesis of osmoprotectants and vitamins that could potentially be involved in increasing plant water stress tolerance. This work provides a better understanding of potential mechanisms involved in beneficial plant-microbe interactions under abiotic stress using a novel S. plymuthica strain as a model.
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Affiliation(s)
- Nathan P Nordstedt
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Michelle L Jones
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
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Bhattacharyya A, Pablo CHD, Mavrodi OV, Weller DM, Thomashow LS, Mavrodi DV. Rhizosphere plant-microbe interactions under water stress. ADVANCES IN APPLIED MICROBIOLOGY 2021; 115:65-113. [PMID: 34140134 DOI: 10.1016/bs.aambs.2021.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Climate change, with its extreme temperature, weather and precipitation patterns, is a major global concern of dryland farmers, who currently meet the challenges of climate change agronomically and with growth of drought-tolerant crops. Plants themselves compensate for water stress by modifying aerial surfaces to control transpiration and altering root hydraulic conductance to increase water uptake. These responses are complemented by metabolic changes involving phytohormone network-mediated activation of stress response pathways, resulting in decreased photosynthetic activity and the accumulation of metabolites to maintain osmotic and redox homeostasis. Phylogenetically diverse microbial communities sustained by plants contribute to host drought tolerance by modulating phytohormone levels in the rhizosphere and producing water-sequestering biofilms. Drylands of the Inland Pacific Northwest, USA, illustrate the interdependence of dryland crops and their associated microbiota. Indigenous Pseudomonas spp. selected there by long-term wheat monoculture suppress root diseases via the production of antibiotics, with soil moisture a critical determinant of the bacterial distribution, dynamics and activity. Those pseudomonads producing phenazine antibiotics on wheat had more abundant rhizosphere biofilms and provided improved tolerance to drought, suggesting a role of the antibiotic in alleviation of drought stress. The transcriptome and metabolome studies suggest the importance of wheat root exudate-derived osmoprotectants for the adaptation of these pseudomonads to the rhizosphere lifestyle and support the idea that the exchange of metabolites between plant roots and microorganisms profoundly affects and shapes the belowground plant microbiome under water stress.
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Affiliation(s)
- Ankita Bhattacharyya
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Clint H D Pablo
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Olga V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - David M Weller
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda S Thomashow
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Dmitri V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States.
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Mavrodi OV, McWilliams JR, Peter JO, Berim A, Hassan KA, Elbourne LDH, LeTourneau MK, Gang DR, Paulsen IT, Weller DM, Thomashow LS, Flynt AS, Mavrodi DV. Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas. Front Microbiol 2021; 12:651282. [PMID: 33936009 PMCID: PMC8079746 DOI: 10.3389/fmicb.2021.651282] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialog between eight well-characterized beneficial strains of the Pseudomonas fluorescens group and Brachypodium distachyon, a model for economically important food, feed, forage, and biomass crops of the grass family. We collected and analyzed root exudates of B. distachyon and demonstrated the presence of multiple carbohydrates, amino acids, organic acids, and phenolic compounds. The subsequent screening of bacteria by Biolog Phenotype MicroArrays revealed that many of these metabolites provide carbon and energy for the Pseudomonas strains. RNA-seq profiling of bacterial cultures amended with root exudates revealed changes in the expression of genes encoding numerous catabolic and anabolic enzymes, transporters, transcriptional regulators, stress response, and conserved hypothetical proteins. Almost half of the differentially expressed genes mapped to the variable part of the strains’ pangenome, reflecting the importance of the variable gene content in the adaptation of P. fluorescens to the rhizosphere lifestyle. Our results collectively reveal the diversity of cellular pathways and physiological responses underlying the establishment of mutualistic interactions between these beneficial rhizobacteria and their plant hosts.
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Affiliation(s)
- Olga V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Janiece R McWilliams
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Jacob O Peter
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Anna Berim
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Karl A Hassan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Liam D H Elbourne
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Melissa K LeTourneau
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - David R Gang
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - David M Weller
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda S Thomashow
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Alex S Flynt
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Dmitri V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
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Sucrose triggers a novel signaling cascade promoting Bacillus subtilis rhizosphere colonization. ISME JOURNAL 2021; 15:2723-2737. [PMID: 33772107 PMCID: PMC8397739 DOI: 10.1038/s41396-021-00966-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/02/2021] [Accepted: 03/15/2021] [Indexed: 11/26/2022]
Abstract
Beneficial rhizobacteria promote plant growth and protect plants against phytopathogens. Effective colonization on plant roots is critical for the rhizobacteria to exert beneficial activities. How bacteria migrate swiftly in the soil of semisolid or solid nature remains unclear. Here we report that sucrose, a disaccharide ubiquitously deployed by photosynthetic plants for fixed carbon transport and storage, and abundantly secreted from plant roots, promotes solid surface motility (SSM) and root colonization by Bacillus subtilis through a previously uncharacterized mechanism. Sucrose induces robust SSM by triggering a signaling cascade, first through extracellular synthesis of polymeric levan, which in turn stimulates strong production of surfactin and hyper-flagellation of the cells. B. subtilis poorly colonizes the roots of Arabidopsis thaliana mutants deficient in root-exudation of sucrose, while exogenously added sucrose selectively shapes the rhizomicrobiome associated with the tomato plant roots, promoting specifically bacilli and pseudomonad. We propose that sucrose activates a signaling cascade to trigger SSM and promote rhizosphere colonization by B. subtilis. Our findings also suggest a practicable approach to boost prevalence of beneficial Bacillus species in plant protection.
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46
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Marzocca MA, Costantino AR, Gentili AR, Oriani AS, Pereyra MT, Lusto J, Baldini MD. Microbiological quality and determination of pesticide residues in the lettuce produced in Bahía Blanca's horticultural belt, Argentina. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2021; 56:439-446. [PMID: 33760685 DOI: 10.1080/03601234.2021.1900693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The aims of this research were 1) to find out the possible microbiological contamination and residues of pesticides (chlorpyrifos and cypermethrin) in lettuce grown in Bahía Blanca's horticultural belt, and bacteriological quality of waters used for irrigation and post-harvest washing, 2) to investigate and compare the internalization capacity of a strain of Escherichia coli isolated from irrigation water with another hospital uropathogenic strain. Some strains of bacteria can internalize into the plant tissue. This capability presents food safety threats as they cannot be removed with standard sanitation practices. To determine bacteriological quality of lettuce, E. coli, Salmonella spp and E. coli O157: H7/NM (n = 10) were investigated. Bacteriological quality of water was determined by quantification of fecal coliforms/100 mL (n = 20). Pesticides were determined by using an improved and validated QuEChERS method combined with GC-MSD. Irrigation water in 19/20 samples did not present health risk. Bacteriological quality of lettuce met demands in 9/10 samples. Pesticides were detected in half of the samples, values exceeding the FAO recommendations. An effort is strongly recommended to implement both, best phytosanitary practices and monitoring programmes. Uropathogenic strain was able to internalize into plant tissue, while the nonpathogenic one was not.
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Affiliation(s)
- María A Marzocca
- Department of Biology, Biochemistry and Pharmacy, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Andrea R Costantino
- INQUISUR, Department of Chemistry, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Alejandro R Gentili
- Department of Biology, Biochemistry and Pharmacy, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Alejandra S Oriani
- Department of Biology, Biochemistry and Pharmacy, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Marcelo T Pereyra
- INQUISUR, Department of Chemistry, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Jorge Lusto
- Department of Agronomy, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Mónica D Baldini
- Department of Biology, Biochemistry and Pharmacy, Universidad Nacional del Sur, Bahía Blanca, Argentina
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47
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Meesungnoen O, Chantiratikul P, Thumanu K, Nuengchamnong N, Hokura A, Nakbanpote W. Elucidation of crude siderophore extracts from supernatants of Pseudomonas sp. ZnCd2003 cultivated in nutrient broth supplemented with Zn, Cd, and Zn plus Cd. Arch Microbiol 2021; 203:2863-2874. [PMID: 33751172 DOI: 10.1007/s00203-021-02274-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/03/2021] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
This research aimed to study siderophores secreted from Pseudomonas sp. PDMZnCd2003, a Zn/Cd tolerant bacterium. The effects of Zn and/or Cd stress were examined in nutrient broth to achieve the actual environmental conditions. Acid and alkali supernatants and liquid-liquid extraction with ethyl acetate and butanol were carried out to obtain crude extracts containing different amounts of the metals. The bacterial growth, UV-visible spectra of the supernatants and siderophore production indicated that the production of siderophores tended to be linked to primary metabolites. Pyocyanin was produced in all treatments, while pyoverdine was induced by stress from the metals, especially Cd. FT-IR spectra showed C=O groups and sulfur functional groups that were involved in binding with the metals. LC-MS revealed that pyocyanin, 1-hydroxy phenazine, pyoverdine, and pyochelin were present in the crude extracts. S K-edge XANES spectra showed that the main sulfur species in the extracts were the reduced forms of sulfide, thiol, and disulfide, and their oxidation states were affected by coordination with Zn and/or Cd. In addition, Zn K-edge EXAFS spectra and Cd K-edge EXAFS spectra presented Zn-O and Cd-O as coordination in the first shell, in case the extracts contained less metal. Although the mix O/S ligands had chelation bonding with Zn and Cd in the other extracts. For the role of S groups in pyochelin binding with the metals, this was the first report. The results of these experiments could be extended to Pseudomonas that respond to metal contaminated environments.
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Affiliation(s)
- Orapan Meesungnoen
- Department of Biology, Faculty of Science, Mahasarakham University, Kamrieng, Kantaravichai, 44150, Mahasarakham, Thailand
| | - Piyanete Chantiratikul
- Department of Chemistry, Faculty of Science, Mahasarakham University, Kamrieng, Kantaravichai, 44150, Mahasarakham, Thailand
| | - Kanjana Thumanu
- Synchrotron Light Research Institute, Muang, Nakhon Ratchasima, 30000, Thailand
| | - Nitra Nuengchamnong
- Science Laboratory Centre, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Akiko Hokura
- Department of Applied Chemistry, Tokyo Denki University, Adachi, Tokyo, 120-8551, Japan
| | - Woranan Nakbanpote
- Department of Biology, Faculty of Science, Mahasarakham University, Kamrieng, Kantaravichai, 44150, Mahasarakham, Thailand.
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Bonkowski M, Tarkka M, Razavi BS, Schmidt H, Blagodatskaya E, Koller R, Yu P, Knief C, Hochholdinger F, Vetterlein D. Spatiotemporal Dynamics of Maize ( Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota. Front Microbiol 2021; 12:619499. [PMID: 33815308 PMCID: PMC8010349 DOI: 10.3389/fmicb.2021.619499] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Numerous studies have shown that plants selectively recruit microbes from the soil to establish a complex, yet stable and quite predictable microbial community on their roots – their “microbiome.” Microbiome assembly is considered as a key process in the self-organization of root systems. A fundamental question for understanding plant-microbe relationships is where a predictable microbiome is formed along the root axis and through which microbial dynamics the stable formation of a microbiome is challenged. Using maize as a model species for which numerous data on dynamic root traits are available, this mini-review aims to give an integrative overview on the dynamic nature of root growth and its consequences for microbiome assembly based on theoretical considerations from microbial community ecology.
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Affiliation(s)
- Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Mika Tarkka
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Bahar S Razavi
- Department of Soil and Plant Microbiome, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Evgenia Blagodatskaya
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,Soil Science, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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49
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Chiniquy D, Barnes EM, Zhou J, Hartman K, Li X, Sheflin A, Pella A, Marsh E, Prenni J, Deutschbauer AM, Schachtman DP, Tringe SG. Microbial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes. Front Microbiol 2021; 12:598180. [PMID: 33767674 PMCID: PMC7985074 DOI: 10.3389/fmicb.2021.598180] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/04/2021] [Indexed: 11/13/2022] Open
Abstract
While the root-associated microbiome is typically less diverse than the surrounding soil due to both plant selection and microbial competition for plant derived resources, it typically retains considerable complexity, harboring many hundreds of distinct bacterial species. Here, we report a time-dependent deviation from this trend in the rhizospheres of field grown sorghum. In this study, 16S rRNA amplicon sequencing was used to determine the impact of nitrogen fertilization on the development of the root-associated microbiomes of 10 sorghum genotypes grown in eastern Nebraska. We observed that early rhizosphere samples exhibit a significant reduction in overall diversity due to a high abundance of the bacterial genus Pseudomonas that occurred independent of host genotype in both high and low nitrogen fields and was not observed in the surrounding soil or associated root endosphere samples. When clustered at 97% identity, nearly all the Pseudomonas reads in this dataset were assigned to a single operational taxonomic unit (OTU); however, exact sequence variant (ESV)-level resolution demonstrated that this population comprised a large number of distinct Pseudomonas lineages. Furthermore, single-molecule long-read sequencing enabled high-resolution taxonomic profiling revealing further heterogeneity in the Pseudomonas lineages that was further confirmed using shotgun metagenomic sequencing. Finally, field soil enriched with specific carbon compounds recapitulated the increase in Pseudomonas, suggesting a possible connection between the enrichment of these Pseudomonas species and a plant-driven exudate profile.
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Affiliation(s)
- Dawn Chiniquy
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States.,Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Department of Energy, Berkeley, CA, United States
| | - Elle M Barnes
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Jinglie Zhou
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Kyle Hartman
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Xiaohui Li
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States.,Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Department of Energy, Berkeley, CA, United States.,Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, United States.,Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Amy Sheflin
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, United States
| | - Allyn Pella
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Ellen Marsh
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Jessica Prenni
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, United States
| | - Adam M Deutschbauer
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Susannah G Tringe
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States.,Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Department of Energy, Berkeley, CA, United States
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Metagenomics of mine tailing rhizospheric communities and its selection for plant establishment towards bioremediation. Microbiol Res 2021; 247:126732. [PMID: 33743500 DOI: 10.1016/j.micres.2021.126732] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/10/2021] [Accepted: 02/17/2021] [Indexed: 11/22/2022]
Abstract
Mining operations often generate tailing dams that contain toxic residues and are a source of contamination when left unconfined. The establishment of a plant community over the tailings has been proposed as a containment strategy known as phytostabilization. Previously, we described naturally occurring mine tailing colonizing plants such as Acacia farnesiana, Brickellia coulteri, Baccharis sarothroides, and Gnaphalium leucocephalum without finding local adaptation. We explored the rhizosphere microbes as contributors in plant establishment and described both the culturable and in situ diversity of rhizospheric bacteria using the 16S rRNA gene and metagenomic shotgun sequencing. We built a synthetic community (SC) of culturable rhizosphere bacteria from the mine tailings. The SC was then the foundation for a serial passes experiment grown in plant-derived nutrient sources, selecting for heavy metals tolerance, community cooperation, and competition. The outcome of the serial passes was named the 'final synthetic community' (FSC). Overall, diversity decreased from in situ uncultivable microbes from roots (399 bacteria genera) to the cultivated communities (291 genera), the SC (94 genera), and the lowest diversity was in the FSC (43 genera). Metagenomic diversity clustered into 94,245 protein families, where we found plant growth promotion-related genes such as the csgBAC and entCEBAH, coded in a metagenome-assembled genome named Kosakonia sp. Nacozari. Finally, we used the FSC to inoculate mine tailing colonizing plants in a greenhouse experiment. The plants with the FSC inocula observed higher relative plant growth rates in sterile substrates. The FSC presents promising features that might make it useful for phytostabilization tailored strategies.
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