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Dove R, Wolfe ER, Stewart NU, Coleman A, Chavez SH, Ballhorn DJ. Root nodules of red alder (Alnus rubra) and sitka alder (Alnus viridis ssp. sinuata) are inhabited by taxonomically diverse cultivable microbial endophytes. Microbiologyopen 2024; 13:e1422. [PMID: 38847331 PMCID: PMC11157421 DOI: 10.1002/mbo3.1422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/10/2024] Open
Abstract
The root nodules of actinorhizal plants are home to nitrogen-fixing bacterial symbionts, known as Frankia, along with a small percentage of other microorganisms. These include fungal endophytes and non-Frankia bacteria. The taxonomic and functional diversity of the microbial consortia within these root nodules is not well understood. In this study, we surveyed and analyzed the cultivable, non-Frankia fungal and bacterial endophytes of root nodules from red and Sitka alder trees that grow together. We examined their taxonomic diversity, co-occurrence, differences between hosts, and potential functional roles. For the first time, we are reporting numerous fungal endophytes of alder root nodules. These include Sporothrix guttuliformis, Fontanospora sp., Cadophora melinii, an unclassified Cadophora, Ilyonectria destructans, an unclassified Gibberella, Nectria ramulariae, an unclassified Trichoderma, Mycosphaerella tassiana, an unclassified Talaromyces, Coniochaeta sp., and Sistotrema brinkmanii. We are also reporting several bacterial genera for the first time: Collimonas, Psychrobacillus, and Phyllobacterium. Additionally, we are reporting the genus Serratia for the second time, with the first report having been recently published in 2023. Pseudomonas was the most frequently isolated bacterial genus and was found to co-inhabit individual nodules with both fungi and bacteria. We found that the communities of fungal endophytes differed by host species, while the communities of bacterial endophytes did not.
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Affiliation(s)
- Robyn Dove
- Portland State University Biology DepartmentPortlandOregonUSA
| | - Emily R. Wolfe
- Portland State University Biology DepartmentPortlandOregonUSA
- Portland State UniversityPortlandOregonUSA
| | - Nathan U. Stewart
- Portland State University Biology DepartmentPortlandOregonUSA
- Portland State UniversityPortlandOregonUSA
| | - Abigail Coleman
- Portland State University Biology DepartmentPortlandOregonUSA
- Oregon Health and Science UniversityPortlandOregonUSA
| | - Sara Herrejon Chavez
- Portland State University Biology DepartmentPortlandOregonUSA
- University of California BerkeleyBerkeleyCaliforniaUSA
| | - Daniel J. Ballhorn
- Portland State University Biology DepartmentPortlandOregonUSA
- Portland State UniversityPortlandOregonUSA
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Zhuang Y, Wang H, Tan F, Wu B, Liu L, Qin H, Yang Z, He M. Rhizosphere metabolic cross-talk from plant-soil-microbe tapping into agricultural sustainability: Current advance and perspectives. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108619. [PMID: 38604013 DOI: 10.1016/j.plaphy.2024.108619] [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: 12/06/2023] [Revised: 03/21/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Rhizosphere interactions from plant-soil-microbiome occur dynamically all the time in the "black microzone" underground, where we can't see intuitively. Rhizosphere metabolites including root exudates and microbial metabolites act as various chemical signalings involving in rhizosphere interactions, and play vital roles on plant growth, development, disease suppression and resistance to stress conditions as well as proper soil health. Although rhizosphere metabolites are a mixture from plant roots and soil microbes, they often are discussed alone. As a rapid appearance of various omics platforms and analytical methods, it offers possibilities and opportunities for exploring rhizosphere interactions in unprecedented breadth and depth. However, our comprehensive understanding about the fine-tuning mechanisms of rhizosphere interactions mediated by these chemical compounds still remain clear. Thus, this review summarizes recent advances systemically including the features of rhizosphere metabolites and their effects on rhizosphere ecosystem, and looks forward to the future research perspectives, which contributes to facilitating better understanding of biochemical communications belowground and helping identify novel rhizosphere metabolites. We also address challenges for promoting the understanding about the roles of rhizosphere metabolites in different environmental stresses.
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Affiliation(s)
- Yong Zhuang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China.
| | - Hao Wang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Furong Tan
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Bo Wu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Linpei Liu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Han Qin
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - ZhiJuan Yang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Mingxiong He
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China.
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3
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Zhao H, He Y, Wang Y, He X, Zhao R, Liu B. Analysis of microbial community evolution, autolysis phenomena, and energy metabolism pathways in Pholiota nameko endophytes. Front Microbiol 2024; 15:1319886. [PMID: 38690362 PMCID: PMC11059008 DOI: 10.3389/fmicb.2024.1319886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/21/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction Pholiota nameko is a widely consumed edible fungus. This study focuses on two crucial developmental stages of Pholiota nameko, namely, mycelium and ascospores. The objectives of this research were to investigate changes in microbial diversity and community structure during the growth of Pholiota nameko and to analyze the adaptability of the dominant strains to their respective habitats through metabolic. Methods Specifically, we conducted second-generation sequencing of the 16S rRNA gene (Illumina) on samples obtained from these stages. In addition, we isolated and characterized endophytes present in Pholiota nameko, focusing on examining the impact of dominant endophyte genera on autolysis. We also conducted a metabolic pathway analysis. Results and discussion The results unveiled 578,414 valid sequences of Pholiota nameko endophytic fungi. At the phylum level, the dominant taxa were Basidiomycota, Ascomycota, Zoopagomycota, and Mucoromycota. At the genus level, the dominant taxa observed were Pholiota, Inocybe, Fusarium, and Hortiboletus. For endophytic bacteria, we obtained 458,475 valid sequences. The dominant phyla were Proteobacteria, TM6, Firmicutes, and Bacteroidetes, while the dominant genera were Edaphobacter, Xanthomonas, Burkholderia, and Pseudomonas. Moreover, we identified the isolated strains in Pholiota nameko using 16S rDNA, and most of them were found to belong to the genus Pseudomonas, with Pseudomonas putida being the most prevalent strain. The findings revealed that the Pseudomonas putida strain has the ability to slow down the breakdown of soluble proteins and partially suppress the metabolic processes that generate superoxide anion radicals in Pholiota nameko, thereby reducing autolysis. Additionally, our results demonstrated that molybdenum enzyme-mediated anaerobic oxidative phosphorylation reactions were the primary energy metabolism pathway in the Pseudomonas putida strain. This suggests that the molybdenum cofactor synthesis pathway might be the main mechanism through which Pholiota nameko adapts to its complex and diverse habitats.
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Affiliation(s)
| | | | | | - Xiaolong He
- College of Life Sciences, Yan’an University, Yan’an, China
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4
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Liu MD, Du Y, Koupaei SK, Kim NR, Fischer MS, Zhang W, Traxler MF. Surface-active antibiotic production as a multifunctional adaptation for postfire microorganisms. THE ISME JOURNAL 2024; 18:wrae022. [PMID: 38366029 PMCID: PMC11069360 DOI: 10.1093/ismejo/wrae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Wildfires affect soils in multiple ways, leading to numerous challenges for colonizing microorganisms. Although it is thought that fire-adapted microorganisms lie at the forefront of postfire ecosystem recovery, the specific strategies that these organisms use to thrive in burned soils remain largely unknown. Through bioactivity screening of bacterial isolates from burned soils, we discovered that several Paraburkholderia spp. isolates produced a set of unusual rhamnolipid surfactants with a natural methyl ester modification. These rhamnolipid methyl esters (RLMEs) exhibited enhanced antimicrobial activity against other postfire microbial isolates, including pyrophilous Pyronema fungi and Amycolatopsis bacteria, compared to the typical rhamnolipids made by organisms such as Pseudomonas spp. RLMEs also showed enhanced surfactant properties and facilitated bacterial motility on agar surfaces. In vitro assays further demonstrated that RLMEs improved aqueous solubilization of polycyclic aromatic hydrocarbons, which are potential carbon sources found in char. Identification of the rhamnolipid biosynthesis genes in the postfire isolate, Paraburkholderia kirstenboschensis str. F3, led to the discovery of rhlM, whose gene product is responsible for the unique methylation of rhamnolipid substrates. RhlM is the first characterized bacterial representative of a large class of integral membrane methyltransferases that are widespread in bacteria. These results indicate multiple roles for RLMEs in the postfire lifestyle of Paraburkholderia isolates, including enhanced dispersal, solubilization of potential nutrients, and inhibition of competitors. Our findings shed new light on the chemical adaptations that bacteria employ to navigate, grow, and outcompete other soil community members in postfire environments.
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Affiliation(s)
- Mira D Liu
- Department of Chemistry, University of California, Berkeley, CA 94720, United States
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, United States
| | - Sara K Koupaei
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States
| | - Nicole R Kim
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States
| | - Monika S Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, United States
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States
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Hata S, Tsuda R, Kojima S, Tanaka A, Kouchi H. Both incompatible and compatible rhizobia inhabit the intercellular spaces of leguminous root nodules. PLANT SIGNALING & BEHAVIOR 2023; 18:2245995. [PMID: 37573516 PMCID: PMC10424618 DOI: 10.1080/15592324.2023.2245995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
In addition to rhizobia, many types of co-existent bacteria are found in leguminous root nodules, but their habitats are unclear. To investigate this phenomenon, we labeled Bradyrhizobium diazoefficiens USDA122 and Bradyrhizobium sp. SSBR45 with Discosoma sp. red fluorescent protein (DsRed) or enhanced green fluorescent protein (eGFP). USDA122 enhances soybean growth by forming effective root nodules, but SSBR45 does not form any nodules. Using low-magnification laser scanning confocal microscopy, we found that infected cells in the central zone of soybean nodules appeared to be occupied by USDA122. Notably, high-magnification microscopy after co-inoculation of non-fluorescent USDA122 and fluorescence-labeled SSBR45 also revealed that SSBR45 inhabits the intercellular spaces of healthy nodules. More unexpectedly, co-inoculation of eGFP-labeled USDA122 and DsRed-labeled SSBR45 (and vice versa) revealed the presence of USDA122 bacteria in both the symbiosomes of infected cells and in the apoplasts of healthy nodules. We then next inspected nodules formed after a mixed inoculation of differently-labeled USDA122, without SSBR45, and confirmed the inhabitation of the both populations of USDA122 in the intercellular spaces. In contrast, infected cells were occupied by single-labeled USDA122. We also observed Mesorhizobium loti in the intercellular spaces of active wild-type nodules of Lotus japonicus using transmission electron microscopy. Compatible intercellular rhizobia have been described during nodule formation of several legume species and in some mutants, but our evidence suggests that this type of colonization may occur much more commonly in leguminous root nodules.
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Affiliation(s)
- Shingo Hata
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Risa Tsuda
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Serina Kojima
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Aiko Tanaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hiroshi Kouchi
- Division of Arts and Sciences, International Christian University, Mitaka, Japan
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Jähne J, Herfort S, Doellinger J, Lasch P, Tam LTT, Borriss R, Vater J. Investigation of the potential of Brevibacillus spp. for the biosynthesis of nonribosomally produced bioactive compounds by combination of genome mining with MALDI-TOF mass spectrometry. Front Microbiol 2023; 14:1286565. [PMID: 38156002 PMCID: PMC10753013 DOI: 10.3389/fmicb.2023.1286565] [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: 08/31/2023] [Accepted: 11/02/2023] [Indexed: 12/30/2023] Open
Abstract
The biosynthetic potential of 11 Brevibacillus spp. strains was investigated by combination of genome mining with mass spectrometric analysis using MALDI-TOF mass spectrometry. These endophytic, plant associated Brevibacillus strains were isolated from crop plants, such as coffee and black pepper, in Vietnam. Draft genomes of these strains were available. They were classified (a) by comparison with type strains and a collection of genome-sequenced Brevibacillus spp. deposited in the NCBI data base as well as (b) by construction of a phylogenetic tree from the core sequences of publicly available genomes of Brevibacillus strains. They were identified as Brevibacillus brevis (1 strain); parabrevis (2 strains); porteri (3 strains); and 5 novel Brevibacillus genomospecies. Our work was specifically focused on the detection and characterization of nonribosomal peptides produced by these strains. Structural characterization of these compounds was performed by LIFT-MALDI-TOF/TOF mass spectrometric sequence analysis. The highlights of our work were the demonstration of the tyrocidines, a well-known family of cyclodecapeptides of great structural variability, as the main products of all investigated strains and the identification of a novel class of pentapeptides produced by B. brevis; B. schisleri; and B. porteri which we designate as brevipentins. Our biosynthetic studies demonstrate that knowledge of their biosynthetic capacity can efficiently assist classification of Brevibacillus species.
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Affiliation(s)
- Jennifer Jähne
- Centre for Biological Threads and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Robert Koch-Institute, Berlin, Germany
| | - Stefanie Herfort
- Centre for Biological Threads and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Robert Koch-Institute, Berlin, Germany
| | - Joerg Doellinger
- Centre for Biological Threads and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Robert Koch-Institute, Berlin, Germany
| | - Peter Lasch
- Centre for Biological Threads and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Robert Koch-Institute, Berlin, Germany
| | - Le Thi Thanh Tam
- Division of Pathology and Phyto-Immunology, Plant Protection Research Institute (PPRI), Ha Noi, Vietnam
| | - Rainer Borriss
- Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
- Institute of Biology, Humboldt University Berlin, Berlin, Germany
| | - Joachim Vater
- Centre for Biological Threads and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Robert Koch-Institute, Berlin, Germany
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7
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Granada Agudelo M, Ruiz B, Capela D, Remigi P. The role of microbial interactions on rhizobial fitness. FRONTIERS IN PLANT SCIENCE 2023; 14:1277262. [PMID: 37877089 PMCID: PMC10591227 DOI: 10.3389/fpls.2023.1277262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023]
Abstract
Rhizobia are soil bacteria that can establish a nitrogen-fixing symbiosis with legume plants. As horizontally transmitted symbionts, the life cycle of rhizobia includes a free-living phase in the soil and a plant-associated symbiotic phase. Throughout this life cycle, rhizobia are exposed to a myriad of other microorganisms that interact with them, modulating their fitness and symbiotic performance. In this review, we describe the diversity of interactions between rhizobia and other microorganisms that can occur in the rhizosphere, during the initiation of nodulation, and within nodules. Some of these rhizobia-microbe interactions are indirect, and occur when the presence of some microbes modifies plant physiology in a way that feeds back on rhizobial fitness. We further describe how these interactions can impose significant selective pressures on rhizobia and modify their evolutionary trajectories. More extensive investigations on the eco-evolutionary dynamics of rhizobia in complex biotic environments will likely reveal fascinating new aspects of this well-studied symbiotic interaction and provide critical knowledge for future agronomical applications.
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Affiliation(s)
- Margarita Granada Agudelo
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Bryan Ruiz
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Delphine Capela
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Philippe Remigi
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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8
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Petrushin IS, Vasilev IA, Markova YA. Drought Tolerance of Legumes: Physiology and the Role of the Microbiome. Curr Issues Mol Biol 2023; 45:6311-6324. [PMID: 37623217 PMCID: PMC10453936 DOI: 10.3390/cimb45080398] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Water scarcity and global warming make drought-tolerant plant species more in-demand than ever. The most drastic damage exerted by drought occurs during the critical growth stages of seed development and reproduction. In the course of their evolution, plants form a variety of drought-tolerance mechanisms, including recruiting beneficial microorganisms. Legumes (one of the three largest groups of higher plants) have unique features and the potential to adapt to abiotic stress. The available literature discusses the genetic (breeding) and physiological aspects of drought tolerance in legumes, neglecting the role of the microbiome. Our review aims to fill this gap: starting with the physiological mechanisms of legume drought adaptation, we describe the symbiotic relationship of the plant host with the microbial community and its role in facing drought. We consider two types of studies related to microbiomes in low-water conditions: comparisons and microbiome engineering (modulation). The first type of research includes diversity shifts and the isolation of microorganisms from the various plant niches to which they belong. The second type focuses on manipulating the plant holobiont through microbiome engineering-a promising biotech strategy to improve the yield and stress-resistance of legumes.
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Affiliation(s)
- Ivan S. Petrushin
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia; (I.A.V.); (Y.A.M.)
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9
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Dhole AM, Shelat HN, Patel HK, Jhala YK. Evaluation of the Co-inoculation Effect of Rhizobium and Plant Growth Promoting Non-rhizobial Endophytes on Vigna radiata. Curr Microbiol 2023; 80:167. [PMID: 37024674 DOI: 10.1007/s00284-023-03266-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/11/2023] [Indexed: 04/08/2023]
Abstract
A unique feature of leguminous plants is the establishment of symbiotic bacterial genera inside root or stem nodules that is being recently re-evaluated for investigating the micro-flora discrete to nitrogen fixation. The present research was carried out to evaluate non-rhizobial endophytes and Rhizobium from root nodules of Vigna radiata and ascertain their co-inoculation effect in pot and field conditions. Each strain displayed one or more plant growth-promoting behaviors in varying degrees. The ability to fix nitrogen was observed in all strains; however, a noticeable enhancement in nitrogen fixation was observed when all three strains were co-inoculated. All three strains were found to possess the nifH gene, which plays a key role in the nitrogen fixation process. However, only Rhizobium sp. AAU B3 also had the nodD gene present. Furthermore, combinations of all three strains produced the highest levels of phosphate solubilization, potash mobilisation, Indole Acetic Acid (IAA), and the stress-relieving enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase. Interestingly, the succession of the root nodule formation within root hairs seedlings was observed under a fluorescence microscope and two NRE were found to be located inside the root nodules, indicating that they are endophytic. Additionally, a pot and field investigation revealed that the combination of chosen Rhizobium and NRE strains had a favorable impact on the growth and yield characteristics of a green gram. Selected bio-inoculants can reduce the utilization of synthetic fertilizers by 75%, which might lead to the restoration of the soil's health. Therefore, these bio-inoculants might be explored commercially for sustainable agriculture production.
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Affiliation(s)
- Archana M Dhole
- B. A. College of Agriculture, Anand Agricultural University, Anand, Gujarat, 388110, India.
| | - Harsha N Shelat
- B. A. College of Agriculture, Anand Agricultural University, Anand, Gujarat, 388110, India
| | - Hiren K Patel
- B. A. College of Agriculture, Anand Agricultural University, Anand, Gujarat, 388110, India
| | - Yogeshvari K Jhala
- B. A. College of Agriculture, Anand Agricultural University, Anand, Gujarat, 388110, India
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10
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Burghardt LT, diCenzo GC. The evolutionary ecology of rhizobia: multiple facets of competition before, during, and after symbiosis with legumes. Curr Opin Microbiol 2023; 72:102281. [PMID: 36848712 DOI: 10.1016/j.mib.2023.102281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 02/27/2023]
Abstract
Rhizobial bacteria have complex lifestyles that involve growth and survival in bulk soil, plant rhizospheres and rhizoplanes, legume infection threads, and mature and senescing legume nodules. In nature, rhizobia coexist and compete with many other rhizobial strains and species to form host associations. We review recent work defining competitive interactions across these environments. We highlight the use of sophisticated measurement tools and sequencing technologies to examine competition mechanisms in planta, and highlight environments (e.g. soil and senescing nodules) where we still know exceedingly little. We argue that moving toward an explicitly ecological framework (types of competition, resources, and genetic differentiation) will clarify the evolutionary ecology of these foundational organisms and open doors for engineering sustainable, beneficial associations with hosts.
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Affiliation(s)
- Liana T Burghardt
- The Pennsylvania State University, Department of Plant Science, University Park, PA 16802, United States; The Pennsylvania State University, Ecology Graduate Program, University Park, PA 16802, United States.
| | - George C diCenzo
- Queen's University, Department of Biology, Kingston, ON K7L 3N6, Canada
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11
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Khan N, Humm EA, Jayakarunakaran A, Hirsch AM. Reviewing and renewing the use of beneficial root and soil bacteria for plant growth and sustainability in nutrient-poor, arid soils. FRONTIERS IN PLANT SCIENCE 2023; 14:1147535. [PMID: 37089637 PMCID: PMC10117987 DOI: 10.3389/fpls.2023.1147535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/16/2023] [Indexed: 05/03/2023]
Abstract
A rapidly increasing human population coupled with climate change and several decades of over-reliance on synthetic fertilizers has led to two pressing global challenges: food insecurity and land degradation. Therefore, it is crucial that practices enabling both soil and plant health as well as sustainability be even more actively pursued. Sustainability and soil fertility encompass practices such as improving plant productivity in poor and arid soils, maintaining soil health, and minimizing harmful impacts on ecosystems brought about by poor soil management, including run-off of agricultural chemicals and other contaminants into waterways. Plant growth promoting bacteria (PGPB) can improve food production in numerous ways: by facilitating resource acquisition of macro- and micronutrients (especially N and P), modulating phytohormone levels, antagonizing pathogenic agents and maintaining soil fertility. The PGPB comprise different functional and taxonomic groups of bacteria belonging to multiple phyla, including Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, among others. This review summarizes many of the mechanisms and methods these beneficial soil bacteria use to promote plant health and asks whether they can be further developed into effective, potentially commercially available plant stimulants that substantially reduce or replace various harmful practices involved in food production and ecosystem stability. Our goal is to describe the various mechanisms involved in beneficial plant-microbe interactions and how they can help us attain sustainability.
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Affiliation(s)
- Noor Khan
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ethan A. Humm
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Akshaya Jayakarunakaran
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ann M. Hirsch
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- *Correspondence: Ann M. Hirsch,
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12
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Ai J, Yu T, Liu X, Jiang Y, Hao Z, Zhao X, Wang E, Deng Z. Nodule-associated diazotrophic community succession is driven by developmental phases combined with microhabitat of Sophora davidii. Front Microbiol 2022; 13:1078208. [PMID: 36532429 PMCID: PMC9751200 DOI: 10.3389/fmicb.2022.1078208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Nodule-associated nitrogen-fixing microorganisms (diazotrophs) residing in legume root nodules, and they have the potential to enhance legume survival. However, the succession characteristics and mechanisms of leguminous diazotrophic communities remain largely unexplored. We performed a high-throughput nifH amplicon sequencing with samples of root nodules and soil in the three developmental phases (young nodules, active nodules and senescent nodules) of the Sophora davidii (Franch.) Skeels root nodules, aiming to investigate the dynamics of nodule-endophytic diazotrophs during three developmental phases of root nodules. The results demonstrated the presence of diverse diazotrophic bacteria and successional community shifting dominated by Mesorhizobium and Bradyrhizobium inside the nodule according to the nodule development. The relative abundance decreased for Mesorhizobium, while decreased first and then increased for Bradyrhizobium in nodule development from young to active to senescent. Additionally, strains M. amorphae BT-30 and B. diazoefficiens B-26 were isolated and selected to test the interaction between them in co-cultured conditions. Under co-culture conditions: B. diazoefficiens B-26 significantly inhibited the growth of M. amorphae BT-30. Intriguingly, growth of B. diazoefficiens B-26 was significantly promoted by co'culture with M. amorphae BT-30 and could utilize some carbon and nitrogen sources that M. amorphae BT-30 could not. Additionally, the composition of microbial community varied in root nodules, in rhizosphere and in bulk soil. Collectively, our study highlights that developmental phases of nodules and the host microhabitat were the key driving factors for the succession of nodule-associated diazotrophic community.
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Affiliation(s)
- Jiamin Ai
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Tianfei Yu
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Xiaodong Liu
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Yingying Jiang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Ziwei Hao
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Xiaoyu Zhao
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Entao Wang
- , Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Zhenshan Deng
- College of Life Sciences, Yan’an University, Yan’an, China,*Correspondence: Zhenshan Deng,
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Li H, Li Z. The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging. Bioengineering (Basel) 2022; 9:707. [PMID: 36421108 PMCID: PMC9687252 DOI: 10.3390/bioengineering9110707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 10/17/2023] Open
Abstract
As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.
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Affiliation(s)
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Liu JQ, Chen SM, Zhang CM, Xu MJ, Xing K, Li CG, Li K, Zhang YQ, Qin S. Abundant and diverse endophytic bacteria associated with medicinal plant Arctium lappa L. and their potential for host plant growth promoting. Antonie Van Leeuwenhoek 2022; 115:1405-1420. [DOI: 10.1007/s10482-022-01785-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/11/2022] [Indexed: 10/31/2022]
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Liu B, Zhang D, Pan X. Nodules of wild legumes as unique natural hotspots of antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156036. [PMID: 35597353 DOI: 10.1016/j.scitotenv.2022.156036] [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: 04/15/2022] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 06/15/2023]
Abstract
Root nodules (RN) of legumes have distinct microenvironment from their symbiotic roots and surrounding soils. The rhizobia can withstand the host-produced phytoalexins and antimicrobial compounds. We thus hypothesize that the wild legume RN may develop unique natural resistome and be antibiotic resistance gene (ARG) hotspots. In this study, in comparison with rhizosphere soil (RS) and bulk soil (BS), we characterized the feature of antibiotic resistance in the RN of two wild legumes, Medicago polymorpha and Astragalus sinicus, by metagenomics. It was shown that the total relative abundance of ARGs followed the order of RN > RS > BS for both legumes. ARGs encoding antibiotic efflux pump predominated in all samples with increased proportion from BS to RN samples for both legumes. Totally 275 ARG subtypes were detected, and diversity of ARGs in RN was significantly lower than in BS samples for both legumes. 32 and 25 unique ARGs subtypes were detected in RN of both legumes. Bacterial community played a key role in shaping nodule-associated resistome because both ARG profiles and bacterial community differed greatly among BS, RS and RN. Rhizobia potentially hosted 10 and 15 ARGs subtypes for both legumes. The number and proportion of plasmid- and ARG-carrying contigs (ACCs) were higher in RN than in BS. Host tracking analysis of plasmid-ACCs suggests that proportion of rhizobial bacteria identified as their hosts decreased from BS to RN samples. No plasmid-ACCs with multiple ARGs were observed in BS samples, whereas they were detected in RN samples of both legumes. Our study showed that even wild legume nodules are unique natural ARG hotspots and enough attention should be paid to the dissemination risk of ARGs posed by globally produced legume crops.
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Affiliation(s)
- Bingshen Liu
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiangliang Pan
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
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Crosbie DB, Mahmoudi M, Radl V, Brachmann A, Schloter M, Kemen E, Marín M. Microbiome profiling reveals that Pseudomonas antagonises parasitic nodule colonisation of cheater rhizobia in Lotus. THE NEW PHYTOLOGIST 2022; 234:242-255. [PMID: 35067935 DOI: 10.1111/nph.17988] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Nodule microbiota are dominated by symbiotic nitrogen-fixing rhizobia, however, other non-rhizobial bacteria also colonise this niche. Although many of these bacteria harbour plant-growth-promoting functions, it is not clear whether these less abundant nodule colonisers impact root-nodule symbiosis. We assessed the relationship between the nodule microbiome and nodulation as influenced by the soil microbiome, by using a metabarcoding approach to characterise the communities inside nodules of healthy and starved Lotus species. A machine learning algorithm and network analyses were used to identify nodule bacteria of interest, which were re-inoculated onto plants in controlled conditions to observe their potential functionality. The nodule microbiome of all tested species differed according to inoculum, but only that of Lotus burttii varied with plant health. Amplicon sequence variants representative of Pseudomonas species were the most indicative non-rhizobial signatures inside healthy L. burttii nodules and negatively correlated with Rhizobium sequences. A representative Pseudomonas isolate co-colonised nodules infected with a beneficial Mesorhizobium, but not with an ineffective Rhizobium isolate and another even reduced the number of ineffective nodules induced on Lotus japonicus. Our results show that nodule endophytes influence the overall outcome of the root-nodule symbiosis, albeit in a plant host-specific manner.
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Affiliation(s)
| | - Maryam Mahmoudi
- Microbial Interactions in Plant Ecosystems, Centre for Plant Molecular Biology, University of Tübingen, Tübingen, 72076, Germany
| | - Viviane Radl
- Comparative Microbiome Analysis, Helmholtz Centre for Environmental Health, Oberschleissheim, 85764, Germany
| | | | - Michael Schloter
- Comparative Microbiome Analysis, Helmholtz Centre for Environmental Health, Oberschleissheim, 85764, Germany
- Chair for Soil Science, Technical University of Munich, Freising, 85354, Germany
| | - Eric Kemen
- Microbial Interactions in Plant Ecosystems, Centre for Plant Molecular Biology, University of Tübingen, Tübingen, 72076, Germany
| | - Macarena Marín
- Genetics, Biocentre, LMU Munich, Martinsried, 82152, Germany
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17
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Dhole A, Shelat H. Non-Rhizobial Endophytes Associated with Nodules of Vigna radiata L. and Their Combined Activity with Rhizobium sp. Curr Microbiol 2022; 79:103. [PMID: 35157135 DOI: 10.1007/s00284-022-02792-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 01/31/2022] [Indexed: 11/27/2022]
Abstract
Root nodules of legume plants are devoted for hosting endophytic symbiotic bacteria that fix atmospheric nitrogen but recently proved as a niche for various non-rhizobial endophytes (NRE) also. In the present investigation, one rhizobial and two NRE were isolated and characterized as Rhizobium sp. AAU B3, Bacillus sp. AAU B6 and Bacillus sp. AAU B12. These isolates were studied for in vitro biocontrol activity against two pathogenic fungi. NRE isolates exhibited antifungal activity against root rot causing Macrophomina phaseolina (ITCC-6749) isolated from Vigna radiata and wilt causing pathogen Fusarium udum Butler isolated from Cajanus cajan in liquid as well as on solid medium. Furthermore, their antagonism was increased markedly when combined with Rhizobium sp. Moreover, Bacillus sp. AAU B6 showed amplification of the zwittermicin A gene (~ 950 bp) which is evident for the production of antibiotics. All three isolates showed HCN production in vitro also, Bacillus sp. AAU B12 exhibited amplification of its gene hcnC. Pathogenic fungal hyphae became thin, transparent, and bent as well as fungi lost their normal growth and branching patterns when exposed to volatile compounds produced by NRE. All the 3 isolates produced siderophores, however siderophore production was increased considerably when all three strains are mixed together. Furthermore, all the three isolates produced cell wall degrading enzymes (chitinase, protease, and cellulase) but lipolytic activity was exhibited only by Rhizobium sp. AAU B3. When NRE inoculated in combination of Rhizobium; overcomes the disease severity against M. phaseolina under pot study. Thus, from present study it is concluded that co-inoculation of NRE and Rhizobium sp. can be exploited as biocontrol bio-agents against M. phaseolina in green gram at field levels.
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Affiliation(s)
- Archana Dhole
- B. A. College of Agriculture, Anand Agricultural University, Anand, Gujarat, 388110, India.
| | - Harsha Shelat
- B. A. College of Agriculture, Anand Agricultural University, Anand, Gujarat, 388110, India
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18
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Pierce EC, Dutton RJ. Putting microbial interactions back into community contexts. Curr Opin Microbiol 2022; 65:56-63. [PMID: 34739927 DOI: 10.1016/j.mib.2021.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 08/31/2021] [Accepted: 10/08/2021] [Indexed: 02/05/2023]
Abstract
Microbial interactions are key aspects of the biology of microbiomes. Recently, there has been a shift in the field towards studying interactions in more representative contexts, whether using multispecies model microbial communities or by looking at interactions in situ. Across diverse microbial systems, these studies have begun to identify common interaction mechanisms. These mechanisms include interactions related to toxic molecules, nutrient competition and cross-feeding, access to metals, signaling pathways, pH changes, and interactions within biofilms. Leveraging technological innovations, many of these studies have used an interdisciplinary approach combining genetic, metabolomic, imaging, and/or microfluidic techniques to gain insight into mechanisms of microbial interactions and into the impact of these interactions on microbiomes.
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Affiliation(s)
- Emily C Pierce
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, USA.
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19
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Costa A, Corallo B, Amarelle V, Stewart S, Pan D, Tiscornia S, Fabiano E. Paenibacillus sp. Strain UY79, Isolated from a Root Nodule of Arachis villosa, Displays a Broad Spectrum of Antifungal Activity. Appl Environ Microbiol 2022; 88:e0164521. [PMID: 34757818 PMCID: PMC8788682 DOI: 10.1128/aem.01645-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
A nodule-inhabiting Paenibacillus sp. strain (UY79) isolated from wild peanut (Arachis villosa) was screened for its antagonistic activity against diverse fungi and oomycetes (Botrytis cinerea, Fusarium verticillioides, Fusarium oxysporum, Fusarium graminearum, Fusarium semitectum, Macrophomina phaseolina, Phomopsis longicolla, Pythium ultimum, Phytophthora sojae, Rhizoctonia solani, Sclerotium rolfsii, and Trichoderma atroviride). The results obtained show that Paenibacillus sp. UY79 was able to antagonize these fungi/oomycetes and that agar-diffusible compounds and volatile compounds (different from HCN) participate in the antagonism exerted. Acetoin, 2,3-butanediol, and 2-methyl-1-butanol were identified among the volatile compounds produced by strain UY79 with possible antagonistic activity against fungi/oomycetes. Paenibacillus sp. strain UY79 did not affect symbiotic association or growth promotion of alfalfa plants when coinoculated with rhizobia. By whole-genome sequence analysis, we determined that strain UY79 is a new species of Paenibacillus within the Paenibacillus polymyxa complex. Diverse genes putatively involved in biocontrol activity were identified in the UY79 genome. Furthermore, according to genome mining and antibiosis assays, strain UY79 would have the capability to modulate the growth of bacteria commonly found in soil/plant communities. IMPORTANCE Phytopathogenic fungi and oomycetes are responsible for causing devastating losses in agricultural crops. Therefore, there is enormous interest in the development of effective and complementary strategies that allow the control of the phytopathogens, reducing the input of agrochemicals in croplands. The discovery of new strains with expanded antifungal activities and with a broad spectrum of action is challenging and of great future impact. Diverse strains belonging to the P. polymyxa complex have been reported to be effective biocontrol agents. Results presented here show that the novel discovered strain of Paenibacillus sp. presents diverse traits involved in antagonistic activity against a broad spectrum of pathogens and is a potential and valuable strain to be further assessed for the development of biofungicides.
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Affiliation(s)
- Andrés Costa
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
| | - Belén Corallo
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Vanesa Amarelle
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
| | - Silvina Stewart
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa Cultivos de Secano. Estación Experimental La Estanzuela, Colonia, Uruguay
| | - Dinorah Pan
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Susana Tiscornia
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Elena Fabiano
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
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Schaedel M, Hidrobo G, Grossman J. From Microns to Meters: Exploring Advances in Legume Microbiome Diversity for Agroecosystem Benefits. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.668195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Legumes are of primary importance for agroecosystems because they provide protein-rich foods and enhance soil fertility through fixed atmospheric nitrogen. The legume-rhizobia symbiosis that makes this possible has been extensively studied, from basic research on biochemical signaling to practical applications in cropping systems. While rhizobia are the most-studied group of associated microorganisms, the functional benefit they confer to their legume hosts by fixing nitrogen is not performed in isolation. Indeed, non-rhizobia members of the rhizosphere and nodule microbiome are now understood to contribute in multiple ways to nodule formation, legume fitness, and other agroecosystem services. In this review, we summarize advances contributing to our understanding of the diversity and composition of bacterial members of the belowground legume microbiome. We also highlight applied work in legume food and forage crops that link microbial community composition with plant functional benefits. Ultimately, further research will assist in the development of multi-species microbial inoculants and cropping systems that maximize plant nutrient benefits, while reducing sources of agricultural pollution.
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21
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Mendoza-Suárez M, Andersen SU, Poole PS, Sánchez-Cañizares C. Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses. FRONTIERS IN PLANT SCIENCE 2021; 12:690567. [PMID: 34489993 PMCID: PMC8416774 DOI: 10.3389/fpls.2021.690567] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Biological nitrogen fixation by Rhizobium-legume symbioses represents an environmentally friendly and inexpensive alternative to the use of chemical nitrogen fertilizers in legume crops. Rhizobial inoculants, applied frequently as biofertilizers, play an important role in sustainable agriculture. However, inoculants often fail to compete for nodule occupancy against native rhizobia with inferior nitrogen-fixing abilities, resulting in low yields. Strains with excellent performance under controlled conditions are typically selected as inoculants, but the rates of nodule occupancy compared to native strains are rarely investigated. Lack of persistence in the field after agricultural cycles, usually due to the transfer of symbiotic genes from the inoculant strain to naturalized populations, also limits the suitability of commercial inoculants. When rhizobial inoculants are based on native strains with a high nitrogen fixation ability, they often have superior performance in the field due to their genetic adaptations to the local environment. Therefore, knowledge from laboratory studies assessing competition and understanding how diverse strains of rhizobia behave, together with assays done under field conditions, may allow us to exploit the effectiveness of native populations selected as elite strains and to breed specific host cultivar-rhizobial strain combinations. Here, we review current knowledge at the molecular level on competition for nodulation and the advances in molecular tools for assessing competitiveness. We then describe ongoing approaches for inoculant development based on native strains and emphasize future perspectives and applications using a multidisciplinary approach to ensure optimal performance of both symbiotic partners.
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Affiliation(s)
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Ochieno DMW, Karoney EM, Muge EK, Nyaboga EN, Baraza DL, Shibairo SI, Naluyange V. Rhizobium-Linked Nutritional and Phytochemical Changes Under Multitrophic Functional Contexts in Sustainable Food Systems. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2020.604396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Rhizobia are bacteria that exhibit both endophytic and free-living lifestyles. Endophytic rhizobial strains are widely known to infect leguminous host plants, while some do infect non-legumes. Infection of leguminous roots often results in the formation of root nodules. Associations between rhizobia and host plants may result in beneficial or non-beneficial effects. Such effects are linked to various biochemical changes that have far-reaching implications on relationships between host plants and the dependent multitrophic biodiversity. This paper explores relationships that exist between rhizobia and various plant species. Emphasis is on nutritional and phytochemical changes that occur in rhizobial host plants, and how such changes affect diverse consumers at different trophic levels. The purpose of this paper is to bring into context various aspects of such interactions that could improve knowledge on the application of rhizobia in different fields. The relevance of rhizobia in sustainable food systems is addressed in context.
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Lucke M, Correa MG, Levy A. The Role of Secretion Systems, Effectors, and Secondary Metabolites of Beneficial Rhizobacteria in Interactions With Plants and Microbes. FRONTIERS IN PLANT SCIENCE 2020; 11:589416. [PMID: 33240304 PMCID: PMC7680756 DOI: 10.3389/fpls.2020.589416] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/14/2020] [Indexed: 05/05/2023]
Abstract
Beneficial rhizobacteria dwell in plant roots and promote plant growth, development, and resistance to various stress types. In recent years there have been large-scale efforts to culture root-associated bacteria and sequence their genomes to uncover novel beneficial microbes. However, only a few strains of rhizobacteria from the large pool of soil microbes have been studied at the molecular level. This review focuses on the molecular basis underlying the phenotypes of three beneficial microbe groups; (1) plant-growth promoting rhizobacteria (PGPR), (2) root nodulating bacteria (RNB), and (3) biocontrol agents (BCAs). We focus on bacterial proteins and secondary metabolites that mediate known phenotypes within and around plants, and the mechanisms used to secrete these. We highlight the necessity for a better understanding of bacterial genes responsible for beneficial plant traits, which can be used for targeted gene-centered and molecule-centered discovery and deployment of novel beneficial rhizobacteria.
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