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Jorrin B, Haskett TL, Knights HE, Martyn A, Underwood TJ, Dolliver J, Ledermann R, Poole PS. Stable, fluorescent markers for tracking synthetic communities and assembly dynamics. MICROBIOME 2024; 12:81. [PMID: 38715147 PMCID: PMC11075435 DOI: 10.1186/s40168-024-01792-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/09/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND After two decades of extensive microbiome research, the current forefront of scientific exploration involves moving beyond description and classification to uncovering the intricate mechanisms underlying the coalescence of microbial communities. Deciphering microbiome assembly has been technically challenging due to their vast microbial diversity but establishing a synthetic community (SynCom) serves as a key strategy in unravelling this process. Achieving absolute quantification is crucial for establishing causality in assembly dynamics. However, existing approaches are primarily designed to differentiate a specific group of microorganisms within a particular SynCom. RESULTS To address this issue, we have developed the differential fluorescent marking (DFM) strategy, employing three distinguishable fluorescent proteins in single and double combinations. Building on the mini-Tn7 transposon, DFM capitalises on enhanced stability and broad applicability across diverse Proteobacteria species. The various DFM constructions are built using the pTn7-SCOUT plasmid family, enabling modular assembly, and facilitating the interchangeability of expression and antibiotic cassettes in a single reaction. DFM has no detrimental effects on fitness or community assembly dynamics, and through the application of flow cytometry, we successfully differentiated, quantified, and tracked a diverse six-member SynCom under various complex conditions like root rhizosphere showing a different colonisation assembly dynamic between pea and barley roots. CONCLUSIONS DFM represents a powerful resource that eliminates dependence on sequencing and/or culturing, thereby opening new avenues for studying microbiome assembly. Video Abstract.
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Affiliation(s)
- Beatriz Jorrin
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Timothy L Haskett
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Hayley E Knights
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Anna Martyn
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Thomas J Underwood
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Jessica Dolliver
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Raphael Ledermann
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Philip S Poole
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
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Diao F, Jia B, Luo J, Ding S, Liu T, Guo W. Arbuscular mycorrhizal fungi drive bacterial community assembly in halophyte Suaeda salsa. Microbiol Res 2024; 282:127657. [PMID: 38422862 DOI: 10.1016/j.micres.2024.127657] [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: 11/29/2023] [Revised: 01/08/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
Halophytes inhabit saline soils, wherein most plants cannot grow, therefore, their ecological value is outstanding. Arbuscular mycorrhizal (AM) fungi can reconstruct microbial communities to assist plants with stress tolerance. However, little information is available on the microbial community assembly of AM fungi in halophytes. A pot experiment was conducted to investigate the effects of AM fungi on rhizosphere bacterial community structure and soil physiochemical characteristics in the halophyte Suaeda salsa at 0, 100, and 400 mM NaCl. The results demonstrated that AM fungi increased soil alkaline phosphatase (ALP) activity at the three NaCl concentrations, and decreased available P, available K, and the activity of soil catalase (CAT) at 100 mM NaCl. AM fungi decreased the Shannon index of the community at 0 and 100 mM NaCl and increased Sobs index at 400 mM NaCl. Regarding the bacterial community structure, AM fungi substantially decreased the abundance of Acidobacteria phylum at 0 and 100 mM NaCl. AM fungi significantly increased the abundance of genus Ramlibacter, an oxyanion-reducing bacteria that can clean out reactive oxygen species (ROS). AM fungi recruited the genera Massilia and Arthrobacter at 0 and 100 mM NaCl, respectively. Some strains in the two genera have been ascribed to plant growth promoting bacteria (PGPB). AM fungi increased the dry weight and promoted halophyte growth at all three NaCl levels. This study supplements the understanding that AM fungi assemble rhizosphere bacterial communities in halophytes.
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Affiliation(s)
- Fengwei Diao
- Shanxi Institute of Organic Dryland Farming, Shanxi Agricultural University, Taiyuan 030031, China; Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Bingbing Jia
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Junqing Luo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Shengli Ding
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Tai Liu
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Wei Guo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China.
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Pacheco-Moreno A, Bollmann-Giolai A, Chandra G, Brett P, Davies J, Thornton O, Poole P, Ramachandran V, Brown JKM, Nicholson P, Ridout C, DeVos S, Malone JG. The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion. PLoS Biol 2024; 22:e3002232. [PMID: 38662644 PMCID: PMC11045101 DOI: 10.1371/journal.pbio.3002232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Plant-associated microbes play vital roles in promoting plant growth and health, with plants secreting root exudates into the rhizosphere to attract beneficial microbes. Exudate composition defines the nature of microbial recruitment, with different plant species attracting distinct microbiota to enable optimal adaptation to the soil environment. To more closely examine the relationship between plant genotype and microbial recruitment, we analysed the rhizosphere microbiomes of landrace (Chevallier) and modern (NFC Tipple) barley (Hordeum vulgare) cultivars. Distinct differences were observed between the plant-associated microbiomes of the 2 cultivars, with the plant-growth promoting rhizobacterial genus Pseudomonas substantially more abundant in the Tipple rhizosphere. Striking differences were also observed between the phenotypes of recruited Pseudomonas populations, alongside distinct genotypic clustering by cultivar. Cultivar-driven Pseudomonas selection was driven by root exudate composition, with the greater abundance of hexose sugars secreted from Tipple roots attracting microbes better adapted to growth on these metabolites and vice versa. Cultivar-driven selection also operates at the molecular level, with both gene expression and the abundance of ecologically relevant loci differing between Tipple and Chevallier Pseudomonas isolates. Finally, cultivar-driven selection is important for plant health, with both cultivars showing a distinct preference for microbes selected by their genetic siblings in rhizosphere transplantation assays.
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Affiliation(s)
- Alba Pacheco-Moreno
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | | | - Govind Chandra
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Brett
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Jack Davies
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Owen Thornton
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Philip Poole
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Vinoy Ramachandran
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - James K. M. Brown
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Nicholson
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Chris Ridout
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Sarah DeVos
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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Cao YH, Zhao XW, Nie G, Wang ZY, Song X, Zhang MX, Hu JP, Zhao Q, Jiang Y, Zhang JL. The salt-tolerance of perennial ryegrass is linked with root exudate profiles and microflora recruitment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170205. [PMID: 38272075 DOI: 10.1016/j.scitotenv.2024.170205] [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: 12/01/2023] [Revised: 01/14/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024]
Abstract
Salinity poses a significant threat to plant growth and development. The root microbiota plays a key role in plant adaptation to saline environments. Nevertheless, it remains poorly understood whether and how perennial grass plants accumulate specific root-derived bacteria when exposed to salinity. Here, we systematically analyzed the composition and variation of rhizosphere and endophytic bacteria, as well as root exudates in perennial ryegrass differing in salt tolerance grown in unsterilized soils with and without salt. Both salt-sensitive (P1) and salt-tolerant (P2) perennial ryegrass genotypes grew better in unsterilized soils compared to sterilized soils under salt stress. The rhizosphere and endophytic bacteria of both P1 and P2 had lower alpha-diversity under salt treatment compared to control. The reduction of alpha-diversity was more pronounced for P1 than for P2. The specific root-derived bacteria, particularly the genus Pseudomonas, were enriched in rhizosphere and endophytic bacteria under salt stress. Changes in bacterial functionality induced by salt stress differed in P1 and P2. Additionally, more root exudates were altered under salt stress in P2 than in P1. The content of important root exudates, mainly including phenylpropanoids, benzenoids, organic acids, had a significantly positive correlation with the abundance of rhizosphere and endophytic bacteria under salt stress. The results indicate that the interactions between root-derived bacteria and root exudates are crucial for the salt tolerance of perennial ryegrass, which provides a potential strategy to manipulate root microbiome for improved stress tolerance of perennial grass species.
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Affiliation(s)
- Yan-Hua Cao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China
| | - Xiong-Wei Zhao
- College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, PR China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Zhi-Yong Wang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agricultural and Forestry, Hainan University, Sanya 572025, PR China
| | - Xin Song
- College of Life Science and Resources and Environment, Yichun University, Yichun 336000, PR China
| | - Ming-Xu Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China
| | - Jin-Peng Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China
| | - Qi Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA.
| | - Jin-Lin Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China; Sanya Institute of Breeding and Multiplication, School of Tropical Agricultural and Forestry, Hainan University, Sanya 572025, PR China.
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Chebotar VK, Zaplatkin AN, Chizhevskaya EP, Gancheva MS, Voshol GP, Malfanova NV, Baganova ME, Khomyakov YV, Pishchik VN. Phytohormone Production by the Endophyte Bacillus safensis TS3 Increases Plant Yield and Alleviates Salt Stress. PLANTS (BASEL, SWITZERLAND) 2023; 13:75. [PMID: 38202382 PMCID: PMC10780329 DOI: 10.3390/plants13010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Endophytic bacteria can be used to overcome the effect of salinity stress and promote plant growth and nutrient uptake. Bacillus safensis colonizes a wide range of habitats due to survival in extreme environments and unique physiological characteristics, such as a high tolerance for salt, heavy metals, and ultraviolet and gamma radiations. The aim of our study was to examine the salt resistance of the endophytic strain TS3 B. safensis and its ability to produce phytohormones and verify its effect on plant yield in field trials and the alleviation of salt stress in pot experiments. We demonstrate that the strain TS3 is capable of producing enzymes and phytohormones such as IAA, ABA and tZ. In pot experiments with radish and oat plants in salinization, the strain TS3 contributed to the partial removal of the negative effect of salinization. The compensatory effect of the strain TS3 on radish plants during salinization was 46.7%, and for oats, it was 108%. We suppose that such a pronounced effect on the plants grown and the salt stress is connected with its ability to produce phytohormones. Genome analysis of the strain TS3 showed the presence of the necessary genes for the synthesis of compounds responsible for the alleviation of the salt stress. Strain B. safensis TS3 can be considered a promising candidate for developing biofertilizer to alleviate salt stress and increase plant yield.
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Affiliation(s)
- Vladimir K. Chebotar
- All-Russia Research Institute for Agricultural Microbiology, Podbel’skogo Shosse 3, Pushkin, 196608 St. Petersburg, Russia; pisemnet-@mail.ru (A.N.Z.); (E.P.C.); (M.S.G.); (M.E.B.); (V.N.P.)
| | - Alexander N. Zaplatkin
- All-Russia Research Institute for Agricultural Microbiology, Podbel’skogo Shosse 3, Pushkin, 196608 St. Petersburg, Russia; pisemnet-@mail.ru (A.N.Z.); (E.P.C.); (M.S.G.); (M.E.B.); (V.N.P.)
| | - Elena P. Chizhevskaya
- All-Russia Research Institute for Agricultural Microbiology, Podbel’skogo Shosse 3, Pushkin, 196608 St. Petersburg, Russia; pisemnet-@mail.ru (A.N.Z.); (E.P.C.); (M.S.G.); (M.E.B.); (V.N.P.)
| | - Maria S. Gancheva
- All-Russia Research Institute for Agricultural Microbiology, Podbel’skogo Shosse 3, Pushkin, 196608 St. Petersburg, Russia; pisemnet-@mail.ru (A.N.Z.); (E.P.C.); (M.S.G.); (M.E.B.); (V.N.P.)
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 St. Petersburg, Russia
| | - Gerben P. Voshol
- Institute of Biology Leiden, Sylviusweg 72, 2333 BE Leiden, The Netherlands; (G.P.V.); (N.V.M.)
| | - Natalia V. Malfanova
- Institute of Biology Leiden, Sylviusweg 72, 2333 BE Leiden, The Netherlands; (G.P.V.); (N.V.M.)
| | - Maria E. Baganova
- All-Russia Research Institute for Agricultural Microbiology, Podbel’skogo Shosse 3, Pushkin, 196608 St. Petersburg, Russia; pisemnet-@mail.ru (A.N.Z.); (E.P.C.); (M.S.G.); (M.E.B.); (V.N.P.)
| | - Yuriy V. Khomyakov
- Agrophysical Scientific Research Institute, Grazhdansky pr. 14, 195220 St. Petersburg, Russia;
| | - Veronika N. Pishchik
- All-Russia Research Institute for Agricultural Microbiology, Podbel’skogo Shosse 3, Pushkin, 196608 St. Petersburg, Russia; pisemnet-@mail.ru (A.N.Z.); (E.P.C.); (M.S.G.); (M.E.B.); (V.N.P.)
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6
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Todorović I, Moënne-Loccoz Y, Raičević V, Jovičić-Petrović J, Muller D. Microbial diversity in soils suppressive to Fusarium diseases. FRONTIERS IN PLANT SCIENCE 2023; 14:1228749. [PMID: 38111879 PMCID: PMC10726057 DOI: 10.3389/fpls.2023.1228749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/10/2023] [Indexed: 12/20/2023]
Abstract
Fusarium species are cosmopolitan soil phytopathogens from the division Ascomycota, which produce mycotoxins and cause significant economic losses of crop plants. However, soils suppressive to Fusarium diseases are known to occur, and recent knowledge on microbial diversity in these soils has shed new lights on phytoprotection effects. In this review, we synthesize current knowledge on soils suppressive to Fusarium diseases and the role of their rhizosphere microbiota in phytoprotection. This is an important issue, as disease does not develop significantly in suppressive soils even though pathogenic Fusarium and susceptible host plant are present, and weather conditions are suitable for disease. Soils suppressive to Fusarium diseases are documented in different regions of the world. They contain biocontrol microorganisms, which act by inducing plants' resistance to the pathogen, competing with or inhibiting the pathogen, or parasitizing the pathogen. In particular, some of the Bacillus, Pseudomonas, Paenibacillus and Streptomyces species are involved in plant protection from Fusarium diseases. Besides specific bacterial populations involved in disease suppression, next-generation sequencing and ecological networks have largely contributed to the understanding of microbial communities in soils suppressive or not to Fusarium diseases, revealing different microbial community patterns and differences for a notable number of taxa, according to the Fusarium pathosystem, the host plant and the origin of the soil. Agricultural practices can significantly influence soil suppressiveness to Fusarium diseases by influencing soil microbiota ecology. Research on microbial modes of action and diversity in suppressive soils should help guide the development of effective farming practices for Fusarium disease management in sustainable agriculture.
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Affiliation(s)
- Irena Todorović
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Yvan Moënne-Loccoz
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Vera Raičević
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | | | - Daniel Muller
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
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Busoms S, Fischer S, Yant L. Chasing the mechanisms of ecologically adaptive salinity tolerance. PLANT COMMUNICATIONS 2023; 4:100571. [PMID: 36883005 PMCID: PMC10721451 DOI: 10.1016/j.xplc.2023.100571] [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: 12/09/2022] [Revised: 02/12/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Plants adapted to challenging environments offer fascinating models of evolutionary change. Importantly, they also give information to meet our pressing need to develop resilient, low-input crops. With mounting environmental fluctuation-including temperature, rainfall, and soil salinity and degradation-this is more urgent than ever. Happily, solutions are hiding in plain sight: the adaptive mechanisms from natural adapted populations, once understood, can then be leveraged. Much recent insight has come from the study of salinity, a widespread factor limiting productivity, with estimates of 20% of all cultivated lands affected. This is an expanding problem, given increasing climate volatility, rising sea levels, and poor irrigation practices. We therefore highlight recent benchmark studies of ecologically adaptive salt tolerance in plants, assessing macro- and microevolutionary mechanisms, and the recently recognized role of ploidy and the microbiome on salinity adaptation. We synthesize insight specifically on naturally evolved adaptive salt-tolerance mechanisms, as these works move substantially beyond traditional mutant or knockout studies, to show how evolution can nimbly "tweak" plant physiology to optimize function. We then point to future directions to advance this field that intersect evolutionary biology, abiotic-stress tolerance, breeding, and molecular plant physiology.
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Affiliation(s)
- Silvia Busoms
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Bellaterra, Barcelona E-08193, Spain
| | - Sina Fischer
- Future Food Beacon of Excellence, University of Nottingham, Nottingham NG7 2RD, UK; School of Biosciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Levi Yant
- Future Food Beacon of Excellence, University of Nottingham, Nottingham NG7 2RD, UK; School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
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Jia F, Chang F, Guan M, Jia Q, Sun Y, Li Z. Effects of rotation and Bacillus on the changes of continuous cropping soil fungal communities in American ginseng. World J Microbiol Biotechnol 2023; 39:354. [PMID: 37874395 PMCID: PMC10598105 DOI: 10.1007/s11274-023-03807-w] [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: 08/03/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023]
Abstract
The continuous cropping obstacle is the main factor in leading to difficulty in American ginseng replanting. The dormant microbiota in the soil may be the cause of American ginseng disease and eventually caused continuous cropping obstacles, but there are few studies on the dynamic changes of soil microenvironment after American ginseng planting. In this study, we tracked short-term variation in physicochemical properties, enzyme activities, and fungal communities over time-series in soils with continuous cropping obstacle under crop rotation and probiotic Bacillus treatments. Furthermore, we examined the relationships between the important fungal compositions and the soil properties. The results showed that sucrase, cellulase, urease and acid phosphatase activities were significantly increased, while catalase and dehydrogenase were decreased with treatments time. Rotation treatment significantly affected the diversity, dissimilarity degree and species distribution of soil fungal community with continuous cropping obstacle over a short-term. Moreover, beneficial fungal biomarkers such as Cladorrhinum, Oidiodendron, and Mariannaea were accumulated at 48 h under rotation treatments. Almost all fungal biomarkers were negatively correlated with hydrolases and positively correlated with oxidoreductases and acid phosphatase under crop rotation treatments. This study suggested that compared to probiotic Bacillus, crop rotation can significantly affect soil fungal community structure, especially the enrichment of specific potentially beneficial fungal species. Our findings provide a scientific basis for understanding the dynamic changes of fungal communities and soil properties with continuous cropping obstacle of American ginseng in initial stage of soil improvement.
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Affiliation(s)
- Fengan Jia
- Shaanxi Institute of Microbiology, Xi'an, 710043, China
| | - Fan Chang
- Shaanxi Institute of Microbiology, Xi'an, 710043, China
| | - Min Guan
- Shaanxi Agricultural Machinery Research Institute, Xianyang, 712000, China
| | - Qingan Jia
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yan Sun
- College of Life Science, Shaanxi Normal University, Xi'an, 710062, China
| | - Zhi Li
- College of Life Science, Shaanxi Normal University, Xi'an, 710062, China.
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Kumar M, Ansari WA, Zeyad MT, Singh A, Chakdar H, Kumar A, Farooqi MS, Sharma A, Srivastava S, Srivastava AK. Core microbiota of wheat rhizosphere under Upper Indo-Gangetic plains and their response to soil physicochemical properties. FRONTIERS IN PLANT SCIENCE 2023; 14:1186162. [PMID: 37255554 PMCID: PMC10226189 DOI: 10.3389/fpls.2023.1186162] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023]
Abstract
Wheat is widely cultivated in the Indo-Gangetic plains of India and forms the major staple food in the region. Understanding microbial community structure in wheat rhizosphere along the Indo-Gangetic plain and their association with soil properties can be an important base for developing strategies for microbial formulations. In the present study, an attempt was made to identify the core microbiota of wheat rhizosphere through a culture-independent approach. Rhizospheric soil samples were collected from 20 different sites along the upper Indo-Gangetic plains and their bacterial community composition was analyzed based on sequencing of the V3-V4 region of the 16S rRNA gene. Diversity analysis has shown significant variation in bacterial diversity among the sites. The taxonomic profile identified Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Planctomycetes, Verrucomicrobia, Firmicutes, and Cyanobacteria as the most dominant phyla in the wheat rhizosphere in the region. Core microbiota analysis revealed 188 taxa as core microbiota of wheat rhizosphere with eight genera recording more than 0.5% relative abundance. The order of most abundant genera in the core microbiota is Roseiflexus> Flavobacterium> Gemmatimonas> Haliangium> Iamia> Flavisolibacter> Ohtaekwangia> Herpetosiphon. Flavobacterium, Thermomonas, Massilia, Unclassified Rhizobiaceae, and Unclassified Crenarchaeota were identified as keystone taxa of the wheat rhizosphere. Correlation studies revealed, pH, organic carbon content, and contents of available nitrogen, phosphorus, and iron as the major factors driving bacterial diversity in the wheat rhizosphere. Redundancy analysis has shown the impact of different soil properties on the relative abundance of different genera of the core microbiota. The results of the present study can be used as a prelude to be developing microbial formulations based on core microbiota.
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Affiliation(s)
- Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Waquar Akhter Ansari
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Mohammad Tarique Zeyad
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Arjun Singh
- ICAR-Central Soil Salinity Research Institute, Regional Research Station (RRS), Lucknow, Uttar Pradesh, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Adarsh Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | | | - Anu Sharma
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Alok Kumar Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
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10
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Huang Q, Wang N, Liu J, Liao H, Zeng Z, Hu C, Wei C, Tan S, Liu F, Li G, Huang H, Chen D, Wei S, Qin Z. Soil bacterial communities associated with marbled fruit in Citrus reticulata Blanco 'Orah'. FRONTIERS IN PLANT SCIENCE 2023; 14:1098042. [PMID: 37223817 PMCID: PMC10200933 DOI: 10.3389/fpls.2023.1098042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/03/2023] [Indexed: 05/25/2023]
Abstract
Citrus reticulata Blanco 'Orah' is grown throughout southern China and provides enormous economic value. However, the agricultural industry has suffered substantial losses during recent years due to marbled fruit disease. The present study focuses on the soil bacterial communities associated with marbled fruit in 'Orah'. The agronomic traits and microbiomes of plants with normal and marbled fruit from three different orchards were compared. No significant differences were found in agronomic traits between the groups, except for higher fruit yields and higher quality of fruits in normal fruit group. Additionally, a total of 2,106,050 16S rRNA gene sequences were generated via the NovoSeq 6000. The alpha diversity index (including the Shannon and Simpson indices), Bray-Curtis similarity, and principal component analyses indicated no significant differences in microbiome diversity between normal and marbled fruit groups. For the healthy 'Orah', the most abundant associated phyla were Bacteroidetes, Firmicutes, and Proteobacteria. In comparison, Burkholderiaceae and Acidobacteria were the most abundant taxa with the marbled fruit group. In addition, the family Xanthomonadaceae and the genus Candidatus Nitrosotalea were prevalent with this group. Analysis using the Kyoto Encyclopedia of Genes and Genomes pathways showed that several pathways related to metabolism significantly differed between the groups. Thus, the present study provides valuable information regarding soil bacterial communities associated with marbled fruit in 'Orah'.
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Affiliation(s)
- Qichun Huang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Nina Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jimin Liu
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huihong Liao
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zhikang Zeng
- Institute of Agricultural Science and Technology Information, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Chengxiao Hu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Chizhang Wei
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Songyue Tan
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Fuping Liu
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Guoguo Li
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hongming Huang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Dongkui Chen
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Shaolong Wei
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zelin Qin
- Institute of Agricultural Science and Technology Information, Guangxi Academy of Agricultural Sciences, Nanning, China
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11
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Jiang X, Lu C, Hu R, Shi W, Zhou L, Wen P, Jiang Y, Lo YM. Nutritional and microbiological effects of vermicompost tea in hydroponic cultivation of maple peas (
Pisum sativum
var.
arvense
L.). Food Sci Nutr 2023. [DOI: 10.1002/fsn3.3299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023] Open
Affiliation(s)
- Xinyi Jiang
- Institute for Advanced Study Shenzhen University Shenzhen China
| | - Ci Lu
- Institute for Advanced Study Shenzhen University Shenzhen China
| | - Runmeng Hu
- Institute for Advanced Study Shenzhen University Shenzhen China
| | - Wenyang Shi
- Institute for Advanced Study Shenzhen University Shenzhen China
| | - Libang Zhou
- Institute for Advanced Study Shenzhen University Shenzhen China
| | - Puzhao Wen
- Institute for Advanced Study Shenzhen University Shenzhen China
| | - Yizhou Jiang
- Institute for Advanced Study Shenzhen University Shenzhen China
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12
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Jamil FN, Hashim AM, Yusof MT, Saidi NB. Association of soil fungal community composition with incidence of Fusarium wilt of banana in Malaysia. Mycologia 2023; 115:178-186. [PMID: 36893072 DOI: 10.1080/00275514.2023.2180975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Banana (Musa spp.), an important food crop in many parts of the world, is threatened by a deadly wilt disease caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (TR4). Increasing evidence indicates that plant actively recruits beneficial microbes in the rhizosphere to suppress soil-borne pathogens. Hence, studies on the composition and diversity of the root-associated microbial communities are important for banana health. Research on beneficial microbial communities has focused on bacteria, although fungi can also influence soil-borne disease. Here, high-throughput sequencing targeting the fungal internal transcribed spacer (ITS) was employed to systematically characterize the difference in the soil fungal community associated with Fusarium wilt (FW) of banana. The community structure of fungi in the healthy and TR4-infected rhizospheres was significantly different compared with that of bulk soil within the same farm. The rhizosphere soils of infected plants exhibited higher richness and diversity compared with healthy plants, with significant abundance of Fusarium genus at 14%. In the healthy rhizosphere soil, Penicillium spp. were more abundant at 7% and positively correlated with magnesium. This study produced a detailed description of fungal community structure in healthy and TR4-infected banana soils in Malaysia and identified candidate biomarker taxa that may be associated with FW disease promotion and suppression. The findings also expand the global inventory of fungal communities associated with the components of asymptomatic and symptomatic banana plants infected by TR4.
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Affiliation(s)
- Fatin Nadiah Jamil
- Institute of Biosciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Amalia Mohd Hashim
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
- Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Mohd Termizi Yusof
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Noor Baity Saidi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
- Laboratory of Sustainable Agronomy and Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
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13
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Yin Y, Wang X, Hu Y, Li F, Cheng H. Soil bacterial community structure in the habitats with different levels of heavy metal pollution at an abandoned polymetallic mine. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130063. [PMID: 36182879 DOI: 10.1016/j.jhazmat.2022.130063] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Heavy metal pollution caused by mining activities can be harmful to soil microbiota, which are highly sensitive to heavy metal stress. This study aimed to investigate the response of soil bacterial communities to varying levels of heavy metal pollution in four types of habitats (i.e., tailing, remediation, natural recovery, and undisturbed areas) at an abandoned polymetallic mine by high-throughput 16 S rRNA gene sequencing, and to determine the dominant ecological processes and major factors driving the variations in bacterial community composition. The diversity and composition of bacterial communities varied significantly between soil habitats (p < 0.05). Heterogeneous selection played a crucial role in shaping the difference of bacterial community composition between distinct soil habitats. Redundancy analysis and Pearson correlation analysis revealed that the total contents of Cu and Zn were key factors causing the difference in bacterial community composition in the tailing and remediation areas, whereas bioavailable Mn and Cd, total nitrogen, available nitrogen, soil organic carbon, vegetation coverage, and plant diversity were key factors shaping the soil bacterial structure in the undisturbed and natural recovery areas. These findings provide insights into the distribution patterns of bacterial communities in soil habitats with different levels of heavy metal pollution, and the dominant ecological processes and the corresponding environmental drivers, and expand knowledge in bacterial assembly mechanisms in mining regions.
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Affiliation(s)
- Yue Yin
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Xiaojie Wang
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China; State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yuanan Hu
- MOE Laboratory of Groundwater Circulation and Evolution, School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Fadong Li
- State Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
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14
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Lidoy J, Berrio E, García M, España-Luque L, Pozo MJ, López-Ráez JA. Flavonoids promote Rhizophagus irregularis spore germination and tomato root colonization: A target for sustainable agriculture. FRONTIERS IN PLANT SCIENCE 2023; 13:1094194. [PMID: 36684723 PMCID: PMC9849897 DOI: 10.3389/fpls.2022.1094194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
The use of arbuscular mycorrhizal (AM) fungi has great potential, being used as biostimulants, biofertilizers and bioprotection agents in agricultural and natural ecosystems. However, the application of AM fungal inoculants is still challenging due to the variability of results when applied in production systems. This variability is partly due to differences in symbiosis establishment. Reducing such variability and promoting symbiosis establishment is essential to improve the efficiency of the inoculants. In addition to strigolactones, flavonoids have been proposed to participate in the pre-symbiotic plant-AM fungus communication in the rhizosphere, although their role is still unclear. Here, we studied the specific function of flavonoids as signaling molecules in AM symbiosis. For that, both in vitro and in planta approaches were used to test the stimulatory effect of an array of different subclasses of flavonoids on Rhizophagus irregularis spore germination and symbiosis establishment, using physiological doses of the compounds. We show that the flavone chrysin and the flavonols quercetin and rutin were able to promote spore germination and root colonization at low doses, confirming their role as pre-symbiotic signaling molecules in AM symbiosis. The results pave the way to use these flavonoids in the formulation of AM fungal-based products to promote the symbiosis. This can improve the efficiency of commercial inoculants, and therefore, help to implement their use in sustainable agriculture.
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15
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Zhou N, Mei CM, Zhu XY, Zhao JJ, Ma MG, Li WD. Research progress of rhizosphere microorganisms in Fritillaria L. medicinal plants. Front Bioeng Biotechnol 2022; 10:1054757. [PMID: 36420438 PMCID: PMC9676442 DOI: 10.3389/fbioe.2022.1054757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/25/2022] [Indexed: 12/01/2023] Open
Abstract
The soil's rhizosphere is a highly active place where the exchange of substances and information occurs among plants, soils, and microorganisms. The microorganisms involved are crucial to the activities of plant growth and development, metabolism, and reproduction. Fritillaria L. medicinal plants are unique Chinese medicinal ingredients, but the continuous cropping obstacles formed in the artificial planting process is severely harmful to the growth and development of these medicinal plants. In this review, we summarized the current species and distribution of Fritillaria L. in China, and analyzed the changes in microbial diversity (mainly among bacteria and fungi) in the rhizosphere of these plants under long-term continuous cropping. The fungi showed an increasing trend in the soil rhizosphere, resulting in the transition of the soil from the high-fertility "bacterial type" to the low-fertility "fungal type" as planting years increased. Furthermore, the interaction between Fritillaria L. medicinal plants and the rhizosphere microorganisms was reviewed, and promising applications for the rhizosphere microbiome in the cultivation of Fritillaria L. medicinal plants were suggested. It is expected that this review will facilitate the in-depth understanding of rhizosphere microorganisms in the growth, accumulation of active ingredients, and disease control of Fritillaria L.
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Affiliation(s)
- Nong Zhou
- College of Pharmacy, Engineering Center of State Ministry of Education for Standardization of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, China
- Chongqing Engineering Laboratory of Green Planting and Deep Processing of Famous-region Drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Chun-Mei Mei
- College of Pharmacy, Engineering Center of State Ministry of Education for Standardization of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xing-Yu Zhu
- College of Pharmacy, Engineering Center of State Ministry of Education for Standardization of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jing-Jing Zhao
- Chongqing Engineering Laboratory of Green Planting and Deep Processing of Famous-region Drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Ming-Guo Ma
- Chongqing Engineering Laboratory of Green Planting and Deep Processing of Famous-region Drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
- Research Center of Biomass Clean Utilization, Beijing Key Laboratory of Lignocellulosic Chemistry, College of Materials Science and Technology, Beijing Forestry University, Beijing, China
| | - Wei-Dong Li
- College of Pharmacy, Engineering Center of State Ministry of Education for Standardization of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, China
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16
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Chebotar VK, Chizhevskaya EP, Baganova ME, Keleinikova OV, Yuzikhin OS, Zaplatkin AN, Khonina OV, Kostitsin RD, Lapenko NG. Endophytes from Halotolerant Plants Aimed to Overcome Salinity and Draught. PLANTS (BASEL, SWITZERLAND) 2022; 11:2992. [PMID: 36365445 PMCID: PMC9658857 DOI: 10.3390/plants11212992] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/30/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
The aim of our research was to study the endosphere of four halophytic plants: Salicornia europaea L., Salsola australis (R.Br.), Bassia sedoides (Pall.) and Kochia prostrata (L.) Schrad. from arid and saline areas of the Stavropol Territory, Russia. In total, 28 endophyte strains were isolated from the roots and stems of these halophytic plants. Most of the isolates (23 out of 28) were identified as Bacillus sp. while others belonged to the genera Oceanobacillus, Paenibacillus, Pantoea, Alcaligenes and Myroides. Three strains of Bacillus sp. (Se5R, Se1-1R, and Se1-3S), isolated from the S. europaea were capable of growth at 55 °C and in 10% of NaCl. Strains Se1-4S, Kp20-2S, and Bs11-2S Bacillus sp. (isolated from the S. australis, K. prostrata and B. sedoides, respectively) demonstrated strong plant growth promoting activity: 85-265% over control lettuce plants and a high degree of growth suppression (59.1-81.2%) of pathogenic fungi Fusarium oxysporum, Bipolaris sorokiniana and Rhizoctonia solani. Selected strains can be promising candidates for the development of bioinoculants to facilitate salt soil phytoremediation and be beneficial for mitigating the salt stress to the plants growing in salt-affected habitats.
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Affiliation(s)
- Vladimir K. Chebotar
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo hwy, 3, Pushkin, St. Petersburg 196608, Russia
| | - Elena P. Chizhevskaya
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo hwy, 3, Pushkin, St. Petersburg 196608, Russia
| | - Maria E. Baganova
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo hwy, 3, Pushkin, St. Petersburg 196608, Russia
| | - Oksana V. Keleinikova
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo hwy, 3, Pushkin, St. Petersburg 196608, Russia
| | - Oleg S. Yuzikhin
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo hwy, 3, Pushkin, St. Petersburg 196608, Russia
| | - Alexander N. Zaplatkin
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo hwy, 3, Pushkin, St. Petersburg 196608, Russia
| | - Olesya V. Khonina
- North Caucasus Federal Scientific Agrarian Center, Federal State Budgetary Scientific Institution, Stavropol Territory, Nikonova str., 49, Shpakovsky District, Mikhailovsk 356241, Russia
| | - Roman D. Kostitsin
- North Caucasus Federal Scientific Agrarian Center, Federal State Budgetary Scientific Institution, Stavropol Territory, Nikonova str., 49, Shpakovsky District, Mikhailovsk 356241, Russia
| | - Nina G. Lapenko
- North Caucasus Federal Scientific Agrarian Center, Federal State Budgetary Scientific Institution, Stavropol Territory, Nikonova str., 49, Shpakovsky District, Mikhailovsk 356241, Russia
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17
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Yang Z, Li L, Zhu W, Xiao S, Chen S, Liu J, Xu Q, Guo F, Lan S. Nitrogen fertilizer amount has minimal effect on rhizosphere bacterial diversity during different growth stages of peanut. PeerJ 2022; 10:e13962. [PMID: 36345480 PMCID: PMC9636873 DOI: 10.7717/peerj.13962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/08/2022] [Indexed: 01/18/2023] Open
Abstract
The impact of short-term nitrogen fertilizer input on the structure and diversity of peanut rhizosphere microbiota (RM) at different growth stages (GSs) was explored in the southern paddy soil planting environment. Three levels of nitrogen were applied in the field: control (LN, 0 kg/hm2), medium nitrogen (MN, 55.68 kg/hm2), and high nitrogen (HN, 111.36 kg/hm2). The rhizosphere soil was collected during four GSs for high-throughput sequencing and chemical properties analysis. The effect of nitrogen fertilizer application on peanut RM was minimal and was obvious only at the seedling stage. In the four peanut GSs, a significant increase in relative abundance was observed for only one operational taxonomic unit (OTU) of Nitrospira under HN conditions at the seedling stage and mature stage, while there was no consistent change in other OTUs. The difference in RM among different peanut GSs was greater than that caused by the amount of nitrogen fertilizer. This may be due to the substantial differences in soil chemical properties (especially alkali-hydrolyzable nitrogen, pH, and available potassium or total potassium) among peanut GSs, as these significantly affected the RM structure. These results are of great value to facilitate deeper understanding of the effect of nitrogen fertilizer on peanut RM structure.
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Affiliation(s)
- Zheng Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Lin Li
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China
| | - Wenjuan Zhu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Siyuan Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Siyu Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Jing Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Qian Xu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Feng Guo
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Shile Lan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
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18
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Tkacz A, Ledermann R, Martyn A, Schornack S, Oldroyd GED, Poole PS. Nodulation and nitrogen fixation in Medicago truncatula strongly alters the abundance of its root microbiota and subtly affects its structure. Environ Microbiol 2022; 24:5524-5533. [PMID: 36054464 PMCID: PMC9804836 DOI: 10.1111/1462-2920.16164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/07/2022] [Indexed: 01/09/2023]
Abstract
The plant common symbiosis signalling (SYM) pathway has shared function between interactions with rhizobia and arbuscular mycorrhizal fungi, the two most important symbiotic interactions between plants and microorganisms that are crucial in plant and agricultural yields. Here, we determine the role of the plant SYM pathway in the structure and abundance of the microbiota in the model legume Medicago truncatula and whether this is controlled by the nitrogen or phosphorus status of the plant. We show that SYM mutants (dmi3) differ substantially from the wild type (WT) in the absolute abundance of the root microbiota, especially under nitrogen limitation. Changes in the structure of the microbiota were less pronounced and depended on both plant genotype and nutrient status. Thus, the SYM pathway has a major impact on microbial abundance in M. truncatula and also subtly alters the composition of the microbiota.
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Affiliation(s)
| | | | - Anna Martyn
- Department of BiologyUniversity of OxfordOxfordUK
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19
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Li CC, Jhou SM, Li YC, Ciou JW, Lin YY, Hung SC, Chang JH, Chang JC, Sun DS, Chou ML, Chang HH. Exposure to low levels of photocatalytic TiO 2 nanoparticles enhances seed germination and seedling growth of amaranth and cruciferous vegetables. Sci Rep 2022; 12:18228. [PMID: 36309586 PMCID: PMC9617883 DOI: 10.1038/s41598-022-23179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/26/2022] [Indexed: 12/31/2022] Open
Abstract
Titanium dioxide (TiO2) is one of the most common compounds on Earth, and it is used in natural forms or engineered bulks or nanoparticles (NPs) with increasing rates. However, the effect of TiO2 NPs on plants remains controversial. Previous studies demonstrated that TiO2 NPs are toxic to plants, because the photocatalytic property of TiO2 produces biohazardous reactive oxygen species. In contrast, another line of evidence suggested that TiO2 NPs are beneficial to plant growth. To verify this argument, in this study, we used seed germination of amaranth and cruciferous vegetables as a model system. Intriguingly, our data suggested that the controversy was due to the dosage effect. The photocatalytic activity of TiO2 NPs positively affected seed germination and growth through gibberellins in a plant-tolerable range (0.1 and 0.2 mg/cm2), whereas overdosing (1 mg/cm2) induced tissue damage. Given that plants are the foundations of the ecosystem; these findings are useful for agricultural application, sustainable development and maintenance of healthy environments.
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Affiliation(s)
- Chi-Cheng Li
- grid.414692.c0000 0004 0572 899XDepartment of Hematology and Oncology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan ,Center of Stem Cell & Precision Medicine, Hualien Tzu Chi Hospital, Hualien, Taiwan
| | - Sian-Ming Jhou
- grid.411824.a0000 0004 0622 7222Tzu-Chi Senior High School Affiliated With Tzu-Chi University, Hualien, Taiwan
| | - Yi-Chen Li
- grid.411824.a0000 0004 0622 7222Tzu-Chi Senior High School Affiliated With Tzu-Chi University, Hualien, Taiwan
| | - Jhih-Wei Ciou
- grid.411824.a0000 0004 0622 7222Tzu-Chi Senior High School Affiliated With Tzu-Chi University, Hualien, Taiwan
| | - You-Yen Lin
- grid.411824.a0000 0004 0622 7222Department of Molecular Biology and Human Genetics, Tzu-Chi University, Hualien, Taiwan
| | - Shih-Che Hung
- grid.411824.a0000 0004 0622 7222Department of Molecular Biology and Human Genetics, Tzu-Chi University, Hualien, Taiwan ,grid.411824.a0000 0004 0622 7222Institute of Medical Sciences, Tzu-Chi University, Hualien, Taiwan
| | - Jen-Hsiang Chang
- grid.445052.20000 0004 0639 3773Department and Graduate School of Computer Science, National Pingtung University, Pingtung, Taiwan
| | | | - Der-Shan Sun
- grid.411824.a0000 0004 0622 7222Department of Molecular Biology and Human Genetics, Tzu-Chi University, Hualien, Taiwan ,grid.411824.a0000 0004 0622 7222Institute of Medical Sciences, Tzu-Chi University, Hualien, Taiwan
| | - Ming-Lun Chou
- grid.411824.a0000 0004 0622 7222Department of Life Sciences, Tzu-Chi University, Hualien, Taiwan
| | - Hsin-Hou Chang
- grid.411824.a0000 0004 0622 7222Department of Molecular Biology and Human Genetics, Tzu-Chi University, Hualien, Taiwan ,grid.411824.a0000 0004 0622 7222Institute of Medical Sciences, Tzu-Chi University, Hualien, Taiwan
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20
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Exploring the core microbiota in scented rice (Oryza sativa L.) rhizosphere through metagenomics approach. Microbiol Res 2022; 263:127157. [PMID: 35944355 DOI: 10.1016/j.micres.2022.127157] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/29/2022] [Accepted: 08/01/2022] [Indexed: 11/22/2022]
Abstract
Rice is a major food crop cultivated around the globe. Specially scented rice varieties are of commercial importance but they are low-yielding. The rhizospheric microflora plays a significant role in improving yield and aroma. However, the core microbiome of the scented rice rhizosphere is comparatively less explored. Here, we analyzed the core microbiome associated with the rhizosphere of the scented (Ambemohar-157 and Dehradun basmati) in comparison with non-scented rice (Kolam and Arize 6444 Gold) cultivated at two different geoclimatic zones of India (Maharashtra and Uttarakhand) using the metagenomics approach. The alpha and beta diversity analysis showed that the microbial communities associated with scented and non-scented varieties significantly changes with respect to richness, diversity, and evenness. The taxonomic profiling revealed the variation in composition, diversity, and abundance of the microbiome in terms of phyla and genera associated with scented rice varieties over non-scented. The cluster analysis distinguishes the microbial communities based on their geographical positions. The core microbiome analysis revealed that scented rice rhizosphere shelters distinct and unique microbiota. 28.6 % of genera were exclusively present only in the scented rice rhizosphere. The putative functional gene annotation revealed the high abundance of genes related to the biosynthesis of 2-acetyl-1-pyrroline (2AP) precursors in scented rice. The precursor feeding analysis revealed proline as a preferred substrate by 2AP synthesizing bacteria. The 2AP precursor proline and proline metabolism genes showed a positive correlation. The scented rice-specific rhizobacteria pointed out in this study can be used as bio-inoculants for enhancing aroma, yield, and sustainable rice cultivation.
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21
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Li Q, Li H, Yang Z, Cheng X, Zhao Y, Qin L, Bisseling T, Cao Q, Willemsen V. Plant growth-promoting rhizobacterium Pseudomonas sp. CM11 specifically induces lateral roots. THE NEW PHYTOLOGIST 2022; 235:1575-1588. [PMID: 35510807 PMCID: PMC9546010 DOI: 10.1111/nph.18199] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/28/2022] [Indexed: 06/10/2023]
Abstract
Plant growth-promoting rhizobacteria are involved in altering secondary root (SR) formation, but hitherto there has been no distinction between the different types of SRs upon induction of soil biota, and the genetic pathways involved. By using plate and soil systems, we studied the effects of the Pseudomonas strains CM11 and WCS417 on plant performance with a focus on root development. Through a combination of cellular, molecular and genetic analyses, we investigated the type of SRs induced upon CM11 and WCS417 root inoculation using genetic pathways associated with specific SR types. CM11 was shown to affect the root architecture differently from WCS417. CM11 inoculation leads to primary root arrest, whereas WCS417 reveals a longer primary root. Both CM11 and WCS417 activate the PLETHORA 3,5,7-controlled lateral root pathway, rather than the WUSCHEL-RELATED HOMEOBOX 11,12-controlled adventitious (lateral) root pathway. In addition, CM11 promotes plant growth in model and various crop species. It improves plant fitness traits, such as bigger shoots, faster bolting and higher yield in terms of seeds. Our results indicate that the root system architecture can be promoted by activation of PLETHORA 3,5,7 dependent primed lateral pre-branch sites upon inoculation with CM11, which creates great potential to gain a better understanding of root plasticity.
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Affiliation(s)
- Qian Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing University of AgricultureBeijing102206China
- Cluster of Plant Developmental BiologyLaboratory of Molecular BiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenthe Netherlands
- Beijing Bei Nong Enterprise Management Co. LtdBeijing102206China
| | - Huchen Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing University of AgricultureBeijing102206China
- Cluster of Plant Developmental BiologyLaboratory of Molecular BiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Zhuang Yang
- Cluster of Plant Developmental BiologyLaboratory of Molecular BiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Xu Cheng
- Cluster of Plant Developmental BiologyLaboratory of Molecular BiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Yaceng Zhao
- College of Plant Science and TechnologyBeijing Key Laboratory for Agricultural Application and New TechniqueBeijing University of AgricultureBeijing102206China
| | - Ling Qin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing University of AgricultureBeijing102206China
- College of Plant Science and TechnologyBeijing Key Laboratory for Agricultural Application and New TechniqueBeijing University of AgricultureBeijing102206China
| | - Ton Bisseling
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing University of AgricultureBeijing102206China
- Cluster of Plant Developmental BiologyLaboratory of Molecular BiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Qingqin Cao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing University of AgricultureBeijing102206China
- College of Plant Science and TechnologyBeijing Key Laboratory for Agricultural Application and New TechniqueBeijing University of AgricultureBeijing102206China
| | - Viola Willemsen
- Cluster of Plant Developmental BiologyLaboratory of Molecular BiologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenthe Netherlands
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22
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Stimulation of Distinct Rhizosphere Bacteria Drives Phosphorus and Nitrogen Mineralization in Oilseed Rape under Field Conditions. mSystems 2022; 7:e0002522. [PMID: 35862821 PMCID: PMC9426549 DOI: 10.1128/msystems.00025-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Advances in DNA sequencing technologies have drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Important ecological interactions being performed by microbes can be investigated by analyzing the extracellular protein fraction. Here, we combined a unique protein extraction method and an iterative bioinformatics pipeline to capture and identify extracellular proteins (metaexoproteomics) synthesized in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analyzed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1,885 plant, insect, and microbial proteins were identified across bulk and rhizosphere samples. Metaexoproteomics identified a significant shift in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This included stimulation of rhizosphere-specialized bacteria, such as Gammaproteobacteria, Betaproteobacteria, and Flavobacteriia, and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralization. Our metaproteomic assessment of the “active” plant microbiome at the field-scale demonstrates the importance of moving beyond metagenomics to determine ecologically important plant-microbe interactions underpinning plant health. IMPORTANCE Plant-microbe interactions are critical to ecosystem function and crop production. While significant advances have been made toward understanding the structure of the plant microbiome, learning about its full functional role is still in its infancy. This is primarily due to an incomplete ability to determine in situ plant-microbe interactions actively operating under field conditions. Proteins are the functional entities of the cell. Therefore, their identification and relative quantification within a microbial community provide the best proxy for which microbes are the most metabolically active and which are driving important plant-microbe interactions. Here, we provide the first metaexoproteomics assessment of the plant microbiome using field-grown oilseed rape as the model crop species, identifying key taxa responsible for specific ecological interactions. Gaining a mechanistic understanding of the plant microbiome is central to developing engineered plant microbiomes to improve sustainable agricultural approaches and reduce our reliance on nonrenewable resources.
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23
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Ho PY, Good BH, Huang KC. Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas. eLife 2022; 11:75168. [PMID: 35404785 PMCID: PMC9000955 DOI: 10.7554/elife.75168] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/24/2022] [Indexed: 12/20/2022] Open
Abstract
Across diverse microbiotas, species abundances vary in time with distinctive statistical behaviors that appear to generalize across hosts, but the origins and implications of these patterns remain unclear. Here, we show that many of these macroecological patterns can be quantitatively recapitulated by a simple class of consumer-resource models, in which the metabolic capabilities of different species are randomly drawn from a common statistical distribution. Our model parametrizes the consumer-resource properties of a community using only a small number of global parameters, including the total number of resources, typical resource fluctuations over time, and the average overlap in resource-consumption profiles across species. We show that variation in these macroscopic parameters strongly affects the time series statistics generated by the model, and we identify specific sets of global parameters that can recapitulate macroecological patterns across wide-ranging microbiotas, including the human gut, saliva, and vagina, as well as mouse gut and rice, without needing to specify microscopic details of resource consumption. These findings suggest that resource competition may be a dominant driver of community dynamics. Our work unifies numerous time series patterns under a simple model, and provides an accessible framework to infer macroscopic parameters of effective resource competition from longitudinal studies of microbial communities.
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Affiliation(s)
- Po-Yi Ho
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Benjamin H Good
- Department of Applied Physics, Stanford University, Stanford, United States.,Chan Zuckerberg Biohub, San Francisco, United States
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, United States.,Chan Zuckerberg Biohub, San Francisco, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
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24
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Yurgel SN, Ajeethan N, Smertenko A. Response of Plant-Associated Microbiome to Plant Root Colonization by Exogenous Bacterial Endophyte in Perennial Crops. Front Microbiol 2022; 13:863946. [PMID: 35479645 PMCID: PMC9037143 DOI: 10.3389/fmicb.2022.863946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
The application of bacterial inoculums for improving plant growth and production is an important component of sustainable agriculture. However, the efficiency of perennial crop inoculums depends on the ability of the introduced endophytes to exert an impact on the host-plant over an extended period of time. This impact might be evaluated by the response of plant-associated microbiome to the inoculation. In this study, we monitored the effect of a single bacterial strain inoculation on the diversity, structure, and cooperation in plant-associated microbiome over 1-year period. An endophyte (RF67) isolated from Vaccinium angustifolium (wild blueberry) roots and annotated as Rhizobium was used for the inoculation of 1-year-old Lonicera caerulea (Haskap) plants. A significant level of bacterial community perturbation was detected in plant roots after 3 months post-inoculation. About 23% of root-associated community variation was correlated with an application of the inoculant, which was accompanied by increased cooperation between taxa belonging to Proteobacteria and Actinobacteriota phyla and decreased cooperation between Firmicutes in plant roots. Additionally, a decrease in bacterial Shannon diversity and an increase in the relative abundances of Rhizobiaceae and Enterobacteriaceae were detected in the roots of inoculated plants relative to the non-inoculated control. A strong effect of the inoculation on the bacterial cooperation was also detected after 1 year of plant field growth, whereas no differences in bacterial community composition and also alpha and beta diversities were detected between bacterial communities from inoculated and non-inoculated roots. These findings suggest that while exogenous endophytes might have a short-term effect on the root microbiome structure and composition, they can boost cooperation between plant-growth-promoting endophytes, which can exist for the extended period of time providing the host-plant with long-lasting beneficial effects.
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Affiliation(s)
- Svetlana N. Yurgel
- Grain Legume Genetics and Physiology Research Unit, U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Prosser, WA, United States
| | - Nivethika Ajeethan
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
- Department of Biosystems Technology, Faculty of Technology, University of Jaffna, Kilinochchi, Sri Lanka
| | - Andrei Smertenko
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
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25
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Bennis M, Perez-Tapia V, Alami S, Bouhnik O, Lamin H, Abdelmoumen H, Bedmar EJ, Missbah El Idrissi M. Characterization of plant growth-promoting bacteria isolated from the rhizosphere of Robinia pseudoacacia growing in metal-contaminated mine tailings in eastern Morocco. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 304:114321. [PMID: 35021593 DOI: 10.1016/j.jenvman.2021.114321] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Mining activity in the Touissit district of Eastern Morocco has led to an unprecedented accumulation of heavy metals, mainly lead and zinc, in the tailing ponds of the open-air mines. This poses a real danger to both the environment and local population. OBJECTIVES The goal of this work was to characterize the Plant Growth Promoting Rhizobacteria (PGPR) isolated from the rhizosphere soil of R. pseudoacacia plants grown wild in the abandoned Pb- and Zn-contaminated tailing ponds in the mining district of Touissit, in Eastern Morocco. MAIN RESULTS One hundred bacterial strains were isolated from the rhizosphere of black locust (Robinia pseudoacacia L.) plants growing naturally in the Touissit mine tailings. Quantitative determination of indole-acetic and siderophores production, inorganic phosphate solubilization, hydrolysis of 1-aminocyclopropane-1-carboxylic acid (ACC deaminase activity), and ability to act as a biocontrol agent allowed selection of the 3 strains, 7MBT, 17MBT and 84MBT with improved PGP properties. The three strains grew well in the presence of high concentration of Pb-acetate and ZnCl2; and the addition of Pb or Zn to the culture medium differently affected the PGP properties analyzed. NOVELTY STATEMENT Inoculation of black locust grown with the 3 selected strains, in the presence 1000 μg ml-1 of Pb-acetate, produced varying effects on the plant dry weight. The strain 84MBT alone or in combination with strains 7MBT and 17MBT increased significantly the dry weight of the plants by 91, 62, and 85% respectively. The 16S rRNA gene sequence analysis of each strain showed that the strains 7MBT 17MBT and 84MBT had 99.34, 100, and had 99.72% similarity with Priestia endophytica (formerly B. endophyticus), B. pumilus NBRC 12092T, and B. halotolerans NBRC 15718T, respectively.
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Affiliation(s)
- Meryeme Bennis
- Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco
| | - Vicente Perez-Tapia
- Departamento de Microbiología del Suelo y Sistemas Simbióticos Estación Experimental del Zaidín, CSIC Apartado Postal 419, 18008, Granada, Spain
| | - Soufiane Alami
- Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco
| | - Omar Bouhnik
- Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco
| | - Hanane Lamin
- Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco
| | - Hanaa Abdelmoumen
- Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco
| | - Eulogio J Bedmar
- Departamento de Microbiología del Suelo y Sistemas Simbióticos Estación Experimental del Zaidín, CSIC Apartado Postal 419, 18008, Granada, Spain
| | - Mustapha Missbah El Idrissi
- Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco.
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26
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Bender SF. Pulling the strings from underground? Soil biota and plant growth-defense tradeoffs. THE NEW PHYTOLOGIST 2022; 233:1015-1017. [PMID: 34766626 DOI: 10.1111/nph.17829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Affiliation(s)
- S Franz Bender
- Department of Agroecology and Environment, Agroscope, Reckenholzstr. 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbiology, University of Zürich, Zollikerstr. 107, CH-8008, Zürich, Switzerland
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27
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Shen MC, Zhang YZ, Bo GD, Yang B, Wang P, Ding ZY, Wang ZB, Yang JM, Zhang P, Yuan XL. Microbial Responses to the Reduction of Chemical Fertilizers in the Rhizosphere Soil of Flue-Cured Tobacco. Front Bioeng Biotechnol 2022; 9:812316. [PMID: 35087808 PMCID: PMC8787768 DOI: 10.3389/fbioe.2021.812316] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/22/2021] [Indexed: 12/23/2022] Open
Abstract
The overuse of chemical fertilizers has resulted in the degradation of the physicochemical properties and negative changes in the microbial profiles of agricultural soil. These changes have disequilibrated the balance in agricultural ecology, which has resulted in overloaded land with low fertility and planting obstacles. To protect the agricultural soil from the effects of unsustainable fertilization strategies, experiments of the reduction of nitrogen fertilization at 10, 20, and 30% were implemented. In this study, the bacterial responses to the reduction of nitrogen fertilizer were investigated. The bacterial communities of the fertilizer-reducing treatments (D10F, D20F, and D30F) were different from those of the control group (CK). The alpha diversity was significantly increased in D20F compared to that of the CK. The analysis of beta diversity revealed variation of the bacterial communities between fertilizer-reducing treatments and CK, when the clusters of D10F, D20F, and D30F were separated. Chemical fertilizers played dominant roles in changing the bacterial community of D20F. Meanwhile, pH, soil organic matter, and six enzymes (soil sucrase, catalase, polyphenol oxidase, urease, acid phosphatase, and nitrite reductase) were responsible for the variation of the bacterial communities in fertilizer-reducing treatments. Moreover, four of the top 20 genera (unidentified JG30-KF-AS9, JG30-KF-CM45, Streptomyces, and Elsterales) were considered as key bacteria, which contributed to the variation of bacterial communities between fertilizer-reducing treatments and CK. These findings provide a theoretical basis for a fertilizer-reducing strategy in sustainable agriculture, and potentially contribute to the utilization of agricultural resources through screening plant beneficial bacteria from native low-fertility soil.
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Affiliation(s)
- Min-Chong Shen
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yu-Zhen Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Guo-Dong Bo
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Bin Yang
- Shandong Qingdao Tobacco Co., Ltd., Qingdao, China
| | - Peng Wang
- Shandong Qingdao Tobacco Co., Ltd., Qingdao, China
| | | | - Zhao-Bao Wang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jian-Ming Yang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Peng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Xiao-Long Yuan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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28
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Abstract
We develop a method to artificially select for rhizosphere microbiomes that confer salt tolerance to the model grass Brachypodium distachyon grown under sodium salt stress or aluminum salt stress. In a controlled greenhouse environment, we differentially propagated rhizosphere microbiomes between plants of a nonevolving, highly inbred plant population; therefore, only microbiomes evolved in our experiment, but the plants did not evolve in parallel. To maximize microbiome perpetuation when transplanting microbiomes between plants and, thus, maximize response to microbiome selection, we improved earlier methods by (i) controlling microbiome assembly when inoculating seeds at the beginning of each selection cycle; (ii) fractionating microbiomes before transfer between plants to harvest, perpetuate, and select on only bacterial and viral microbiome components; (iii) ramping of salt stress gradually from minor to extreme salt stress with each selection cycle to minimize the chance of overstressing plants; (iv) using two nonselection control treatments (e.g., nonselection microbial enrichment and null inoculation) that permit comparison to the improving fitness benefits that selected microbiomes impart on plants. Unlike previous methods, our selection protocol generated microbiomes that enhance plant fitness after only 1 to 3 rounds of microbiome selection. After nine rounds of microbiome selection, the effect of microbiomes selected to confer tolerance to aluminum salt stress was nonspecific (these artificially selected microbiomes equally ameliorate sodium and aluminum salt stresses), but the effect of microbiomes selected to confer tolerance to sodium salt stress was specific (these artificially selected microbiomes do not confer tolerance to aluminum salt stress). Plants with artificially selected microbiomes had 55 to 205% greater seed production than plants with unselected control microbiomes. IMPORTANCE We developed an experimental protocol that improves earlier methods of artificial selection on microbiomes and then tested the efficacy of our protocol to breed root-associated bacterial microbiomes that confer salt tolerance to a plant. Salt stress limits growth and seed production of crop plants, and artificially selected microbiomes conferring salt tolerance may ultimately help improve agricultural productivity. Unlike previous experiments of microbiome selection, our selection protocol generated microbiomes that enhance plant productivity after only 1 to 3 rounds of artificial selection on root-associated microbiomes, increasing seed production under extreme salt stress by 55 to 205% after nine rounds of microbiome selection. Although we artificially selected microbiomes under controlled greenhouse conditions that differ from outdoor conditions, increasing seed production by 55 to 205% under extreme salt stress is a remarkable enhancement of plant productivity compared to traditional plant breeding. We describe a series of additional experimental protocols that will advance insights into key parameters that determine efficacy and response to microbiome selection.
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29
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Jones CY, Engelhardt I, Patko D, Dupuy L, Holden N, Willats WGT. High-resolution 3D mapping of rhizosphere glycan patterning using molecular probes in a transparent soil system. ACTA ACUST UNITED AC 2021; 7:100059. [PMID: 34557617 PMCID: PMC8445887 DOI: 10.1016/j.tcsw.2021.100059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/02/2021] [Accepted: 07/12/2021] [Indexed: 12/27/2022]
Abstract
Rhizospheres are microecological zones at the interface of roots and soils. Interactions between bacteria and roots are critical for maintaining plant and soil health but are difficult to study because of constraints inherent in working with underground systems. We have developed an in-situ rhizosphere imaging system based on transparent soils and molecular probes that can be imaged using confocal microscopy. We observed spatial patterning of polysaccharides along roots and on cells deposited into the rhizosphere and also co-localised fluorescently tagged soil bacteria. These studies provide insight into the complex glycan landscape of rhizospheres and suggest a means by which root / rhizobacteria interactions can be non-disruptively studied.
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Affiliation(s)
- Catherine Y Jones
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle-Upon-Tyne NE1 7RU, UK
| | - Ilonka Engelhardt
- Neiker, Department of Conservation of Natural Resources, Derio, Spain
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Daniel Patko
- Neiker, Department of Conservation of Natural Resources, Derio, Spain
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Lionel Dupuy
- Neiker, Department of Conservation of Natural Resources, Derio, Spain
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| | - Nicola Holden
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - William G T Willats
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle-Upon-Tyne NE1 7RU, UK
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30
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Examining the Effects of the Nitrogen Environment on Growth and N 2-Fixation of Endophytic Herbaspirillum seropedicae in Maize Seedlings by Applying 11C Radiotracing. Microorganisms 2021; 9:microorganisms9081582. [PMID: 34442661 PMCID: PMC8401641 DOI: 10.3390/microorganisms9081582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 11/17/2022] Open
Abstract
Herbaspirillum seropedicae, as an endophyte and prolific root colonizer of numerous cereal crops, occupies an important ecological niche in agriculture because of its ability to promote plant growth and potentially improve crop yield. More importantly, there exists the untapped potential to harness its ability, as a diazotroph, to fix atmospheric N2 as an alternative nitrogen resource to synthetic fertilizers. While mechanisms for plant growth promotion remain controversial, especially in cereal crops, one irrefutable fact is these microorganisms rely heavily on plant-borne carbon as their main energy source in support of their own growth and biological functions. Biological nitrogen fixation (BNF), a microbial function that is reliant on nitrogenase enzyme activity, is extremely sensitive to the localized nitrogen environment of the microorganism. However, whether internal root colonization can serve to shield the microorganisms and de-sensitize nitrogenase activity to changes in the soil nitrogen status remains unanswered. We used RAM10, a GFP-reporting strain of H. seropedicae, and administered radioactive 11CO2 tracer to intact 3-week-old maize leaves and followed 11C-photosynthates to sites within intact roots where actively fluorescing microbial colonies assimilated the tracer. We examined the influence of administering either 1 mM or 10 mM nitrate during plant growth on microbial demands for plant-borne 11C. Nitrogenase activity was also examined under the same growth conditions using the acetylene reduction assay. We found that plant growth under low nitrate resulted in higher nitrogenase activity as well as higher microbial demands for plant-borne carbon than plant growth under high nitrate. However, carbon availability was significantly diminished under low nitrate growth due to reduced host CO2 fixation and reduced allocation of carbon resources to the roots. This response of the host caused significant inhibition of microbial growth. In summary, internal root colonization did little to shield these endophytic microorganisms from the nitrogen environment.
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31
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Ióca LP, Dai Y, Kunakom S, Diaz‐Espinosa J, Krunic A, Crnkovic CM, Orjala J, Sanchez LM, Ferreira AG, Berlinck RGS, Eustáquio AS. A Family of Nonribosomal Peptides Modulate Collective Behavior in
Pseudovibrio
Bacteria Isolated from Marine Sponges**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202017320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Laura P. Ióca
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Instituto de Química de São Carlos Universidade de São Paulo São Carlos SP 13560-970 Brazil
| | - Yitao Dai
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Sylvia Kunakom
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Jennifer Diaz‐Espinosa
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Aleksej Krunic
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Camila M. Crnkovic
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Jimmy Orjala
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Laura M. Sanchez
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
| | - Antonio G. Ferreira
- Departamento de Química Universidade Federal de São Carlos São Carlos SP 13565-905 Brazil
| | - Roberto G. S. Berlinck
- Instituto de Química de São Carlos Universidade de São Paulo São Carlos SP 13560-970 Brazil
| | - Alessandra S. Eustáquio
- Department of Pharmaceutical Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences College of Pharmacy University of Illinois at Chicago Chicago IL 60607 USA
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32
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Ióca LP, Dai Y, Kunakom S, Diaz-Espinosa J, Krunic A, Crnkovic CM, Orjala J, Sanchez LM, Ferreira AG, Berlinck RGS, Eustáquio AS. A Family of Nonribosomal Peptides Modulate Collective Behavior in Pseudovibrio Bacteria Isolated from Marine Sponges*. Angew Chem Int Ed Engl 2021; 60:15891-15898. [PMID: 33961724 PMCID: PMC8269750 DOI: 10.1002/anie.202017320] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/01/2021] [Indexed: 11/08/2022]
Abstract
Although swarming motility and biofilms are opposed collective behaviors, both contribute to bacterial survival and host colonization. Pseudovibrio bacteria have attracted attention because they are part of the microbiome of healthy marine sponges. Two-thirds of Pseudovibrio genomes contain a member of a nonribosomal peptide synthetase-polyketide synthase gene cluster family, which is also found sporadically in Pseudomonas pathogens of insects and plants. After developing reverse genetics for Pseudovibrio, we isolated heptapeptides with an ureido linkage and related nonadepsipeptides we termed pseudovibriamides A and B, respectively. A combination of genetics and imaging mass spectrometry experiments showed heptapetides were excreted, promoting motility and reducing biofilm formation. In contrast to lipopeptides widely known to affect motility/biofilms, pseudovibriamides are not surfactants. Our results expand current knowledge on metabolites mediating bacterial collective behavior.
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Affiliation(s)
- Laura P. Ióca
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP 13560-970, Brazil
| | - Yitao Dai
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Sylvia Kunakom
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jennifer Diaz-Espinosa
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Aleksej Krunic
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Camila M. Crnkovic
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jimmy Orjala
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Laura M. Sanchez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Antonio G. Ferreira
- Departamento de Química, Universidade Federal de São Carlos, São Carlos, SP 13565-905, Brazil
| | - Roberto G. S. Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP 13560-970, Brazil
| | - Alessandra S. Eustáquio
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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Welmillage SU, Zhang Q, Sreevidya VS, Sadowsky MJ, Gyaneshwar P. Inoculation of Mimosa Pudica with Paraburkholderia phymatum Results in Changes to the Rhizoplane Microbial Community Structure. Microbes Environ 2021; 36. [PMID: 33716243 PMCID: PMC7966945 DOI: 10.1264/jsme2.me20153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Nitrogen fixing symbiosis between rhizobia and legumes contributes significant amounts of N to agricultural and natural environments. In natural soils, rhizobia compete with indigenous bacterial communities to colonize legume roots, which leads to symbiotic interactions. However, limited information is currently available on the effects of the rhizobial symbiont on the resident microbial community in the legume rhizosphere, rhizoplane, and endosphere, which is partly due to the presence of native nodulating rhizobial strains. In the present study, we used a symbiotic system comprised of Paraburkholderia phymatum and Mimosa pudica to examine the interaction of an inoculant strain with indigenous soil bacteria. The effects of a symbiont inoculation on the native bacterial community was investigated using high throughput sequencing and an analysis of 16S rRNA gene amplicons. The results obtained revealed that the inoculation induced significant alterations in the microbial community present in the rhizoplane+endosphere of the roots, with 13 different taxa showing significant changes in abundance. No significant changes were observed in the rhizospheric soil. The relative abundance of P. phymatum significantly increased in the rhizoplane+endosphere of the root, but significant decreased in the rhizospheric soil. While the rhizosphere, rhizoplane, and root endosphere contained a wide diversity of bacteria, the nodules were predominantly colonized by P. phymatum. A network analysis revealed that the operational taxonomic units of Streptomyces and Phycicoccus were positively associated with P. phymatum as potential keystone taxa. Collectively, these results suggest that the success of an inoculated symbiont depends on its ability to colonize the roots in the face of competition by other soil bacteria. A more detailed understanding of the mechanisms by which an inoculated strain colonizes its plant host is crucial for realizing the full potential of microbial inoculants in sustainable agriculture.
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Affiliation(s)
| | - Qian Zhang
- Department of Soil and Water and Climate, University of Minnesota
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LaMontagne MG, Tran PL, Benavidez A, Morano LD. Development of an inexpensive matrix-assisted laser desorption-time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize. PeerJ 2021; 9:e11359. [PMID: 34123583 PMCID: PMC8166240 DOI: 10.7717/peerj.11359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/06/2021] [Indexed: 12/14/2022] Open
Abstract
Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety c ontained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize.
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Affiliation(s)
- Michael G LaMontagne
- Department of Biology and Biotechnology, University of Houston, Clear Lake, Houston, Texas, United States
| | - Phi L Tran
- Department of Biology and Biotechnology, University of Houston, Clear Lake, Houston, Texas, United States
| | - Alexander Benavidez
- Department of Natural Sciences, University of Houston, Downtown, Houston, Texas, United States
| | - Lisa D Morano
- Department of Natural Sciences, University of Houston, Downtown, Houston, Texas, United States
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Sohn SI, Ahn JH, Pandian S, Oh YJ, Shin EK, Kang HJ, Cho WS, Cho YS, Shin KS. Dynamics of Bacterial Community Structure in the Rhizosphere and Root Nodule of Soybean: Impacts of Growth Stages and Varieties. Int J Mol Sci 2021; 22:5577. [PMID: 34070397 PMCID: PMC8197538 DOI: 10.3390/ijms22115577] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/20/2021] [Accepted: 05/22/2021] [Indexed: 11/17/2022] Open
Abstract
Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max (L.) Merr.). In this report, we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology, respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina sequencing analysis, the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria, and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.
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Affiliation(s)
- Soo-In Sohn
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (S.P.); (E.-K.S.); (H.-J.K.); (W.-S.C.); (Y.-S.C.)
| | - Jae-Hyung Ahn
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Jeonju 55365, Korea;
| | - Subramani Pandian
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (S.P.); (E.-K.S.); (H.-J.K.); (W.-S.C.); (Y.-S.C.)
| | - Young-Ju Oh
- Institute for Future Environmental Ecology Co., Ltd., Jeonju 54883, Korea;
| | - Eun-Kyoung Shin
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (S.P.); (E.-K.S.); (H.-J.K.); (W.-S.C.); (Y.-S.C.)
| | - Hyeon-Jung Kang
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (S.P.); (E.-K.S.); (H.-J.K.); (W.-S.C.); (Y.-S.C.)
| | - Woo-Suk Cho
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (S.P.); (E.-K.S.); (H.-J.K.); (W.-S.C.); (Y.-S.C.)
| | - Youn-Sung Cho
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (S.P.); (E.-K.S.); (H.-J.K.); (W.-S.C.); (Y.-S.C.)
| | - Kong-Sik Shin
- Audit and Inspection Office, Rural Development of Administration, Jeonju 54875, Korea;
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Wu AL, Jiao XY, Wang JS, Dong EW, Guo J, Wang LG, Sun AQ, Hu HW. Sorghum rhizosphere effects reduced soil bacterial diversity by recruiting specific bacterial species under low nitrogen stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:144742. [PMID: 33736399 DOI: 10.1016/j.scitotenv.2020.144742] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/25/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
Rhizosphere microbiota play a pivotal role in promoting plant growth and defending against pathogens, but their responses to abiotic environmental stress remain largely elusive. Here, we investigated the influences of low-N stress on rhizosphere bacteria of six sorghum cultivars in a glasshouse experiment. The alpha diversity of bacteria (as revealed by Shannon diversity and Chao1 richness indices) was remarkably lower in rhizosphere soils than in bulk soils, and was significantly higher under low-N stress than under N addition. Principal coordinates analysis revealed that the bacterial community compositions in rhizosphere soils were clearly separated from bulk soils, and the rhizosphere soils under low-N stress or with N fertilization were clearly separated, indicating that both rhizosphere effects and N fertilization impacted the rhizosphere bacterial community. Notably, the relative abundances of beneficial bacteria such as Bacillaceae and Streptomycetaceae significantly increased in rhizosphere soils under low-N stress, which had significantly positive correlations with the sorghum N uptake. The relative abundance of Nitrosomonadaceae in rhizosphere soils was significantly lower than that in bulk soils, while the relative abundance of Rhizobiaceae showed an opposite pattern. Taken together, our results suggested that sorghum rhizosphere effects can reduce soil bacterial diversity possibly through recruiting specific bacterial species under low N stress.
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Affiliation(s)
- Ai-Lian Wu
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Xiao-Yan Jiao
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China.
| | - Jin-Song Wang
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Er-Wei Dong
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Jun Guo
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Li-Ge Wang
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - An-Qi Sun
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
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Christakis CA, Daskalogiannis G, Chatzaki A, Markakis EA, Mermigka G, Sagia A, Rizzo GF, Catara V, Lagkouvardos I, Studholme DJ, Sarris PF. Endophytic Bacterial Isolates From Halophytes Demonstrate Phytopathogen Biocontrol and Plant Growth Promotion Under High Salinity. Front Microbiol 2021; 12:681567. [PMID: 34017321 PMCID: PMC8129196 DOI: 10.3389/fmicb.2021.681567] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/07/2021] [Indexed: 01/22/2023] Open
Abstract
Halophytic endophytes potentially contribute to the host's adaptation to adverse environments, improving its tolerance against various biotic and abiotic stresses. Here, we identified the culturable endophytic bacteria of three crop wild relative (CWR) halophytes: Cakile maritima, Matthiola tricuspidata, and Crithmum maritimum. In the present study, the potential of these isolates to improve crop adaptations to various stresses was investigated, using both in vitro and in-planta approaches. Endophytic isolates were identified by their 16S rRNA gene sequence and evaluated for their ability to: grow in vitro in high levels of NaCl; inhibit the growth of the economically important phytopathogens Verticillium dahliae, Ralstonia solanacearum, and Clavibacter michiganensis and the human pathogen Aspergillus fumigatus; provide salt tolerance in-planta; and provide growth promoting effect in-planta. Genomes of selected isolates were sequenced. In total, 115 endophytic isolates were identified. At least 16 isolates demonstrated growth under increased salinity, plant growth promotion and phytopathogen antagonistic activity. Three showed in-planta suppression of Verticillium growth. Furthermore, representatives of three novel species were identified: two Pseudomonas species and one Arthrobacter. This study provides proof-of-concept that the endophytes from CWR halophytes can be used as "bio-inoculants," for the enhancement of growth and stress tolerance in crops, including the high-salinity stress.
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Affiliation(s)
- Christos A Christakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
| | | | - Anastasia Chatzaki
- Laboratory of Mycology, Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization DIMITRA, Heraklion, Greece
| | - Emmanouil A Markakis
- Laboratory of Mycology, Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization DIMITRA, Heraklion, Greece
| | - Glykeria Mermigka
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
| | - Angeliki Sagia
- Department of Biology, University of Crete, Heraklion, Greece
| | - Giulio Flavio Rizzo
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Ilias Lagkouvardos
- ZIEL-Institute for Food and Health, Technical University of Munich, Freising, Germany
| | | | - Panagiotis F Sarris
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece.,Department of Biology, University of Crete, Heraklion, Greece.,Biosciences, University of Exeter, Exeter, United Kingdom
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Effects of Compost Amendment on Glycophyte and Halophyte Crops Grown on Saline Soils: Isolation and Characterization of Rhizobacteria with Plant Growth Promoting Features and High Salt Resistance. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11052125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Soil salinization and desertification due to climate change are the most relevant challenges for the agriculture of the 21st century. Soil compost amendment and plant growth promoting rhizobacteria (PGP-R) are valuable tools to mitigate salinization and desertification impacts on agricultural soils. Selection of novel halo/thermo-tolerant bacteria from the rhizosphere of glicophytes and halophytes, grown on soil compost amended and watered with 150/300 mM NaCl, was the main objective of our study. Beneficial effects on the biomass, well-being and resilience, exerted on the assayed crops (maize, tomato, sunflower and quinoa), were clearly observable when soils were amended with 20% compost despite the very high soil electric conductivity (EC). Soil compost amendment not only was able to increase crop growth and biomass, but also their resilience to the stress caused by very high soil EC (up to 20 dS m−1). Moreover, compost amendment has proved itself a valuable source of highly halo-(4.0 M NaCl)/thermo tolerant rhizobacteria (55 °C), showing typical PGP features. Among the 13 rhizobacterial isolates, molecularly and biochemically characterized, two bacterial strains showed several biochemical PGP features. The use of compost is growing all around the world reducing considerably for farmers soil fertilization costs. In fact, only in Italy its utilization has ensured, in the last years, a saving of 650 million euro for the farmers, without taking into account the environment and human health benefits. Furthermore, the isolation of halo/thermo-tolerant PGPR strains and their use will allow the recovery and cultivation of hundreds of thousands of hectares of saline and arid soils now unproductive, making agriculture more respectful of agro-ecosystems also in view of upcoming climate change.
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Ahmad MZ, Zhang Y, Zeng X, Li P, Wang X, Benedito VA, Zhao J. Isoflavone malonyl-CoA acyltransferase GmMaT2 is involved in nodulation of soybean by modifying synthesis and secretion of isoflavones. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1349-1369. [PMID: 33130852 DOI: 10.1093/jxb/eraa511] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/26/2020] [Indexed: 05/20/2023]
Abstract
Malonyl-CoA:flavonoid acyltransferases (MaTs) modify isoflavones, but only a few have been characterized for activity and assigned to specific physiological processes. Legume roots exude isoflavone malonates into the rhizosphere, where they are hydrolyzed into isoflavone aglycones. Soybean GmMaT2 was highly expressed in seeds, root hairs, and nodules. GmMaT2 and GmMaT4 recombinant enzymes used isoflavone 7-O-glucosides as acceptors and malonyl-CoA as an acyl donor to generate isoflavone glucoside malonates. GmMaT2 had higher activity towards isoflavone glucosides than GmMaT4. Overexpression in hairy roots of GmMaT2 and GmMaT4 produced more malonyldaidzin, malonylgenistin, and malonylglycitin, and resulted in more nodules than control. However, only GmMaT2 knockdown (KD) hairy roots showed reduced levels of malonyldaidzin, malonylgenistin, and malonylglycitin, and, likewise, reduced nodule numbers. These were consistent with the up-regulation of only GmMaT2 by rhizobial infection, and higher expression levels of early nodulation genes in GmMaT2- and GmMaT4-overexpressing roots, but lower only in GmMaT2-KD roots compared with control roots. Higher malonyl isoflavonoid levels in transgenic hairy roots were associated with higher levels of isoflavones in root exudates and more nodules, and vice versa. We suggest that GmMaT2 participates in soybean nodulation by catalyzing isoflavone malonylation and affecting malonyl isoflavone secretion for activation of Nod factor and nodulation.
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Affiliation(s)
- Muhammad Zulfiqar Ahmad
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yanrui Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xiangsheng Zeng
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xiaobo Wang
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Vagner A Benedito
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
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Kandasamy S, Weerasuriya N, Subramanian G, Thorn RG, Patterson G, Ali S, Lazarovits G. Disentangling the Association of Corn Root Mycobiome With Plant Productivity and the Importance of Soil Physicochemical Balance in Shaping Their Relationship. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.617332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Soil bacteria and fungi are integral parts of healthy ecosystem functioning in production agriculture. The effects of fungal abundance and diversity on crop productivity is poorly understood. We sampled 10 corn farms at the V10 growth stage across southwestern Ontario, Canada, using aerial infrared imaging to identify zones of low and high productive corn plants. Roots and soils were sampled from low and high yield zones and soil physical and chemical properties were measured in conjunction with assessment of the root mycobiome communities using Illumina MiSeq sequencing of 4 rRNA amplicons. Higher crop yields were associated with sites having greater fungal phylogenetic diversity and Fisher's α diversity. Indicator species associated with high and low yield sites within a farm could be identified but there were no shared fungal indicators of productivity differences across farms. Communities largely varied across locations despite crop genetics, demonstrating a major influence of soil texture and chemistry in shaping the mycobiome in a site-specific manner. Across all 4 primers, roots from high-yielding sites shared 35 major OTUs including Penicillium spp., Trichoderma, Chalara fungorum, and Gibellulopsis. Low-yielding sites shared 31 OTUs including Fusarium spp., Pythium, Setophoma terrestris, and Neonectria. Soil physical and chemical parameters that contributed to broad scale differences in yield and mycobiome diversity included: %clay, %sand, %phosphorus saturation, cation exchange capacity, aluminum, pH, iron, potassium, %moisture, organic matter, and chlorine. The results show the importance of physicochemical balance in shaping the relationship between root mycobiome and plant productivity.
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Sinong GF, Yasuda M, Nara Y, Lee CG, Dastogeer KMG, Tabuchi H, Nakai H, Djedidi S, Okazaki S. Distinct Root Microbial Communities in Nature Farming Rice Harbor Bacterial Strains With Plant Growth-Promoting Traits. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2020.629942] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A nature farming system is an ecological farming practice that entails cultivating crops without using chemical fertilizers and pesticides. To understand the diversity and functions of root microbiomes associated with nature farming systems, we compared the root microbial community of rice under nature farming conditions with those under conventional farming conditions. High-throughput amplicon analysis demonstrated a higher abundance and greater diversity of the root microbiome under unfertilized nature farming conditions than under conventional conditions. The application of chemical fertilizers reduced the microbial diversity and abundance of some beneficial taxa important for plant growth and health. Subsequently, we isolated and identified 46 endo- and epiphytic bacteria from rice roots grown under nature farming conditions and examined their plant growth-promoting activity. Six potential isolates were selected for plant growth assessment in insoluble P- and K-containing media. Most of the isolates promoted rice growth, and Pseudomonas koreensis AEPR1 was able to enhance rice growth significantly in both insoluble P- and K-containing media. Our data indicated that nature farming systems create a distinct root microbiome that is comparatively more diverse and supports plant growth under low-input cultivation practices than under conventional practices. The potential isolates could be exploited as sources with potential applications in sustainable agriculture.
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Zia H, Ayub MA, Fattah El Baroudy AAE, Rehman MZU, Khalid H, Haq AU, Umar W, Ahmad Z. Microbial associations in ecological reclamation and restoration of marginal lands. MICROBES IN LAND USE CHANGE MANAGEMENT 2021:239-266. [DOI: 10.1016/b978-0-12-824448-7.00014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Impact of Inoculation with Pseudomonas aestus CMAA 1215 T on the Non-target Resident Bacterial Community in a Saline Rhizosphere Soil. Curr Microbiol 2020; 78:218-228. [PMID: 33236213 DOI: 10.1007/s00284-020-02285-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/05/2020] [Indexed: 10/22/2022]
Abstract
Plant growth reduction caused by osmotic stress, pathogens, and nutrient scarcity can be overcome by inoculation with plant growth-promoting rhizobacteria (PGPR). Knowing the effects of PGPR on the microbial community beyond those on plant growth can bring new options of soil microbiota management. The present study aimed to investigate the effect of inoculation with the newly described Pseudomonas aestus CMAA 1215T [a 1-aminocyclopropane-1-carboxylate (ACC) deaminase and glycine-betaine producer] on the rhizosphere bacterial community of Zea mays in natural (non-salinized) and saline soil. The bacterial community structure was assessed by sequencing the V6-V7 16S ribosomal RNA using the Ion Personal Genome Machine™. The non-metric multidimensional scaling (NMDS) of the OTU profile (ANOSIM P < 0.01) distinguishes all the treatments (with and without inoculation under saline and natural soils). Inoculated samples shared 1234 OTUs with non-inoculated soil. The most abundant classes in all samples were Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Acidobacteriia, Bacteroidia, Thermoleophilia, Verrucomicrobiae, Ktenodobacteria, and Bacilli. The inoculation, on the other hand, caused an increase in the abundance of the genera Bacillus, Bryobacter, Bradyrhizobium, "Candidatus Xiphinematobacter", and "Candidatus Udaeobacter" independent of soil salinization. "Candidatus Udaeobacter" has the largest Mean Decrease in Gini Values with higher abundance on inoculated salted soil. In addition, Pseudomonas inoculation reduced the abundance of Gammaproteobacteria and Phycisphaerae. Understanding how inoculation modifies the bacterial community is essential to manage the rhizospheric microbiome to create a multi-inoculant approach and to understand its effects on ecological function.
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Rice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites. mSystems 2020; 5:5/6/e00721-20. [PMID: 33234605 PMCID: PMC7687028 DOI: 10.1128/msystems.00721-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives. Some plant-specific resistance genes could affect rhizosphere microorganisms by regulating the release of root exudates. In a previous study, the SST (seedling salt tolerant) gene in rice (Oryza sativa) was identified, and loss of SST function resulted in better plant adaptation to salt stress. However, whether the rice SST variation could alleviate salt stress via regulating soil metabolites and microbiota in the rhizosphere is still unknown. Here, we used transgenic plants with SST edited in the Huanghuazhan (HHZ) and Zhonghua 11 (ZH11) cultivars by the CRISPR/Cas9 system and found that loss of SST function increased the accumulation of potassium and reduced the accumulation of sodium ions in rice plants. Using 16S rRNA gene amplicon high-throughput sequencing, we found that the mutant material shifted the rhizobacterial assembly under salt-free stress. Importantly, under salt stress, the sst, HHZcas, and ZH11cas plants significantly changed the assembly of the rhizobacteria. Furthermore, the rice SST gene also affected the soil metabolites, which were closely related to the dynamics of rhizosphere microbial communities, and we further determined the relationship between the rhizosphere microbiota and soil metabolites. Overall, our results show the effects of the rice SST gene on the response to salt stress associated with the soil microbiota and metabolites in the rhizosphere. This study reveals a helpful linkage among the rice SST gene, soil metabolites, and rhizobacterial community assembly and also provides a theoretical basis for improving crop adaptation through soil microbial management practices. IMPORTANCE Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives.
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Dellagi A, Quillere I, Hirel B. Beneficial soil-borne bacteria and fungi: a promising way to improve plant nitrogen acquisition. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4469-4479. [PMID: 32157312 PMCID: PMC7475097 DOI: 10.1093/jxb/eraa112] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/09/2020] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) is an essential element for plant productivity, thus, it is abundantly applied to the soil in the form of organic or chemical fertilizers that have negative impacts on the environment. Exploiting the potential of beneficial microbes and identifying crop genotypes that can capitalize on symbiotic associations may be possible ways to significantly reduce the use of N fertilizers. The best-known example of symbiotic association that can reduce the use of N fertilizers is the N2-fixing rhizobial bacteria and legumes. Bacterial taxa other than rhizobial species can develop associative symbiotic interactions with plants and also fix N. These include bacteria of the genera Azospirillum, Azotobacter, and Bacillus, some of which are commercialized as bio-inoculants. Arbuscular mycorrhizal fungi are other microorganisms that can develop symbiotic associations with most terrestrial plants, favoring access to nutrients in a larger soil volume through their extraradical mycelium. Using combinations of different beneficial microbial species is a promising strategy to boost plant N acquisition and foster a synergistic beneficial effect between symbiotic microorganisms. Complex biological mechanisms including molecular, metabolic, and physiological processes dictate the establishment and efficiency of such multipartite symbiotic associations. In this review, we present an overview of the current knowledge and future prospects regarding plant N nutrition improvement through the use of beneficial bacteria and fungi associated with plants, individually or in combination.
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Affiliation(s)
- Alia Dellagi
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Isabelle Quillere
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Bertrand Hirel
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
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Exploring Rice Root Microbiome; The Variation, Specialization and Interaction of Bacteria and Fungi In Six Tropic Savanna Regions in Ghana. SUSTAINABILITY 2020. [DOI: 10.3390/su12145835] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We investigated the root microbiomes of rice sampled from six major rice-producing regions in Ghana using Illumina MiSeq high-throughput amplicon sequencing analysis. The result showed that both bacterial and fungal community compositions were significantly varied across the regions. Bacterial communities were shaped predominantly by biotic factors, including root fungal diversity and abundance. In contrast, fungal communities were influenced by abiotic factors such as soil nitrate, total carbon and soil pH. A negative correlation between the diversity and abundance of root fungi with soil nitrate (NO3-) level was observed. It suggested that there were direct and indirect effects of NO3- on the root-associated bacterial and fungal community composition. The gradient of soil nitrate from North to South parts of Ghana may influence the composition of rice root microbiome. Bacterial community composition was shaped by fungal diversity and abundance; whereas fungal community composition was shaped by bacterial abundance. It suggested the mutualistic interaction of bacteria and fungi at the community level in the rice root microbiome. Specific bacterial and fungal taxa were detected abundantly in the ‘Northern’ regions of Ghana, which were very low or absent from the samples of other regions. The analysis of indicator species suggested that an ‘ecological specialization’ may have occurred which enabled specific microbial taxa to adapt to the local environment, such as the low-nitrate condition in the Northern regions.
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Wang X, Wang M, Xie X, Guo S, Zhou Y, Zhang X, Yu N, Wang E. An amplification-selection model for quantified rhizosphere microbiota assembly. Sci Bull (Beijing) 2020; 65:983-986. [PMID: 36659026 DOI: 10.1016/j.scib.2020.03.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/06/2020] [Accepted: 03/01/2020] [Indexed: 01/21/2023]
Affiliation(s)
- Xiaolin Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Mingxing Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xingguang Xie
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Siyi Guo
- Center for Multi-Omics Research, Collaborative Innovation Center of Crop Stress Biology, Henan Province, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Yun Zhou
- Center for Multi-Omics Research, Collaborative Innovation Center of Crop Stress Biology, Henan Province, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Xuebin Zhang
- Center for Multi-Omics Research, Collaborative Innovation Center of Crop Stress Biology, Henan Province, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China.
| | - Nan Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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Insights into the Physiological and Biochemical Impacts of Salt Stress on Plant Growth and Development. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10070938] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Climate change is causing soil salinization, resulting in crop losses throughout the world. The ability of plants to tolerate salt stress is determined by multiple biochemical and molecular pathways. Here we discuss physiological, biochemical, and cellular modulations in plants in response to salt stress. Knowledge of these modulations can assist in assessing salt tolerance potential and the mechanisms underlying salinity tolerance in plants. Salinity-induced cellular damage is highly correlated with generation of reactive oxygen species, ionic imbalance, osmotic damage, and reduced relative water content. Accelerated antioxidant activities and osmotic adjustment by the formation of organic and inorganic osmolytes are significant and effective salinity tolerance mechanisms for crop plants. In addition, polyamines improve salt tolerance by regulating various physiological mechanisms, including rhizogenesis, somatic embryogenesis, maintenance of cell pH, and ionic homeostasis. This research project focuses on three strategies to augment salinity tolerance capacity in agricultural crops: salinity-induced alterations in signaling pathways; signaling of phytohormones, ion channels, and biosensors; and expression of ion transporter genes in crop plants (especially in comparison to halophytes).
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Peñaloza Atuesta GC, Murillo Arango W, Eras J, Oliveros DF, Méndez Arteaga JJ. Rice-Associated Rhizobacteria as a Source of Secondary Metabolites against Burkholderia glumae. Molecules 2020; 25:molecules25112567. [PMID: 32486494 PMCID: PMC7321088 DOI: 10.3390/molecules25112567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022] Open
Abstract
Various diseases, including bacterial panicle blight (BPB) and sheath rot, threaten rice production. It has been established that Burkholderia glumae (B. glumae) is the causative agent of the above mentioned pathologies. In the present study, antagonistic activity, growth promotion, and the metabolite profiles of two rhizobacteria, isolated in different paddy fields, were assessed against B. glumae. Strains were identified based on 16S rRNA gene sequences, and the phylogenetic analyses showed that both strains belong to the genus Enterobacter, with high similarity to the strain Enterobacter tabaci NR146667.2 (99%). The antagonistic activity was assessed with the disc diffusion method. Active fractions were isolated through a liquid/liquid extraction with ethyl acetate (EtOAc) from the fermentation media, and their antibacterial activities were evaluated following the Clinical and Laboratory Standards Institute (CLSI) guidelines. The Pikovskaya modified medium was used to test the ability of in vitro inorganic phosphorus solubilization, and BSB1 proved to be the best inorganic phosphorus solubilizer, with a solubilization index (SI) of 4.5 ± 0.2. The glass-column fractionation of the EtOAc extracted from BCB11 produced an active fraction (25.9 mg) that inhibited the growth of five B. glumae strains by 85-95%. Further, metabolomic analysis, based on GC-MS, showed 3-phenylpropanoic acid (3-PPA) to be the main compound both in this fraction (46.7%), and in the BSB1 extract (28.6%). This compound showed antibacterial activity against all five strains of B. glumae with a minimum inhibitory concentration (MIC) of 1000 mg/L towards all of them. The results showed that rice rhizosphere microorganisms are a source of compounds that inhibit B. glumae growth and are promising plant growth promoters (PGP).
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Affiliation(s)
| | - Walter Murillo Arango
- Chemistry Department, Faculty of Sciences, University of Tolima, Ibagué 730006299, Colombia
| | - Jordi Eras
- Chemistry Department, Scientific Technical Services-TCEM, University of Lleida, 25198 Lleida, Spain
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Quantifying Plant-Borne Carbon Assimilation by Root-Associating Bacteria. Microorganisms 2020; 8:microorganisms8050700. [PMID: 32397579 PMCID: PMC7285072 DOI: 10.3390/microorganisms8050700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 11/17/2022] Open
Abstract
Herbaspirillum seropedicae is a rhizobacteria that occupies a specialized ecological niche in agriculture. As an endophyte and prolific grass root colonizer it has the potential to promote plant growth, enhancing crop yield in many cereal crops. While the mechanisms for plant growth promotion are controversial, the one irrefutable fact is these microorganisms rely heavily on plant-borne carbon as their main energy source in support of their biological functions. Unfortunately, the tools and technology enabling researchers to trace carbon exchange between plants and the microorganisms associating with them has been limiting. Here, we demonstrate that radioactive 11CO2 administered to intact maize leaves with translocation of 11C-photosynthates to roots can provide a ‘traceable’ source of carbon whose assimilation by microbial organisms can be quantified with enormous sensitivity. Fluorescence root imaging of RAM10, a green fluorescent protein (GFP) reporting strain of H. seropedicae, was used to identify regions of high microbial colonization. Microbes were mechanically removed from these regions via sonication in saline solution and extracts were subjected to fluorescence measurement and gamma counting to correlate carbon-11 atoms with numbers of colony forming units. The method has potential to translate to other microorganisms provided they possess an optical reporting trait.
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