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Difficult-to-culture bacteria in the rhizosphere:The underexplored signature microbial groups

Pedosphere 2022年第1期32卷 75-89页

作者： Sadaf KALAM Anirban BASU Appa Rao PODILE Department of plant Sciences School of Life SciencesUniversity of HyderabadHyderabad 500046(India)

Microorganisms represent a substantial portion of the earth’s biodiversity and biomass, and the plant rhizosphere is an innate reservoir teeming with heterogeneous microbes predominated by bacterial communities. Rhizospheric microbial diversity (genetic, phenotypic, and metabolic) has been extensively studied to understand the key ecological roles played by the microbial members, including plant growth promotion. The application of 16S rRNA gene sequencing and next-generation sequencing (NGS) technologies has revolutionized the discovery of novel bacterial groups that have remained undetected by traditional cultivation-based approaches. Such technological advancements have opened new vistas in our current understanding of predominant but concealed and missed bacterial diversity referred to as difficult-to-culture bacterial lineages, especially the predominant phyla Acidobacteria, Verrucomicrobia,Planctomycetes, and Gemmatimonadetes. Regardless of their ubiquity and prevalence, little is known about their ecophysiology because of the non-availability of culturable members. More recently, there has been increased interest in understanding the cosmopolitan distribution and diversity of the difficult-to-culture bacteria, focusing on their role in driving complex plant-microbial interactions and mobilizing nutrients in soil and their potential as sources of novel bioactive metabolites. As an initial step, we review the distribution and significance of such bacterial phyla in soil, their ecophysiological roles, and their hidden plant growth promoting potential. The ability to select and deploy plant probiotic bacteria from the difficult-to-culture fraction of the bacterial community might open new avenues for improving crop health.

关键词： Acidobacteria ecophysiological roles Gemmatimonadetes microbial diversity Planctomycetes plant growth promotion Verrucomicrobia

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Utilization of lignocellulosic plant residues for compost formation and its role in improving soil fertility

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Pedosphere 2023年第5期33卷 700-716页

作者： ALOKIKA ANU Bijender SINGH Laboratory of Bioprocess Technology Departmentof MicrobiologyMaharshi Dayanand UniversityRohtakHaryana 124001India Department of Biotechnology Central University of HaryanaJant-PaliMahendergarhHaryana 123031India

Globally,urbanization and a steady increase in population generate a huge amount of wastes,which leads to a series of economic,social,and environmental changes,mainly in developing countries.There is an utmost need for efficient management strategies for the beneficial utilization of these wastes into useful products.Among these strategies,composting is gaining attention due to its benefits of solid waste management,such as proper sterilization,and economical and effective bioconversion of lignocellulosic wastes to valuable products.Composting is an effective and sustainable approach for the management of various lignocellulosic wastes.This process comprises a series of effective waste treatment steps to ensure sustainable agriculture.Different composting methods have been explored for solid waste management.Furthermore,the influence of various factors relevant to composting has been elucidated.Microbes play a significant role in enhancing the degradation of lignocellulosic residues by secreting different hydrolytic enzymes.Compost has been utilized for increasing soil properties and improving plant growth.

关键词： abiotic factors composting method plant growth promotion remediation sustainable agriculture vermicomposting waste management

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The rhizosphere microbial complex in plant health:A review of interaction dynamics

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Journal of Integrative Agriculture 2022年第8期21卷 2168-2182页

作者： Oluwaseyi Samuel OLANREWAJU Olubukola Oluranti BABALOLA Food Security and Safety Focus Area Faculty of Natural and Agricultural SciencesNorth-West UniversityMmabatho 2735South Africa

Climate change,urbanization,and population increase limit food availability.To sustain human existence,there is the need to increase food and agricultural production to mitigate the impact of these factors.Scientists have been working for years on ways to increase food production.From plant breeding techniques to soil science,scientists have made tremendous progress.The rhizobiome has been proven to be important to crop production,and the impact of the rhizobiome on plant health cannot be overemphasized.Being rich in diverse complex microbial interactions,the rhizosphere has become a major force in recent plant growth promotion studies.The upsurge in next-generation sequencing applications with the various“omics”technologies is helping to unearth information relating to rhizosphere impact on plant growth.Explaining the complex interactions between and across microbial species present in the rhizosphere is important to further enhance our understanding of their mechanistic and mutualistic functions.Knowledge from this can be used in rhizosphere biome engineering for improved plant growth and yield in the face of the various biotic and abiotic challenges.

关键词： below-ground interactions climate change plant growth promotion plant microbiome root exudation

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Mutualistic fungus Piriformospora indica modulates cadmium phytoremediation properties of host plant via concerted action of enzymatic and non-enzymatic biochemicals

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Pedosphere 2022年第2期32卷 256-267页

作者： Muhammad KHALID Saeed UR-RAHMAN Haoxin TAN Lantian SU Pei ZHOU Nan HUI Key Laboratory of Urban Agriculture School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Joint International Research Laboratory of Metabolic&Developmental Sciences Key Laboratory of Urban Agriculture(South)Ministry of AgriculturePlant Biotechnology Research CenterFudan-SJTU-Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station Ministry of Science and TechnologyMinistry of Education800 Dongchuan Rd.Shanghai 200240China Shanghai Urban Forest Ecosystem Research Station National Forestry and Grassland Administration800 Dongchuan Rd.Shanghai 200240China

Soils and ecosystems contaminated with cadmium (Cd) threaten human health and adversely affect morphological,physiological,and biochemical parameters of plants.The symbiotic association of endophytic fungi with their host plants is the best strategy to improve various plant characteristics and remediate soils polluted with heavy metal(loid)s (HMs).Being a well-known plant growth-promoting fungus,Piriformospora indica confers resistance against a number of abiotic stresses,including HM stress.This pot experiment explored the potential and ameliorative effects of P.indica on Artemisia annua L.plants treated with different concentrations (0,40,80,and 120 mg kg-1) of Cd.Inoculation with P.indica significantly increased plant performance,especially by enhancing chlorophyll concentration and water potential and by decreasing electrolytic leakage,when compared with un-inoculated plants,despite the high Cd levels.Similarly,P.indica enhanced antioxidant enzyme activities,thereby reducing the drastic effects of Cd in inoculated plants.In addition,P.indica accumulated Cd in the roots of colonized plants,as revealed by atomic absorption spectroscopy,and restricted Cd translocation to aerial parts.Furthermore,P.indica showed in vitro resistance (up to a certain level) to Cd stress;however,fungus growth was inhibited at very high Cd concentrations,proving it an excellent candidate for use as a potential phytoremediator in fields affected by Cd contamination.The transcriptional analysis showed that the signaling genes and artemisinin and flavonoid biosynthetic pathway genes were significantly upregulated in P.indica-co-cultivated plants when compared with un-inoculated plants,suggesting a fine collaboration between primary and secondary metabolisms to modulate resistance capacity and to enhance the phytoremediation capability of A.annua against Cd toxicity.

关键词： Artemisia annua defence-related gene endophytic fungi fungal inoculation heavy metal stress plant growth promotion soil contamination transcripts

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Prospecting microbial biofilms as climate smart strategies for improving plant and soil health: A review

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Pedosphere 2023年第1期33卷 129-152页

作者： Kulandaivelu VELMOUROUGANE Shobit THAPA Radha PRASANNA Division of Crop Production Indian Council of Agricultural Research-Central Institute for Cotton Research(CICR)Nagpur 440010India Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms KushmaurMau Nath Bhanjan 275103India Division of Microbiology Indian Council of Agricultural Research-Indian Agricultural Research InstituteNew Delhi 110012India

Microbes and their products play key roles in complementing chemical fertilizers and plant protection chemicals by eliciting defence mechanisms in crop plants,thereby providing immunity and resistance against diverse stresses.Among the different environmental technologies used to mitigate climate change,several microbiological interventions are promising,among which biofilms,both naturally-existing and laboratory-developed,and their application have gained momentum recently.Microbial biofilms are aggregations of microbial cells in a self-generated polymeric matrix,which are produced by several genera of bacteria,yeasts,cyanobacteria,and fungi as a mode of reproductive fitness,thereby advantageous in successful proliferation,even in extreme environments.The propensity of microbial biofilms to grow in diverse niches and adapt to biotic and abiotic stresses illustrates their immense potential as biofertilizers and disease suppression options in various crops across diverse ecologies.In the inhospitable habitats of deserts and denudated land,biofilms play an important role in preventing soil erosion and sustaining vegetation,microflora,and fauna.Biofilms represent a mode of growth for several microbes with plant growth-promoting and biocontrol potential,which are important in seed establishment and the facilitation of exchanging nutrients and metabolites from the environment.In this review,we discuss the prospects of microbial biofilms as a green option in agriculture in general and,more specifically,their potential in mitigating climate change.

关键词： biocontrol bioremediation climate change environmental stress nutrient sequestration plant growth promotion

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Endophytic Bacteria Promote the growth of Suaeda glauca in Saline-Alkali Stress:Regulation of Osmotic Pressure and Antioxidative Defense System

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Journal of Ocean University of China 2023年第4期22卷 1109-1118页

作者： FENG Kanghong SUN Ping CHEN Youyuan GUO Jiameng College of Environmental Science and Engineering Ocean University of ChinaQingdao 266100China Key Laboratory of Marine Environment and Ecology Ministry of EducationOcean University of ChinaQingdao 266100China Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering Ocean University of ChinaQingdao 266100China

Endophytic bacteria are promising bacterial fertilizers to improve plant growth under adverse environment.For ecological remediation of coastal wetlands,it was necessary to investigate the effect and interaction of endophytes on halophytes under saline-alkali stress.In this study,an endophytic bacterium strain HK1 isolated from halophytes was selected to infect Suaeda glauca under pH(7 and 8)and salinity gradient(150,300 and 450mmolL^(-1)).Strain HK1 was identified as Pantoea ananatis and it had ability to fix nitrogen,dissolve inorganic phosphorus and produce indole-3-aceticacid(IAA).The results showed that strain HK1 could promote the growth of S.glauca seedings when the salinity was less than 300mmolL^(-1),in view of longer shoot length and heavier fresh weight.The infected plants could produce more proline to decrease the permeability of cells,which content increased by 26.2%–61.1%compared to the non-infected group.Moreover,the oxidative stress of infected plants was relieved with the malondialdehyde(MDA)content decreased by 16.8%–32.9%,and the peroxidase(POD)activity and catalase(CAT)activity increased by 100%–500%and 6.2%–71.4%,respectively.Statistical analysis revealed that increasing proline content and enhancing CAT and POD activities were the main pathways to alleviate saline-alkali stress by strain HK1 infection,and the latter might be more important.This study illustrated that endophytic bacteria could promote the growth of halophytes by regulation of osmotic substances and strengthening antioxidant activities.This finding would be helpful for the bioremediation of coastal soil.

关键词： endophytic bacteria Suaeda glauca plant growth promotion plant-microorganism interaction antioxidant enzyme

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Transcriptomic insights into growth promotion effect of Trichoderma afroharzianum TM2-4 microbial agent on tomato plants

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Journal of Integrative Agriculture 2021年第5期20卷 1266-1276页

作者： ZHAO Juan LIU Ting LIU Wei-cheng ZHANG Dian-peng DONG Dan WU Hui-ling ZHANG Tao-tao LIU De-wen Institute of plant and Environment Protection Beijing Academy of Agriculture and Forestry SciencesBeijing 100097P.R.China

plant growth promoting fungi are receiving increased attention as valuable beneficial microorganisms in crop cultivation due to their capacity to produce bioactive substances,promote plant growth and enhance immune defense functions.In this study,a novel Trichoderma isolate,designated as TM2-4,was screened from healthy tomato rhizosphere soil and identified as Trichoderma afroharzianum.Culture filtrate of the isolate TM2-4 displayed obvious bioactive substance production and an evident effect in promoting tomato seed germination,with hypocotyl length,radical length and vigor index increased by 28.7,19.4 and 62.1%,respectively,after a 100-fold dilution treatment.To assess the promotion effect and related mechanism of isolate TM2-4,the plant biological indexes and gene expression profiles of tomato plants treated with or without T.afroharzianum TM2-4 microbial agent were investigated by greenhouse pot experiment and RNA sequencing.The results demonstrated that T.afroharzianum TM2-4 significantly promoted tomato plant growth in terms of plant height,dry weight,number of leaves per plant and root activity,through efficient colonization in the rhizosphere and root system of the plants.Transcriptome analyses identified a total of 984 differentially expressed genes in T.afroharzianum microbial agent inoculated tomato roots,which were mainly engaged in the biological process of phytohormone homeostasis,antioxidant activity,as well as metabolic pathways including phenylpropanoid biosynthesis and glutathione metabolism.These findings provide useful information for understanding the mechanism of isolate TM2-4 for tomato plant growth promotion,which would facilitate further development of T.afroharzianum TM2-4 microbial agent for use in vegetable crop production.

关键词： Trichoderma afroharzianum Solanum lycopersicum L. plant growth promotion transcriptome analyses qRTPCR

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Benefits of a root fungal endophyte on physiological processes and growth of the vulnerable legume tree Prosopis chilensis(Fabaceae)

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Journal of plant Ecology 2019年第2期12卷 264-271页

作者： Marcia González-Teuber Alejandro Urzúa Andrea Morales Cristian Ibáñez Luisa Bascuñán-Godoy Max Planck Partner Group Departamento de Ciencias del AmbienteUniversidad de Santiago de ChileAv.Libertador Bernardo O'Higgins 3363SantiagoChile Instituto de Investigación Multidisciplinario en Ciencias y Tecnología Universidad de La SerenaAv.Raúl Bitrán 1305La SerenaChile Laboratorio de Química Ecológica Universidad de Santiago de ChileAv.Libertador Bernardo O'Higgins 3363SantiagoChile Departamento de Biología Universidad de La SerenaAv.Raúl Bitrán 1305La SerenaChile Departamento de Botánica Universidad de ConcepciónBarrio Universitario s/nConcepciónChile

Aims Desertification is a major concern in arid and semi-arid regions globally.Understanding interactions between vulnerable plant spe-cies and associated microbial symbionts may have important appli-cations for conservation and restoration strategies in affected areas.Methods In this study,we evaluated the root-associated fungal endophyte community in Prosopis chilensis,a vulnerable and threatened arid-adapted tree of northern Chile.Host benefits in terms of physiologi-cal performance and plant growth were also assessed.Endophytic fungi were isolated from asymptomatic roots by the culture method for molecular identification of the 18S rRNA gene.The dominant fungal endophyte(Penicillium sp.)in the community was later used in inoculation experiments to assess its effect on maximum quan-tum efficiency of photosystem II(_(PSII)),(Fv/Fm)actual _(PSII) efficiency(Φ_(PSII)),and non-photochemical quenching(NPQ).Total sugars,starch content,malonaldehyde(MDA),nitrogen content(%)and growth traits were also measured.Important Findings WhereasΦ_(PSII) increased significantly in endophyte-inoculated plants,NPQ was found to decrease.No effect of endophyte inocula-tion on sugars and MDA was detected,but starch content,leaf nitro-gen content,number of leaves and shoot biomass were found to increase.Results revealed that inoculation of endophytic Penicillium fungal isolate can provide significant physiological benefits to the host plant P.chilensis.Its presence resulted in greater _(PSII) efficiency and higher leaf nitrogen and carbohydrate content,enhancing host plant growth.These findings highlight the importance of consider-ing the fungal endophyte community of this vulnerable species as an important tool to the design of further revegetation and conserva-tion programs.

关键词： root endophytic fungi PSII efficiency nitrogen content plant growth promotion starch accumulation arid habitats

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plant growth-promoting characteristics of root fungal endophytes isolated from a traditional Cordillera rice landrace

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Studies in Fungi 2020年第1期5卷 536-549页

作者： Pablo CHD Pagaduan JRR Langres HKC Hipol RM Department of Biology College of ScienceUniversity of the Philippines Baguio

This study was conducted to isolate and characterize the plant growth-promoting potential of fungal endophytes from the roots of Diket red,a traditional rice plant from the Cordillera,Northern Luzon.Eighteen morphospecies of filamentous endophytes were isolated of which twelve isolates were successfully identified to the species level.These isolates were identified as Aspergillus versicolor,Aspergillus sp.,Chaetosphaeria sp.,Cladosporium cladosporioides,Hypocrea lixii,Microascus murinus,and Trichoderma harzianum.The identified twelve isolates were selected to screen in vitro for their plant growth-promoting characteristics,and evaluated in vivo for their beneficial effects on seedling vigor and early seedling growth.Isolate PPL14 produced the highest IAA at 55.5μg ml^(-1)and M.murinus PPL10 produced the highest amount of IAA at 3.73μg IAA mg^(-1)dry mycelia wt.The seedling vigor assay and in vivo plant growth promotion bioassay indicated overall positive effects of culture filtrate(CF)application of the endophyte isolates.Rice seeds and seedlings grown in aseptic condition and treated with endophyte CFs displayed significantly enhanced levels of germination,seedling vigor,shoot,root,and total plant growth,and biomass compared to non-treated control.Other plant growth-promoting characteristics were also studied including phosphate solubilization,siderophore production,ammonia production,and catalase activity.This study supports the potential use of fungal endophytes as bio-inoculants for plant growth promotion and enhancement of nutrient assimilation of agriculturally important crops.

关键词： 18S rDNA Endophytic fungi plant growth promotion Rice landrace Seedling vigor

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Phenotypic, Stress Tolerance and plant growth Promoting Characteristics of Rhizobial Isolates from Selected Wild Legumes of Semiarid Region, Tirupati, India

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Advances in Microbiology 2016年第1期6卷 1-12页

作者： Y. Bhargava J. S. R. Murthy T. V. Rajesh Kumar M. Narayana Rao Department of Biotechnology S. V. University Tirupati India Department of Botany S. V. University Tirupati India

Rhizobia are vital for nitrogen input, fertility of soil and legume plant growth. Knowledge on rhizobial diversity from arid and semiarid areas is important for dry land agriculture in the context of climatic change and for economic utilization. This study provides morphological, biochemical, stress tolerance and plant growth promoting characteristics of fifteen rhizobial isolates from the nodules of same number of wild legumes and one isolate from cultivated Arachis hypogea from semi-arid region, Tirupati. The bacterial isolates were confirmed as rhizobia based on colony morphology and biochemical tests. Based on the colour change of YMA-BTB medium, eight isolates were identified as slow growers and six were fast growers. The isolates differed in growth pattern, colony morphology, antibiotic resistance at higher concentrations and uniformity in utilization of carbon and nitrogen sources. The isolates are tolerant to NaCl up to one percent, displayed normal growth at temperatures 28℃ - 30℃, at neutral pH and poor growth at pH 5and 9. The isolates varied in the production of EPS and IAA, positive for phosphate solubilization and siderophore formation. This functional diversity displayed by the isolates can be utilised for the legume crop production by cross inoculation.

关键词： Wild Legumes Rhizobia Characterization Stress Tolerance plant growth promotion

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