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Zhang H, Li S, Zhou S, Guo W, Chen P, Li Y, Wu W. Divergence of Phyllosphere Microbial Community Assemblies and Components of Volatile Organic Compounds between the Invasive Sphagneticola trilobata, the Native Sphagneticola calendulacea and Their Hybrids, and Its Implications for Invasiveness. Genes (Basel) 2024; 15:955. [PMID: 39062734 PMCID: PMC11275861 DOI: 10.3390/genes15070955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 07/18/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Closely-related plant groups with distinct microbiomes, chemistries and ecological characteristics represent tractable models to explore mechanisms shaping species spread, competitive dynamics and community assembly at the interface of native and introduced ranges. We investigated phyllosphere microbial communities, volatile organic compound (VOC) compositions, and potential interactions among introduced S. trilobata, native S. calendulacea and their hybrid in South China. S. trilobata exhibited higher α diversity but significantly different community composition compared to the native and hybrid groups. However, S. calendulacea and the hybrid shared certain microbial taxa, suggesting potential gene flow or co-existence. The potent antimicrobial VOC profile of S. trilobata, including unique compounds like p-cymene (13.33%), likely contributes to its invasion success. The hybrid's intermediate microbial and VOC profiles suggest possible consequences for species distribution, genetic exchange, and community assembly in heterogeneous environments. This hybrid deserves further study as both an opportunity for and threat to diversity maintenance. These differentiating yet connected plant groups provide insight into ecological and evolutionary dynamics shaping microbiome structure, species co-occurrence and competitive outcomes during biological exchange and habitat transformation. An interdisciplinary approach combining chemical and microbial ecology may reveal mechanisms underlying community stability and change, informing management of species spread in a globalized world.
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Affiliation(s)
| | | | | | | | | | | | - Wei Wu
- Scarce and Quality Economic Forest Engineering Technology Research Center, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (H.Z.); (S.L.); (S.Z.); (W.G.); (P.C.); (Y.L.)
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2
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Zhang C, Zhou DF, Wang MY, Song YZ, Zhang C, Zhang MM, Sun J, Yao L, Mo XH, Ma ZX, Yuan XJ, Shao Y, Wang HR, Dong SH, Bao K, Lu SH, Sadilek M, Kalyuzhnaya MG, Xing XH, Yang S. Phosphoribosylpyrophosphate synthetase as a metabolic valve advances Methylobacterium/Methylorubrum phyllosphere colonization and plant growth. Nat Commun 2024; 15:5969. [PMID: 39013920 PMCID: PMC11252147 DOI: 10.1038/s41467-024-50342-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 07/06/2024] [Indexed: 07/18/2024] Open
Abstract
The proficiency of phyllosphere microbiomes in efficiently utilizing plant-provided nutrients is pivotal for their successful colonization of plants. The methylotrophic capabilities of Methylobacterium/Methylorubrum play a crucial role in this process. However, the precise mechanisms facilitating efficient colonization remain elusive. In the present study, we investigate the significance of methanol assimilation in shaping the success of mutualistic relationships between methylotrophs and plants. A set of strains originating from Methylorubrum extorquens AM1 are subjected to evolutionary pressures to thrive under low methanol conditions. A mutation in the phosphoribosylpyrophosphate synthetase gene is identified, which converts it into a metabolic valve. This valve redirects limited C1-carbon resources towards the synthesis of biomass by up-regulating a non-essential phosphoketolase pathway. These newly acquired bacterial traits demonstrate superior colonization capabilities, even at low abundance, leading to increased growth of inoculated plants. This function is prevalent in Methylobacterium/Methylorubrum strains. In summary, our findings offer insights that could guide the selection of Methylobacterium/Methylorubrum strains for advantageous agricultural applications.
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Affiliation(s)
- Cong Zhang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Di-Fei Zhou
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Meng-Ying Wang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Ya-Zhen Song
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Chong Zhang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, PR China
| | - Ming-Ming Zhang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Jing Sun
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Lu Yao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong, PR China
| | - Xu-Hua Mo
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Zeng-Xin Ma
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Xiao-Jie Yuan
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Yi Shao
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Hao-Ran Wang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Si-Han Dong
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Kai Bao
- School of Life Sciences, Hubei University, Wuhan, Hubei, PR China
| | - Shu-Huan Lu
- CABIO Biotech (Wuhan) Co. Ltd., Wuhan, Hubei, PR China
| | - Martin Sadilek
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | | | - Xin-Hui Xing
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, PR China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, PR China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, PR China
| | - Song Yang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China.
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China.
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China.
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, PR China.
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, PR China.
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3
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Baruah N, Haajanen R, Rahman MT, Pirttilä AM, Koskimäki JJ. Biosynthesis of polyhydroxybutyrate by Methylorubrum extorquens DSM13060 is essential for intracellular colonization in plant endosymbiosis. FRONTIERS IN PLANT SCIENCE 2024; 15:1302705. [PMID: 38390299 PMCID: PMC10883064 DOI: 10.3389/fpls.2024.1302705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
Methylorubrum extorquens DSM13060 is an endosymbiont that lives in the cells of shoot tip meristems. The bacterium is methylotrophic and consumes plant-derived methanol for the production of polyhydroxybutyrate (PHB). The PHB provides protection against oxidative stress for both host and endosymbiont cells through its fragments, methyl-esterified 3-hydroxybutyrate (ME-3HB) oligomers. We evaluated the role of the genes involved in the production of ME-3HB oligomers in the host colonization by the endosymbiont M. extorquens DSM13060 through targeted genetic mutations. The strains with deletions in PHB synthase (phaC), PHB depolymerase (phaZ1), and a transcription factor (phaR) showed altered PHB granule characteristics, as ΔphaC had a significantly low number of granules, ΔphaR had a significantly increased number of granules, and ΔphaZ1 had significantly large PHB granules in the bacterial cells. When the deletion strains were exposed to oxidative stress, the ΔphaC strain was sensitive to 10 mM HO· and 20 mM H2O2. The colonization of the host, Scots pine (Pinus sylvestris L.), by the deletion strains varied greatly. The deletion strain ΔphaR colonized the host mainly intercellularly, whereas the ΔphaZ1 strain was a slightly poorer colonizer than the control. The deletion strain ΔphaC lacked the colonization potential, living mainly on the surfaces of the epidermis of pine roots and shoots in contrast to the control, which intracellularly colonized all pine tissues within the study period. In earlier studies, deletions within the PHB metabolic pathway have had a minor effect on plant colonization by rhizobia. We have previously shown the association between ME-3HB oligomers, produced by PhaC and PhaZ1, and the ability to alleviate host-generated oxidative stress during plant infection by the endosymbiont M. extorquens DSM13060. Our current results show that the low capacity for PHB synthesis leads to poor tolerance of oxidative stress and loss of colonization potential by the endosymbiont. Altogether, our findings demonstrate that the metabolism of PHB in M. extorquens DSM13060 is an important trait in the non-rhizobial endosymbiosis.
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Affiliation(s)
- Namrata Baruah
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roosa Haajanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Mohammad Tanvir Rahman
- Disease Networks, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - Janne J Koskimäki
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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4
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Torres Vera R, Bernabé García AJ, Carmona Álvarez FJ, Martínez Ruiz J, Fernández Martín F. Application and effectiveness of Methylobacterium symbioticum as a biological inoculant in maize and strawberry crops. Folia Microbiol (Praha) 2024; 69:121-131. [PMID: 37526803 PMCID: PMC10876812 DOI: 10.1007/s12223-023-01078-4] [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] [Accepted: 07/14/2023] [Indexed: 08/02/2023]
Abstract
The effectiveness of Methylobacterium symbioticum in maize and strawberry plants was measured under different doses of nitrogen fertilisation. The biostimulant effect of the bacteria was observed in maize and strawberry plants treated with the biological inoculant under different doses of nitrogen fertiliser compared to untreated plants (control). It was found that bacteria allowed a 50 and 25% decrease in the amount of nitrogen applied in maize and strawberry crops, respectively, and the photosynthetic capacity increased compared with the control plant under all nutritional conditions. A decrease in nitrate reductase activity in inoculated maize plants indicated that the bacteria affects the metabolism of the plant. In addition, inoculated strawberry plants grown with a 25% reduction in nitrogen had a higher concentration of nitrogen in leaves than control plants under optimal nutritional conditions. Again, this indicates that Methylobacterium symbioticum provide an additional supply of nitrogen.
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5
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Bawane P, Deshpande S, Yele S. Industrial and Pharmaceutical Applications of Microbial Diversity of Hypersaline Ecology from Lonar Soda Crater. Curr Pharm Biotechnol 2024; 25:1564-1584. [PMID: 38258768 DOI: 10.2174/0113892010265978231109085224] [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: 07/30/2023] [Revised: 09/16/2023] [Accepted: 10/04/2023] [Indexed: 01/24/2024]
Abstract
The unidentified geochemical and physiochemical characteristics of Soda Lakes across the globe make it a novel reservoir and bring attention to scientific civic for its conceivable industrial and pharmaceutical applications. In India, in the Maharashtra state, Lonar Lake is a naturally created Soda Lake by a meteorite impact. Phylogenetic data from this lake explored a diverse array of microorganisms like haloalkaliphilic bacteria and Archaea. Previously reported studies postulated the major microbial communities present in this lake ecosystem are Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria. Furthermore, it also contains Bacteroidetes, Nitrospirae, and Verrucomicrobia. This lake is also rich in phytoplankton, with the predominant presence of the Spirulina plantensis. Unique microbial strains from Lonar Lake ecosystems have fascinated consideration as a source of biological molecules with medicinal, industrial, and biotechnological potential. Recent literature revealed the isolation of antibioticproducing bacteria and alkaline proteases-producing alkaliphilic bacterium, as well as novel species of rare methylotrophs, other bacterial strains involved in producing vital enzymes, and unique actinomycetes are also reported. It indicates that the novel bacterial assemblage not reached hitherto may exist in this modified and unique ecology. This comprehensive review provides information about microbial diversity and its industrial and pharmaceutical interests that exist in Lonar Lake, which could be the future source of bioactive enzymes, biosurfactants, and biofuel and also useful in bioremediation. Furthermore, the novel species of microorganisms isolated from Lonar Lake have applications in the biosynthesis of medicines like antibiotics, antivirals, antifungals, anti-inflammatory agents, and precursors for synthesising valuable products. Data consolidated in the present review will cater to the needs of emerging industrial sectors for their commercial and therapeutic applications.
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Affiliation(s)
- Pradip Bawane
- Department of Pharmacognosy, SVKM's NMIMS, Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, Mumbai, 400056, India
- Department of Pharmacognosy, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule, Maharashtra, India
| | - Shirish Deshpande
- Department of Pharmaceutical Chemistry, SVKM's NMIMS, School of Pharmacy & Technology Management, Telangana Hyderabad, 509301, India
| | - Santosh Yele
- Department of Pharmacognosy, SVKM's NMIMS, School of Pharmacy & Technology Management, Telangana Hyderabad, 509301, India
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6
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Gaube P, Marchenko P, Müller C, Schweiger R, Tenhaken R, Keller A, Junker RR. Inter- and intraspecific phytochemical variation correlate with epiphytic flower and leaf bacterial communities. Environ Microbiol 2023; 25:1624-1643. [PMID: 37011905 DOI: 10.1111/1462-2920.16382] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023]
Abstract
Microbes associated with flowers and leaves affect plant health and fitness and modify the chemical phenotypes of plants with consequences for interactions of plants with their environment. However, the drivers of bacterial communities colonizing above-ground parts of grassland plants in the field remain largely unknown. We therefore examined the relationships between phytochemistry and the epiphytic bacterial community composition of flowers and leaves of Ranunculus acris and Trifolium pratense. On 252 plant individuals, we characterized primary and specialized metabolites, that is, surface sugars, volatile organic compounds (VOCs), and metabolic fingerprints, as well as epiphytic flower and leaf bacterial communities. The genomic potential of bacterial colonizers concerning metabolic capacities was assessed using bacterial reference genomes. Phytochemical composition displayed pronounced variation within and between plant species and organs, which explained part of the variation in bacterial community composition. Correlation network analysis suggests strain-specific correlations with metabolites. Analysis of bacterial reference genomes revealed taxon-specific metabolic capabilities that corresponded with genes involved in glycolysis and adaptation to osmotic stress. Our results show relationships between phytochemistry and the flower and leaf bacterial microbiomes suggesting that plants provide chemical niches for distinct bacterial communities. In turn, bacteria may induce alterations in the plants' chemical phenotype. Thus, our study may stimulate further research on the mechanisms of trait-based community assembly in epiphytic bacteria.
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Affiliation(s)
- Paul Gaube
- Department of Bioinformatics, University of Würzburg, D-97074, Würzburg, Germany
- Center for Computational and Theoretical Biology, University of Würzburg, D-97074, Würzburg, Germany
| | - Polina Marchenko
- Department of Environment and Biodiversity, University of Salzburg, A-5020, Salzburg, Austria
| | - Caroline Müller
- Department of Chemical Ecology, Bielefeld University, D-33615, Bielefeld, Germany
| | - Rabea Schweiger
- Department of Chemical Ecology, Bielefeld University, D-33615, Bielefeld, Germany
| | - Raimund Tenhaken
- Department of Environment and Biodiversity, University of Salzburg, A-5020, Salzburg, Austria
| | - Alexander Keller
- Cellular and Organismic Networks, Center for Organismic Adaptation (CORA), Faculty of Biology, LMU Munich, Planegg-Martinsried, D-82152, Germany
| | - Robert R Junker
- Department of Environment and Biodiversity, University of Salzburg, A-5020, Salzburg, Austria
- Evolutionary Ecology of Plants, Department of Biology, University of Marburg, D-35032, Marburg, Germany
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7
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Barros-Rodríguez A, García-Gálvez C, Pacheco P, Kalyuzhnaya MG, Manzanera M. Isolation of Methane Enriched Bacterial Communities and Application as Wheat Biofertilizer under Drought Conditions: An Environmental Contribution. PLANTS (BASEL, SWITZERLAND) 2023; 12:2487. [PMID: 37447048 DOI: 10.3390/plants12132487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023]
Abstract
The search for methanotrophs as plant-growth-promoting rhizobacteria (PGPR) presents an important contribution to mitigating the impact of global warming by restoring the natural soil potential for consuming methane while benefiting plants during droughts. Our in silico simulations suggest that water, produced as a byproduct of methane oxidation, can satisfy the cell growth requirement. In addition to water, methanotrophs can produce metabolites that stimulate plant growth. Considering this, we proposed that applying methanotrophs as PGPR can alleviate the effect of droughts on crops, while stimulating atmospheric methane consumption. In this work, we isolated a series of methanotrophic communities from the rhizospheres of different crops, including Italian sweet pepper and zucchini, using an atmosphere enriched with pure methane gas, to determine their potential for alleviating drought stress in wheat plants. Subsequently, 23 strains of nonmethanotrophic bacteria present in the methanotrophic communities were isolated and characterized. We then analyzed the contribution of the methane-consuming consortia to the improvement of plant growth under drought conditions, showing that some communities contributed to increases in the wheat plants' lengths and weights, with statistically significant differences according to ANOVA models. Furthermore, we found that the presence of methane gas can further stimulate the plant-microbe interactions, resulting in larger plants and higher drought tolerance.
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Affiliation(s)
- Adoración Barros-Rodríguez
- Institute for Water Research and Department of Microbiology, University of Granada, 18071 Granada, Spain
- VitaNtech Biotechnology S.L., 18008 Granada, Spain
| | - Carlos García-Gálvez
- Institute for Water Research and Department of Microbiology, University of Granada, 18071 Granada, Spain
- VitaNtech Biotechnology S.L., 18008 Granada, Spain
| | - Pamela Pacheco
- Institute for Water Research and Department of Microbiology, University of Granada, 18071 Granada, Spain
| | | | - Maximino Manzanera
- Institute for Water Research and Department of Microbiology, University of Granada, 18071 Granada, Spain
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8
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Di Lorenzo F, Nicolardi S, Marchetti R, Vanacore A, Gallucci N, Duda K, Nieto Fabregat F, Nguyen HNA, Gully D, Saenz J, Giraud E, Paduano L, Molinaro A, D’Errico G, Silipo A. Expanding Knowledge of Methylotrophic Capacity: Structure and Properties of the Rough-Type Lipopolysaccharide from Methylobacterium extorquens and Its Role on Membrane Resistance to Methanol. JACS AU 2023; 3:929-942. [PMID: 37006758 PMCID: PMC10052234 DOI: 10.1021/jacsau.3c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
The ability of Methylobacterium extorquens to grow on methanol as the sole carbon and energy source has been the object of intense research activity. Unquestionably, the bacterial cell envelope serves as a defensive barrier against such an environmental stressor, with a decisive role played by the membrane lipidome, which is crucial for stress resistance. However, the chemistry and the function of the main constituent of the M. extorquens outer membrane, the lipopolysaccharide (LPS), is still undefined. Here, we show that M. extorquens produces a rough-type LPS with an uncommon, non-phosphorylated, and extensively O-methylated core oligosaccharide, densely substituted with negatively charged residues in the inner region, including novel monosaccharide derivatives such as O-methylated Kdo/Ko units. Lipid A is composed of a non-phosphorylated trisaccharide backbone with a distinctive, low acylation pattern; indeed, the sugar skeleton was decorated with three acyl moieties and a secondary very long chain fatty acid, in turn substituted by a 3-O-acetyl-butyrate residue. Spectroscopic, conformational, and biophysical analyses on M. extorquens LPS highlighted how structural and tridimensional features impact the molecular organization of the outer membrane. Furthermore, these chemical features also impacted and improved membrane resistance in the presence of methanol, thus regulating membrane ordering and dynamics.
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Affiliation(s)
- Flaviana Di Lorenzo
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Simone Nicolardi
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Roberta Marchetti
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Adele Vanacore
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Noemi Gallucci
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
- CSGI, Consorzio
Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Katarzyna Duda
- Research
Center Borstel Leibniz Lung Center, Parkallee 4a, 23845 Borstel, Germany
| | - Ferran Nieto Fabregat
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Ha Ngoc Anh Nguyen
- B-CUBE
Center for Molecular Bioengineering, Technische
Universität Dresden, Tatzberg 41, 01307 Dresden, Germany
| | - Djamel Gully
- IRD,
Laboratoire des Symbioses Tropicales et Méditerranéennes
(LSTM) UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J, Campus de Baillarguet, 34398 Montpellier Cedex 5, France
| | - James Saenz
- B-CUBE
Center for Molecular Bioengineering, Technische
Universität Dresden, Tatzberg 41, 01307 Dresden, Germany
| | - Eric Giraud
- IRD,
Laboratoire des Symbioses Tropicales et Méditerranéennes
(LSTM) UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J, Campus de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Luigi Paduano
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
- CSGI, Consorzio
Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Antonio Molinaro
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Gerardino D’Errico
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
- CSGI, Consorzio
Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Alba Silipo
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
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9
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Hernández-Tasco AJ, Tronchini RA, Apaza-Castillo GA, Hosaka GK, Quiñones NR, Goulart MC, Fantinatti-Garboggini F, Salvador MJ. Diversity of bacterial and fungal endo phytic communities presents in the leaf blades of Sinningia magnifica, Sinningia schiffneri and Sinningia speciosa from different cladus of Gesneriaceae family: a comparative analysis in three consecutive years. Microbiol Res 2023; 271:127365. [PMID: 37011509 DOI: 10.1016/j.micres.2023.127365] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/24/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
Sinningia is a genus of plants of Gesneriaceae family with species native to Brazil and is a source of several classes of bioactive secondary metabolites, such as quinones, terpenoids, flavonoids, and phenylethanoid glycosides. However, the diversity of endophytic microorganisms associated with them and the impact of endophytes on the biosynthesis of bioactive substances is unknown. Therefore, we sought to evaluate the microbial diversity, behavior, and frequency of endophytes in leaves blades of S. magnifica, S. schiffneri, and S. speciosa. These plants were collected in different regions and environments of Brazil and were studied comparatively for three consecutive years. The total DNA obtained from the blades of the plant leaves were sequenced by the Illumina MiSeq platform, followed by bioinformatics analysis to assess the microbial diversity of endophytes associated with each plant species and study year. The results of the taxonomic diversity showed a dynamic microbial community, which contained several bacterial phyla among them, Actinomycetota, Bacteroidota, Bacillota, and Pseudomonadota, and for the fungal phyla Ascomycota and Basidiomycota. Comparing the three years of study, the richness of the genera, over time, was decreasing, with signs of recovery towards the third year. The alpha and beta diversity indices confirm a great phylogenetic richness in the endophytic communities of bacteria and fungi associated with the leaf blades of Sinningia. However, these communities are comparatively little conserved, showing population and taxonomic changes of the microorganisms over time, possibly as a measure of adjustment to environmental conditions, evidencing both its fragility and versatility against the effects of environmental change on its endophytic microbial communities.
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Affiliation(s)
- Alvaro José Hernández-Tasco
- Institute of Biology, Department of Plant Biology, PPG-BTPB, University of Campinas (UNICAMP), 13083-970 Campinas, SP, Brazil.
| | - Rafaela Aparecida Tronchini
- Institute of Biology, Department of Plant Biology, PPG-BTPB, University of Campinas (UNICAMP), 13083-970 Campinas, SP, Brazil
| | | | - Guilherme Kenichi Hosaka
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Nataly Ruiz Quiñones
- Research Center for Chemical, Biological and Agricultural Pluridisciplinary (CPQBA), Division of Microbiol Resources, University of Campinas (UNICAMP), Av. Alexandre Cazellato, 999, 13148-218 Paulínia, SP, Brazil
| | - Marcela Cristina Goulart
- Research Center for Chemical, Biological and Agricultural Pluridisciplinary (CPQBA), Division of Microbiol Resources, University of Campinas (UNICAMP), Av. Alexandre Cazellato, 999, 13148-218 Paulínia, SP, Brazil
| | - Fabiana Fantinatti-Garboggini
- Research Center for Chemical, Biological and Agricultural Pluridisciplinary (CPQBA), Division of Microbiol Resources, University of Campinas (UNICAMP), Av. Alexandre Cazellato, 999, 13148-218 Paulínia, SP, Brazil
| | - Marcos José Salvador
- Institute of Biology, Department of Plant Biology, PPG-BTPB, University of Campinas (UNICAMP), 13083-970 Campinas, SP, Brazil.
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10
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Gamit HA, Naik H, Chandarana KA, Chandwani S, Amaresan N. Secondary metabolites from methylotrophic bacteria: their role in improving plant growth under a stressed environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:28563-28574. [PMID: 36710311 DOI: 10.1007/s11356-023-25505-8] [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: 11/14/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Climate change is considered a natural disaster that causes the ecosystem to fluctuate and increase temperature, as well as the amount of UV radiation (UV-A and UV-B) on the Earth's surface. Consequently, greenhouse gases such as chlorofluorocarbons, methane, nitrogen oxide, and carbon dioxide have become obstacles to the development of sustainable agriculture. To overcome environmental stress such as phytopathogens, drought, salinity, heavy metals, and high-low temperatures, the utilization of microorganisms is a viable option. The synthesis of secondary metabolites by methylotrophic bacteria improves plant metabolism, enhances tolerance, and facilitates growth. The genus Methylobacterium is a pink-pigmented facultative methylotrophs which abundantly colonizes plants, especially young leaves, owing to the availability of methanol. Secondary metabolites such as amino acids, carotenoids, hormones, antimicrobial compounds, and other compounds produced by methylotrophic bacteria enhance plant metabolism under stress conditions. Therefore, in this review, we discuss the role of secondary metabolites produced by methylotrophic bacteria and their role in promoting plant growth under stress.
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Affiliation(s)
- Harshida A Gamit
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, 394 350, Gujarat, India
| | - Hetvi Naik
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, 394 350, Gujarat, India
| | - Komal A Chandarana
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, 394 350, Gujarat, India
| | - Sapna Chandwani
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, 394 350, Gujarat, India
| | - Natarajan Amaresan
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, 394 350, Gujarat, India.
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11
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Insights into the genome of Methylobacterium sp. NMS14P, a novel bacterium for growth promotion of maize, chili, and sugarcane. PLoS One 2023; 18:e0281505. [PMID: 36749783 PMCID: PMC9904496 DOI: 10.1371/journal.pone.0281505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant (Coffea arabica) in Thailand. The 16S rRNA sequence analysis revealed that this new isolate belongs to the genus Methylobacterium, and its novelty was clarified by genomic and comparative genomic analyses, in which NMS14P exhibited low levels of relatedness with other Methylobacterium-type strains. NMS14P genome consists of a 6,268,579 bp chromosome, accompanied by a 542,519 bp megaplasmid and a 66,590 bp plasmid, namely pNMS14P1 and pNMS14P2, respectively. Several genes conferring plant growth promotion are aggregated on both chromosome and plasmids, including phosphate solubilization, indole-3-acetic acid (IAA) biosynthesis, cytokinins (CKs) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, sulfur-oxidizing activity, trehalose synthesis, and urea metabolism. Furthermore, pangenome analysis showed that NMS14P possessed the highest number of strain-specific genes accounting for 1408 genes, particularly those that are essential for colonization and survival in a wide array of host environments, such as ABC transporter, chemotaxis, quorum sensing, biofilm formation, and biosynthesis of secondary metabolites. In vivo tests have supported that NMS14P significantly promoted the growth and development of maize, chili, and sugarcane. Collectively, NMS14P is proposed as a novel plant growth-promoting Methylobacterium that could potentially be applied to a broad range of host plants as Methylobacterium-based biofertilizers to reduce and ultimately substitute the use of synthetic agrochemicals for sustainable agriculture.
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12
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Jahan R, McDonald IR. Diversity of Methylobacterium species associated with New Zealand native plants. FEMS Microbiol Lett 2023; 370:fnad124. [PMID: 37985695 PMCID: PMC10699869 DOI: 10.1093/femsle/fnad124] [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: 05/24/2023] [Revised: 09/26/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023] Open
Abstract
Methylobacterium species are abundant colonizers of the phyllosphere due to the availability of methanol, a waste product of pectin metabolism during plant cell division. The phyllosphere is an extreme environment, with a landscape that is heterogeneous and continuously changing as the plant grows and is exposed to high levels of ultraviolet irradiation. Geographically, New Zealand (NZ) has been isolated for over a million years, has a biologically diverse flora, and is considered a biodiversity hotspot, with most native plants being endemic. We therefore hypothesize that the phyllosphere of NZ native plants harbor diverse groups of Methylobacterium species. Leaf imprinting using methanol-supplemented agar medium was used to isolate bacteria, and diversity was determined using ARDRA and 16S rRNA gene sequencing. Methylobacterium species were successfully isolated from the phyllosphere of 18 of the 20 native NZ plant species in this study, and six different species were identified: M. marchantiae, M. mesophilicum, M. adhaesivum, M. komagatae, M. extorquens, and M. phyllosphaerae. Other α, β, and γ-Proteobacteria, Actinomycetes, Bacteroidetes, and Firmicutes were also isolated, highlighting the presence of other potentially novel methanol utilizers within this ecosystem. This study identified that Methylobacterium are abundant members of the NZ phyllosphere, with species diversity and composition dependent on plant species.
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Affiliation(s)
- Rowshan Jahan
- Te Aka Mātuatua—School of Science, Te Whare Wānanga o Waikato—University of Waikato, Private Bag 3105, Hamilton 3240, Aotearoa, New Zealand
| | - Ian R McDonald
- Te Aka Mātuatua—School of Science, Te Whare Wānanga o Waikato—University of Waikato, Private Bag 3105, Hamilton 3240, Aotearoa, New Zealand
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13
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Yurimoto H, Sakai Y. Interaction between C1-microorganisms and plants: contribution to the global carbon cycle and microbial survival strategies in the phyllosphere. Biosci Biotechnol Biochem 2022; 87:1-6. [PMID: 36367545 DOI: 10.1093/bbb/zbac176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
C1-microorganisms that can utilize C1-compounds, such as methane and methanol, are ubiquitous in nature, and contribute to drive the global carbon cycle between two major greenhouse gases, CO2 and methane. Plants emit C1-compounds from their leaves and provide habitats for C1-microorganisms. Among C1-microorganisms, Methylobacterium spp., representative of methanol-utilizing methylotrophic bacteria, predominantly colonize the phyllosphere and are known to promote plant growth. This review summarizes the interactions between C1-mircroorganisms and plants that affect not only the fixation of C1-compounds produced by plants but also CO2 fixation by plants. We also describe our recent understanding of the survival strategy of C1-microorganisms in the phyllosphere and the application of Methylobacterium spp. to improve rice crop yield.
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Affiliation(s)
- Hiroya Yurimoto
- D ivision of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Yasuyoshi Sakai
- D ivision of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
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14
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Vanacore A, Forgione MC, Cavasso D, Nguyen HNA, Molinaro A, Saenz JP, D'Errico G, Paduano L, Marchetti R, Silipo A. Role of EPS in mitigation of plant abiotic stress: The case of Methylobacterium extorquens PA1. Carbohydr Polym 2022; 295:119863. [DOI: 10.1016/j.carbpol.2022.119863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022]
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15
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Micallef SA, Han S, Martinez L. Tomato Cultivar Nyagous Fruit Surface Metabolite Changes during Ripening Affect Salmonella Newport. J Food Prot 2022; 85:1604-1613. [PMID: 36048925 DOI: 10.4315/jfp-22-160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/30/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Tomatoes are a valuable crop consumed year-round. Ripe fruit is picked for local sale, whereas tomatoes intended for transit may be harvested at late mature green or breaker stages when fruit firmness preserves quality. In this study, we evaluated Solanum lycopersicum cv. BHN602 association with three Salmonella serotypes and S. lycopersicum cv. Nyagous with Salmonella Newport using fruit at two ripeness stages. Counts of Salmonella Javiana and Typhimurium were higher from red ripe fruit surfaces of BHN602, and counts of Salmonella Newport were higher from ripe Nyagous fruit than from mature green fruit (P < 0.05). Aqueous fruit washes containing fruit surface compounds collected from ripe Nyagous fruit supported more Salmonella Newport growth than green fruit washes (P < 0.05). Growth curve analysis showed that between 2 and 6 h, Salmonella Newport grew at a rate of 0.25 log CFU/h in red fruit wash compared with 0.17 log CFU/h in green fruit wash (P < 0.05). The parallel trend in Salmonella interaction between fruit and wash suggested that surface metabolite differences between unripe and ripe fruit affect Salmonella dynamics. Untargeted phytochemical profiling of tomato fruit surface washes with gas chromatography time-of-flight mass spectrometry showed that ripe fruit had threefold-lower amino acid and fourfold-higher sugar (fructose, glucose, and xylose) levels than green fruit. Green fruit had higher levels of lauric, palmitic, margaric, and arachidic acids, whereas red fruit had more capric acid. The phenolics ferulic, chlorogenic, and vanillic acid, as well as tyrosol, also decreased with ripening. Although limitations of this study preclude conclusions on how specific compounds affect Salmonella, our study highlights the complexity of the plant niche for foodborne pathogens and the importance of understanding the metabolite landscape Salmonella encounters on fresh produce. Fruit surface phytochemical profiling generated testable hypotheses for future studies exploring the differential Salmonella interactions with tomato varieties and fruit at various ripeness stages. HIGHLIGHTS
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Affiliation(s)
- Shirley A Micallef
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742, USA.,Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland 20742, USA
| | - Sanghyun Han
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742, USA
| | - Louisa Martinez
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742, USA
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16
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Kröber E, Mankowski A, Schäfer H. Microorganisms associated with Sporobolus anglicus, an invasive dimethylsulfoniopropionate producing salt marsh plant, are an unrecognized sink for dimethylsulfide. Front Microbiol 2022; 13:950460. [PMID: 36246216 PMCID: PMC9563715 DOI: 10.3389/fmicb.2022.950460] [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: 05/22/2022] [Accepted: 08/12/2022] [Indexed: 11/23/2022] Open
Abstract
Background Saltmarshes are hotspots of organosulfur compound cycling due to production of dimethylsulfoniopropionate (DMSP) by benthic microorganisms, macroalgae, and saltmarsh vegetation. Degradation of DMSP is a source of dimethylsulfide (DMS), an important precursor for formation of secondary organic aerosol. Microorganisms degrading DMS play a role in controlling the amount of DMS available for emission into the atmosphere. Previous work has implicated sediment microbial populations as a major sink for DMS. Here, we show that Sporobolus anglicus (previously known as Spartina anglica), a widely distributed saltmarsh plant, is colonized by DMS-degrading microorganisms. Methods Dimethylsulfide degradation potential was assessed by gas chromatography and 13C-DMS stable isotope probing, microbial community diversity and functional genetic potential in phyllosphere and rhizosphere samples was assessed by high-throughput sequencing of 16S rRNA gene amplicons, cloning and sequencing of methanethiol oxidase genes, and by metagenomic analysis of phyllosphere microbial communities. Results The DMS degradation potential of microbial communities recovered from phyllosphere and rhizosphere samples was similar. Active DMS-degraders were identified by 13C-DMS stable isotope probing and included populations related to Methylophaga and other Piscirickettsiaceae in rhizosphere samples. DMS-degraders in the phyllosphere included Xanthomonadaceae and Halothiobacillaceae. The diversity in sediment samples of the methanethiol oxidase (mtoX) gene, a marker for metabolism of methanethiol during DMS and DMSP degradation, was similar to previously detected saltmarsh mtoX, including those of Methylophaga and Methylococcaeae. Phyllosphere mtoX genes were distinct from sediment mtoX and did not include close relatives of cultivated bacteria. Microbial diversity in the phyllosphere of S. anglicus was distinct compared to those of model plants such as rice, soybean, clover and Arabidopsis and showed a dominance of Gammaproteobacteria rather than Alphaproteobacteria. Conclusion The potential for microbial DMS degradation in the phyllosphere and rhizosphere of Sporobolus anglicus suggest that DMS cycling in saltmarshes is more complex than previously recognised and calls for a more detailed assessment of how aboveground activities affect fluxes of DMS.
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Affiliation(s)
- Eileen Kröber
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Anna Mankowski
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hendrik Schäfer
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
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17
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Juma PO, Fujitani Y, Alessa O, Oyama T, Yurimoto H, Sakai Y, Tani A. Siderophore for Lanthanide and Iron Uptake for Methylotrophy and Plant Growth Promotion in Methylobacterium aquaticum Strain 22A. Front Microbiol 2022; 13:921635. [PMID: 35875576 PMCID: PMC9301485 DOI: 10.3389/fmicb.2022.921635] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/09/2022] [Indexed: 11/15/2022] Open
Abstract
Methylobacterium and Methylorubrum species are facultative methylotrophic bacteria that are abundant in the plant phyllosphere. They have two methanol dehydrogenases, MxaF and XoxF, which are dependent on either calcium or lanthanides (Lns), respectively. Lns exist as insoluble minerals in nature, and their solubilization and uptake require a siderophore-like substance (lanthanophore). Methylobacterium species have also been identified as plant growth-promoting bacteria although the actual mechanism has not been well-investigated. This study aimed to reveal the roles of siderophore in Methylobacterium aquaticum strain 22A in Ln uptake, bacterial physiology, and plant growth promotion. The strain 22A genome contains an eight-gene cluster encoding the staphyloferrin B-like (sbn) siderophore. We demonstrate that the sbn siderophore gene cluster is necessary for growth under low iron conditions and was complemented by supplementation with citrate or spent medium of the wild type or other strains of the genera. The siderophore exhibited adaptive features, including tolerance to oxidative and nitrosative stress, biofilm formation, and heavy metal sequestration. The contribution of the siderophore to plant growth was shown by the repressive growth of duckweed treated with siderophore mutant under iron-limited conditions; however, the siderophore was dispensable for strain 22A to colonize the phyllosphere. Importantly, the siderophore mutant could not grow on methanol, but the siderophore could solubilize insoluble Ln oxide, suggesting its critical role in methylotrophy. We also identified TonB-dependent receptors (TBDRs) for the siderophore–iron complex, iron citrate, and Ln, among 12 TBDRs in strain 22A. Analysis of the siderophore synthesis gene clusters and TBDR genes in Methylobacterium genomes revealed the existence of diverse types of siderophores and TBDRs. Methylorubrum species have an exclusive TBDR for Ln uptake that has been identified as LutH. Collectively, the results of this study provide insight into the importance of the sbn siderophore in Ln chelation, bacterial physiology, and the diversity of siderophore and TBDRs in Methylobacterium species.
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Affiliation(s)
- Patrick Otieno Juma
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Ola Alessa
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Tokitaka Oyama
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hiroya Yurimoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasuyoshi Sakai
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
- *Correspondence: Akio Tani,
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18
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Becker MF, Hellmann M, Knief C. Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees. ENVIRONMENTAL MICROBIOME 2022; 17:31. [PMID: 35715810 PMCID: PMC9205072 DOI: 10.1186/s40793-022-00427-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/30/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Studies about spatio-temporal variation of the root-associated microbiome focused so far primarily on community-compositional changes of annual plants, while little is known about their perennial counterparts. The aim of this work was to get deep insight into the spatial patterns and temporal dynamics of the root associated microbiota of apple trees. RESULTS The bacterial community structure in rhizospheric soil and endospheric root material from orchard-grown apple trees was characterized based on 16S rRNA gene amplicon sequencing. At the small scale, the rhizosphere and endosphere bacterial communities shifted gradually with increasing root size diameter (PERMANOVA R2-values up to 0.359). At the larger scale, bulk soil heterogeneity introduced variation between tree individuals, especially in the rhizosphere microbiota, while the presence of a root pathogen was contributing to tree-to-tree variation in the endosphere microbiota. Moreover, the communities of both compartments underwent seasonal changes and displayed year-to-year variation (PERMANOVA R2-values of 0.454 and 0.371, respectively). CONCLUSIONS The apple tree root-associated microbiota can be spatially heterogeneous at field scale due to soil heterogeneities, which particularly influence the microbiota in the rhizosphere soil, resulting in tree-to-tree variation. The presence of pathogens can contribute to this variation, though primarily in the endosphere microbiota. Smaller-scale spatial heterogeneity is observed in the rhizosphere and endosphere microbiota related to root diameter, likely influenced by root traits and processes such as rhizodeposition. The microbiota is also subject to temporal variation, including seasonal effects and annual variation. As a consequence, responses of the tree root microbiota to further environmental cues should be considered in the context of this spatio-temporal variation.
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Affiliation(s)
- Maximilian Fernando Becker
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Nussallee 13, 53115, Bonn, Germany
| | - Manfred Hellmann
- Dienstleistungszentrum Ländlicher Raum (DLR) Rheinpfalz, Kompetenzzentrum Gartenbau Klein-Altendorf, 53359, Rheinbach, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Nussallee 13, 53115, Bonn, Germany.
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Ikeda S, Okazaki K, Tsurumaru H, Suzuki T, Hirafuji M. Effects of Different Types of Additional Fertilizers on Root-associated Microbes of Napa Cabbage Grown in an Andosol Field in Japan. Microbes Environ 2022; 37. [PMID: 35650110 PMCID: PMC9530736 DOI: 10.1264/jsme2.me22013] [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] [Indexed: 11/12/2022] Open
Abstract
The effects of different types of additional fertilizations (a compound fertilizer and Chiyoda-kasei) on the root-associated microbes of napa cabbage grown in an Andosol field were investigated by molecular community ana-lyses. Most of the closest known species of the bacterial sequences whose relative abundance significantly differed among fertilizers were sensitive to nitrogen fertilization and/or related to the geochemical cycles of nitrogen. The fungal community on the roots of napa cabbage was dominated by two genera, Bipolaris and Olpidium. The relative abundance of these two genera was affected by the types of fertilizers to some extent and showed a strong negative correlation.
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Affiliation(s)
- Seishi Ikeda
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| | - Kazuyuki Okazaki
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
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20
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Palberg D, Kisiała A, Jorge GL, Emery RJN. A survey of Methylobacterium species and strains reveals widespread production and varying profiles of cytokinin phytohormones. BMC Microbiol 2022; 22:49. [PMID: 35135483 PMCID: PMC8822675 DOI: 10.1186/s12866-022-02454-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/21/2022] [Indexed: 12/02/2022] Open
Abstract
Background Symbiotic Methylobacterium strains comprise a significant part of plant microbiomes. Their presence enhances plant productivity and stress resistance, prompting classification of these strains as plant growth-promoting bacteria (PGPB). Methylobacteria can synthesize unusually high levels of plant hormones, called cytokinins (CKs), including the most active form, trans-Zeatin (tZ). Results This study provides a comprehensive inventory of 46 representatives of Methylobacterium genus with respect to phytohormone production in vitro, including 16 CK forms, abscisic acid (ABA) and indole-3-acetic acid (IAA). High performance-liquid chromatography—tandem mass spectrometry (HPLC–MS/MS) analyses revealed varying abilities of Methylobacterium strains to secrete phytohormones that ranged from 5.09 to 191.47 pmol mL−1 for total CKs, and 0.46 to 82.16 pmol mL−1 for tZ. Results indicate that reduced methanol availability, the sole carbon source for bacteria in the medium, stimulates CK secretion by Methylobacterium. Additionally, select strains were able to transform L-tryptophan into IAA while no ABA production was detected. Conclusions To better understand features of CKs in plants, this study uncovers CK profiles of Methylobacterium that are instrumental in microbe selection for effective biofertilizer formulations. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02454-9.
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Affiliation(s)
- Daniel Palberg
- Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Anna Kisiała
- Department of Biology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada.
| | - Gabriel Lemes Jorge
- Department of Biology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada.,Department of Technology, Sao Paulo State University, Jaboticabal, Sao Paulo, Brazil
| | - R J Neil Emery
- Department of Biology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
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21
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Wang S, Li J, Zhao J, Dong Z, Shao T. An investigation of fermentative profile, microbial numbers, bacterial community diversity and their predicted metabolic characteristics in Sudangrass ( Sorghum sudanense Stapf.) silages. Anim Biosci 2022; 35:1162-1173. [PMID: 34991212 PMCID: PMC9262718 DOI: 10.5713/ab.21.0326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022] Open
Abstract
Objective This study aimed to investigate the fermentation profiles, bacterial community and predicted metabolic characteristics of Sudangrass (Sorghum sudanense Stapf.) during ensiling. Methods First-cutting Sudangrass was harvested at the vegetative stage and ensiled in laboratory-scale silos (1 L capacity). Triplicate silos were sampled after 1, 3, 7, 15, 30, and 60 days of ensiling, respectively. The bacterial communities on day 3 and 60 were assessed through high-throughput sequencing technology, and 16S rRNA-gene predicted functional profiles were analyzed according to the Kyoto encyclopedia of genes and genomes using Tax4Fun. Results The Sudangrass silages showed good fermentation quality, indicated by higher lactic acid contents, and lower pH, butyric acid and ammonia nitrogen contents. The dominant genus Lactococcus on day 3 was replaced by Lactobacillus on day 60. The metabolism of amino acid, energy, cofactors and vitamins was restricted, and metabolism of nucleotide and carbohydrate was promoted after ensiling. The 1-phosphofructokinase and pyruvate kinase of bacterial community seemed to play important roles in stimulating the lactic acid fermentation, and the promotion of arginine deiminase could help lactic acid bacteria to tolerate the acidic environment. Conclusion High-throughput sequencing technology combined with 16S rRNA gene-predicted functional analyses revealed the differences during the early and late stages of Sudangrass ensiling not only for distinct bacterial community but also for specific functional metabolites. The results could provide a comprehensive insight into bacterial community and metabolic characteristics to further improve the silage quality.
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Alessa O, Ogura Y, Fujitani Y, Takami H, Hayashi T, Sahin N, Tani A. Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species. Front Microbiol 2021; 12:740610. [PMID: 34737731 PMCID: PMC8561711 DOI: 10.3389/fmicb.2021.740610] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/06/2021] [Indexed: 01/06/2023] Open
Abstract
The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: Methylobacterium and Methylorubrum. They have been separated into three major clades: A, B (Methylorubrum), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other Methylobacteriaceae. The Methylobacterium species in clade A, including the type species Methylobacterium organophilum, were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to Methylorubrum species; this finding led us to reunite the two genera into a single genus Methylobacterium. Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the H4MPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.
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Affiliation(s)
- Ola Alessa
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Hideto Takami
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nurettin Sahin
- Egitim Fakultesi, Mugla Sitki Kocman University, Mugla, Turkey
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
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Yan K, Han W, Zhu Q, Li C, Dong Z, Wang Y. Leaf surface microtopography shaping the bacterial community in the phyllosphere: evidence from 11 tree species. Microbiol Res 2021; 254:126897. [PMID: 34710835 DOI: 10.1016/j.micres.2021.126897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/27/2021] [Accepted: 10/13/2021] [Indexed: 10/20/2022]
Abstract
Phyllosphere bacteria are an important component of environmental microbial communities and are closely related to plant health and ecosystem stability. However, the relationships between the inhabitation and assembly of phyllosphere bacteria and leaf microtopography are still obscure. In this study, the phyllosphere bacterial communities and leaf microtopographic features (vein density, stomatal length, and density) of eleven tree species were fully examined. Both the absolute abundance and diversity of phyllosphere bacterial communities were significantly different among the tree species, and leaf vein density dominated the variation. TITAN analysis showed that leaf vein density also played more important roles in regulating the relative abundance of bacteria than stomatal features, and 6 phyla and 62 genera of phyllosphere bacteria showed significant positive responses to leaf vein density. Moreover, LEfSe analysis showed that the leaves with higher vein density had more bacterial biomarkers. Leaf vein density also changed the co-occurrence pattern of phyllosphere bacteria, and the co-occurrence network demonstrated more negative correlations and more nodes on the leaves with larger leaf vein density, indicating that higher densities of leaf veins improved the stability of the phyllosphere bacterial community. Phylogenetic analysis showed that deterministic processes (especially homogeneous selection) dominated the assembly process of phyllosphere bacterial communities. The leaf vein density increased the degree of bacterial clustering at the phylogenetic level. Therefore, the inhabitation and assembly of the phyllosphere bacterial community are related to leaf microtopography, which provides deeper insight into the interaction between plants and bacteria.
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Affiliation(s)
- Kun Yan
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Wenhao Han
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Qiliang Zhu
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Chuanrong Li
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Zhi Dong
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Yanping Wang
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an, 271018, PR China.
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Potential of pink pigmented methylotrophic bacteria on growth and physiology of cluster bean and soil microbial community. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Wang S, Li J, Zhao J, Dong Z, Shao T. Exploring the ensiling characteristics and bacterial community of red clover inoculated with the epiphytic bacteria from temperate gramineous grasses. J Appl Microbiol 2021; 132:177-188. [PMID: 34309950 DOI: 10.1111/jam.15234] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/07/2021] [Accepted: 07/16/2021] [Indexed: 11/29/2022]
Abstract
AIMS To explore the microbiological factors that cause the difference in silage fermentation characteristics between temperate gramineous (Italian ryegrass and oat) grass and legume forage. METHODS AND RESULTS Through γ-ray irradiation sterilization and bacterial transplantation technology, the sterilized red clover was inoculated as follows: (i) aseptic water (STRC); (ii) epiphytic bacteria on red clover (RCRC); (iii) epiphytic bacteria on oat (RCOT); and (iv) epiphytic bacteria on Italian ryegrass (RCIR). Red clover was ensiled in laboratory-scale silos made of vacuum-packed plastic bags for 1, 3, 7, 14, 30 and 60 days. STRC remained unfermented state based on similar chemical components with fresh red clover. Compared with RCRC and RCIR, higher lactic acid content and ratio of lactic acid to acetic acid, and lower pH, acetic acid and ammonia nitrogen contents were observed in RCOT after 60 days of ensiling. Using next-generation sequencing, higher abundances of Methylobacterium and Sphingomonas were observed in the epiphytic bacteria on red clover. Pediococcus was dominant in RCRC after 3 days of ensiling. Lactobacillus was the most predominant in each group after 60 days of fermentation. RCRC and RCIR had a more hetero-fermentative process, while RCOT possessed a more homo-fermentative pathway. According to the 16S rRNA gene-predicted functional profiles, the metabolism of amino acids was accelerated by the epiphytic bacteria from red clover. CONCLUSIONS Inoculating the epiphytic bacteria from oat could alter the fermentation characteristics and bacterial compositions of red clover silage. The relative abundance and activity of Methylobacterium, Sphingomonas, Enterobacteriaceae and hetero-fermentative Lactobacillus in red clover silage could be changed by the epiphytic bacteria on temperate gramineous grass. SIGNIFICANCE AND IMPACT OF THE STUDY The exogenous micro-organisms inhibiting the metabolism of amino acids can be a good potential source to improve the silage quality of legume forage.
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Affiliation(s)
- Siran Wang
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Junfeng Li
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Jie Zhao
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Zhihao Dong
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Tao Shao
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
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Tong W, Yu J, Wu Q, Hu L, Tabys D, Wang Y, Wei C, Ling T, Ali Inayat M, Bennetzen JL. Black Tea Quality is Highly Affected during Processing by its Leaf Surface Microbiome. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:7115-7126. [PMID: 34152762 DOI: 10.1021/acs.jafc.1c01607] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Microbiomes can greatly affect the quality of fermented food and beverages, including tea. In this study, microbial populations were characterized during black and green tea manufacturing, revealing that tea processing steps can drive both the bacterial and fungal community structure. Tea leaves were found to mostly harbor Proteobacteria, Bacteriodetes, Firmicutes, and Actinobacteria among bacteria and Ascomycetes among fungi. During processing, tea microbial populations changed especially between sterilized and unsterilized samples. The surface sterilization of fresh leaves before processing can remove many microbes, especially the bacteria of the genera Sphingomonas and Methylobacteria, indicating that these are mostly phylloplane microbes on tea leaves. The surface sterilization removed most fungi, except the Debaryomyces. We also observed a fluctuation in the content of several tea quality-related metabolites during processing. Caffeine and theanine were found in the same quantities in green tea with or without leaf surface sterilization. However, the sterilization process dramatically decreased the content of total catechins and theanine in black tea, indicating that microbes on the surface of tea leaf may be involved in maintaining the formation of these important metabolites during black tea processing.
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Affiliation(s)
- Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Jie Yu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
- Sericultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230061, China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Lizhen Hu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Dina Tabys
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan
| | - Yijun Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Tiejun Ling
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Mallano Ali Inayat
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Jeffrey L Bennetzen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
- Department of Genetics, University of Georgia, Athens, Georgia 30602, United States
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Dela Rosa CJO, Lee AC, Rivera WL. Pink Pigmented Facultative Methylotrophic Bacteria Isolated from Fermented Philippine Shrimp Paste. Trop Life Sci Res 2021; 32:147-161. [PMID: 34367520 PMCID: PMC8300941 DOI: 10.21315/tlsr2021.32.2.10] [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] [Indexed: 11/23/2022] Open
Abstract
Pink pigmented facultative methylotrophic (PPFM) bacteria are ecologically distributed microorganisms. They have been isolated in many types of ecosystems like soil, water, air, in association with plants and even as pathogens in humans. However, a yet unexplored area for PPFM bacteria research is in food. Hence, the objective of this study was to establish the presence of PPFM bacteria in Philippine fermented food, in particular shrimp paste, and characterise them phenotypically and genotypically. A total of 13 PPFM bacteria were obtained from Philippine shrimp paste. Sequencing of the 16S rRNA gene revealed that the PPFM bacterial isolates belong to the genus Methylobacterium. A total of 35 phenotypic characterisations were performed that included morphological, biochemical and physiological tests. Phylogenetic tree was constructed to establish the genetic relatedness of the isolates. Morphological test results showed that all 13 isolates were consistent with the established phenotypic characters of the genus such as pink colony colour, Gram negative and rod-shaped. Biochemically, the use of API® 20 NE tests showed heterogeneity of results and physiological tests exhibited that the isolates are primarily mesophilic and halotolerant, being able to grow at 2% salt. Phylogenetic analysis showed that the isolates are Methylobacterium populi, M. dankookense, M. lusitanum, M. radiotolerans and M. zatmanii. This study confirmed the presence and diversity of PPFM bacteria in Philippine shrimp paste. Further studies are needed to show the functional activity of Methylobacterium in Philippine shrimp paste production.
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Affiliation(s)
- Christian Jordan O Dela Rosa
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines.,Biology Department, College of Science, De La Salle University, City of Manila 0922, Philippines
| | - Anthony C Lee
- Biology Department, College of Science, De La Salle University, City of Manila 0922, Philippines
| | - Windell L Rivera
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
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Müller-Santos M, Koskimäki JJ, Alves LPS, de Souza EM, Jendrossek D, Pirttilä AM. The protective role of PHB and its degradation products against stress situations in bacteria. FEMS Microbiol Rev 2021; 45:fuaa058. [PMID: 33118006 DOI: 10.1093/femsre/fuaa058] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022] Open
Abstract
Many bacteria produce storage biopolymers that are mobilized under conditions of metabolic adaptation, for example, low nutrient availability and cellular stress. Polyhydroxyalkanoates are often found as carbon storage in Bacteria or Archaea, and of these polyhydroxybutyrate (PHB) is the most frequently occurring PHA type. Bacteria usually produce PHB upon availability of a carbon source and limitation of another essential nutrient. Therefore, it is widely believed that the function of PHB is to serve as a mobilizable carbon repository when bacteria face carbon limitation, supporting their survival. However, recent findings indicate that bacteria switch from PHB synthesis to mobilization under stress conditions such as thermal and oxidative shock. The mobilization products, 3-hydroxybutyrate and its oligomers, show a protective effect against protein aggregation and cellular damage caused by reactive oxygen species and heat shock. Thus, bacteria should have an environmental monitoring mechanism directly connected to the regulation of the PHB metabolism. Here, we review the current knowledge on PHB physiology together with a summary of recent findings on novel functions of PHB in stress resistance. Potential applications of these new functions are also presented.
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Affiliation(s)
- Marcelo Müller-Santos
- Department of Biochemistry and Molecular Biology, Federal University of Paraná - UFPR, Setor de Ciências Biológicas, Centro Politécnico, Jardim da Américas, CEP: 81531-990, Caixa Postal: 190-46, Curitiba, Paraná, Brazil
| | - Janne J Koskimäki
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, P.O. Box 3000, FI-90014 Oulu, Finland
| | - Luis Paulo Silveira Alves
- Department of Biochemistry and Molecular Biology, Federal University of Paraná - UFPR, Setor de Ciências Biológicas, Centro Politécnico, Jardim da Américas, CEP: 81531-990, Caixa Postal: 190-46, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná - UFPR, Setor de Ciências Biológicas, Centro Politécnico, Jardim da Américas, CEP: 81531-990, Caixa Postal: 190-46, Curitiba, Paraná, Brazil
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Anna Maria Pirttilä
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, P.O. Box 3000, FI-90014 Oulu, Finland
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Physiology of Methylotrophs Living in the Phyllosphere. Microorganisms 2021; 9:microorganisms9040809. [PMID: 33921272 PMCID: PMC8069551 DOI: 10.3390/microorganisms9040809] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 01/06/2023] Open
Abstract
Methanol is abundant in the phyllosphere, the surface of the above-ground parts of plants, and its concentration oscillates diurnally. The phyllosphere is one of the major habitats for a group of microorganisms, the so-called methylotrophs, that utilize one-carbon (C1) compounds, such as methanol and methane, as their sole source of carbon and energy. Among phyllospheric microorganisms, methanol-utilizing methylotrophic bacteria, known as pink-pigmented facultative methylotrophs (PPFMs), are the dominant colonizers of the phyllosphere, and some of them have recently been shown to have the ability to promote plant growth and increase crop yield. In addition to PPFMs, methanol-utilizing yeasts can proliferate and survive in the phyllosphere by using unique molecular and cellular mechanisms to adapt to the stressful phyllosphere environment. This review describes our current understanding of the physiology of methylotrophic bacteria and yeasts living in the phyllosphere where they are exposed to diurnal cycles of environmental conditions.
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Formaldehyde-responsive proteins, TtmR and EfgA, reveal a tradeoff between formaldehyde resistance and efficient transition to methylotrophy in Methylorubrum extorquens. J Bacteriol 2021; 203:JB.00589-20. [PMID: 33619153 PMCID: PMC8092166 DOI: 10.1128/jb.00589-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
For bacteria to thrive they must be well-adapted to their environmental niche, which may involve specialized metabolism, timely adaptation to shifting environments, and/or the ability to mitigate numerous stressors. These attributes are highly dependent on cellular machinery that can sense both the external and intracellular environment. Methylorubrum extorquens is an extensively studied facultative methylotroph, an organism that can use single-carbon compounds as their sole source of carbon and energy. In methylotrophic metabolism, carbon flows through formaldehyde as a central metabolite; thus, formaldehyde is both an obligate metabolite and a metabolic stressor. Via the one-carbon dissimilation pathway, free formaldehyde is rapidly incorporated by formaldehyde activating enzyme (Fae), which is constitutively expressed at high levels. In the presence of elevated formaldehyde levels, a recently identified formaldehyde-sensing protein, EfgA, induces growth arrest. Herein, we describe TtmR, a formaldehyde-responsive transcription factor that, like EfgA, modulates formaldehyde resistance. TtmR is a member of the MarR family of transcription factors and impacts the expression of 75 genes distributed throughout the genome, many of which are transcription factors and/or involved in stress response, including efgA Notably, when M. extorquens is adapting its metabolic network during the transition to methylotrophy, efgA and ttmR mutants experience an imbalance in formaldehyde production and a notable growth delay. Although methylotrophy necessitates that M. extorquens maintain a relatively high level of formaldehyde tolerance, this work reveals a tradeoff between formaldehyde resistance and the efficient transition to methylotrophic growth and suggests that TtmR and EfgA play a pivotal role in maintaining this balance.Importance: All organisms produce formaldehyde as a byproduct of enzymatic reactions and as a degradation product of metabolites. The ubiquity of formaldehyde in cellular biology suggests all organisms have evolved mechanisms of mitigating formaldehyde toxicity. However, formaldehyde-sensing is poorly described and prevention of formaldehyde-induced damage is primarily understood in the context of detoxification. Here we use an organism that is regularly exposed to elevated intracellular formaldehyde concentrations through high-flux one-carbon utilization pathways to gain insight into the role of formaldehyde-responsive proteins that modulate formaldehyde resistance. Using a combination of genetic and transcriptomic analyses, we identify dozens of genes putatively involved in formaldehyde resistance, determined the relationship between two different formaldehyde response systems and identified an inherent tradeoff between formaldehyde resistance and optimal transition to methylotrophic metabolism.
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Mass spectrometry-based approaches to study lanthanides and lanthanide-dependent proteins in the phyllosphere. Methods Enzymol 2021; 650:215-236. [PMID: 33867023 DOI: 10.1016/bs.mie.2021.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Rare-earth elements (REEs) were recently discovered to be biologically significant. The finding was originally made with the methanol dehydrogenase XoxF, which depends on REEs for its activity, and reports of lanthanide-utilizing bacteria have since expanded. Environmental proteomics allows the identification of proteins specifically induced by the presence of lanthanides or can provide insights into the preferred use of lanthanide-dependent and -independent isoenzymes, for example. Here we describe protocols for the growth and subsequent mass spectrometry-based proteome analysis of bacteria obtained from controlled artificial media and from the phyllosphere of the model plant Arabidopsis thaliana. In addition, the use of inductively coupled plasma mass spectrometry (ICP-MS) is described for the quantification of REEs in biological samples.
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Neelakandan P, Young CC, Hameed A, Wang YN, Chen KN, Shen FT. Volatile 1-octanol of tea (Camellia sinensis L.) fuels cell division and indole-3-acetic acid production in phylloplane isolate Pseudomonas sp. NEEL19. Sci Rep 2021; 11:2788. [PMID: 33531600 PMCID: PMC7854675 DOI: 10.1038/s41598-021-82442-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 01/20/2021] [Indexed: 01/30/2023] Open
Abstract
Tea leaves possess numerous volatile organic compounds (VOC) that contribute to tea's characteristic aroma. Some components of tea VOC were known to exhibit antimicrobial activity; however, their impact on bacteria remains elusive. Here, we showed that the VOC of fresh aqueous tea leaf extract, recovered through hydrodistillation, promoted cell division and tryptophan-dependent indole-3-acetic acid (IAA) production in Pseudomonas sp. NEEL19, a solvent-tolerant isolate of the tea phylloplane. 1-octanol was identified as one of the responsible volatiles stimulating cell division, metabolic change, swimming motility, putative pili/nanowire formation and IAA production, through gas chromatography-mass spectrometry, microscopy and partition petri dish culture analyses. The bacterial metabolic responses including IAA production increased under 1-octanol vapor in a dose-dependent manner, whereas direct-contact in liquid culture failed to elicit such response. Thus, volatile 1-octanol emitting from tea leaves is a potential modulator of cell division, colonization and phytohormone production in NEEL19, possibly influencing the tea aroma.
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Affiliation(s)
- Poovarasan Neelakandan
- grid.260542.70000 0004 0532 3749Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 40227 Taiwan, ROC
| | - Chiu-Chung Young
- grid.260542.70000 0004 0532 3749Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 40227 Taiwan, ROC ,grid.260542.70000 0004 0532 3749Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University, Taichung, 40227 Taiwan, ROC
| | - Asif Hameed
- grid.260542.70000 0004 0532 3749Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 40227 Taiwan, ROC ,Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore, 575018 India
| | - Yu-Ning Wang
- grid.260542.70000 0004 0532 3749Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 40227 Taiwan, ROC
| | - Kui-Nuo Chen
- grid.260542.70000 0004 0532 3749Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 40227 Taiwan, ROC
| | - Fo-Ting Shen
- grid.260542.70000 0004 0532 3749Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 40227 Taiwan, ROC ,grid.260542.70000 0004 0532 3749Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University, Taichung, 40227 Taiwan, ROC
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Chaudhry V, Runge P, Sengupta P, Doehlemann G, Parker JE, Kemen E. Shaping the leaf microbiota: plant-microbe-microbe interactions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:36-56. [PMID: 32910810 PMCID: PMC8210630 DOI: 10.1093/jxb/eraa417] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/07/2020] [Indexed: 05/28/2023]
Abstract
The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. The leaf's physical and chemical properties, combined with fluctuating and often challenging environmental factors, create surfaces that require a high degree of adaptation for microbial colonization. As a consequence, specific interactive processes have evolved to establish a plant leaf niche. Little is known about the impact of the host immune system on phyllosphere colonization by non-pathogenic microbes. These organisms can trigger plant basal defenses and benefit the host by priming for enhanced resistance to pathogens. In most disease resistance responses, microbial signals are recognized by extra- or intracellular receptors. The interactions tend to be species specific and it is unclear how they shape leaf microbial communities. In natural habitats, microbe-microbe interactions are also important for shaping leaf communities. To protect resources, plant colonizers have developed direct antagonistic or host manipulation strategies to fight competitors. Phyllosphere-colonizing microbes respond to abiotic and biotic fluctuations and are therefore an important resource for adaptive and protective traits. Understanding the complex regulatory host-microbe-microbe networks is needed to transfer current knowledge to biotechnological applications such as plant-protective probiotics.
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Affiliation(s)
- Vasvi Chaudhry
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
| | - Paul Runge
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Priyamedha Sengupta
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Jane E Parker
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Eric Kemen
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
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Herrmann M, Geesink P, Richter R, Küsel K. Canopy Position Has a Stronger Effect than Tree Species Identity on Phyllosphere Bacterial Diversity in a Floodplain Hardwood Forest. MICROBIAL ECOLOGY 2021; 81:157-168. [PMID: 32761502 PMCID: PMC7794210 DOI: 10.1007/s00248-020-01565-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 07/27/2020] [Indexed: 05/17/2023]
Abstract
The phyllosphere is a challenging microbial habitat in which microorganisms can flourish on organic carbon released by plant leaves but are also exposed to harsh environmental conditions. Here, we assessed the relative importance of canopy position-top, mid, and bottom at a height between 31 and 20 m-and tree species identity for shaping the phyllosphere microbiome in a floodplain hardwood forest. Leaf material was sampled from three tree species-maple (Acer pseudoplatanus L.), oak (Quercus robur L.), and linden (Tilia cordata MILL.)-at the Leipzig canopy crane facility (Germany). Estimated bacterial species richness (Chao1) and bacterial abundances approximated by quantitative PCR of 16S rRNA genes exhibited clear vertical trends with a strong increase from the top to the mid and bottom position of the canopy. Thirty operational taxonomic units (OTUs) formed the core microbiome, which accounted for 77% of all sequence reads. These core OTUs showed contrasting trends in their vertical distribution within the canopy, pointing to different ecological preferences and tolerance to presumably more extreme conditions at the top position of the canopy. Co-occurrence analysis revealed distinct tree species-specific OTU networks, and 55-57% of the OTUs were unique to each tree species. Overall, the phyllosphere microbiome harbored surprisingly high fractions of Actinobacteria of up to 66%. Our results clearly demonstrate strong effects of the position in the canopy on phyllosphere bacterial communities in a floodplain hardwood forest and-in contrast to other temperate or tropical forests-a strong predominance of Actinobacteria.
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Affiliation(s)
- Martina Herrmann
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
| | - Patricia Geesink
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743, Jena, Germany
| | - Ronny Richter
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Systematic Botany and Functional Biodiversity, Institute for Biology, Leipzig University, Johannisallee 21, 04103, Leipzig, Germany
- Geoinformatics and Remote Sensing, Institute of Geography, Leipzig University, Johannisallee 19a, 04103, Leipzig, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
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Kumar A, Zhimo Y, Biasi A, Salim S, Feygenberg O, Wisniewski M, Droby S. Endophytic Microbiome in the Carposphere and Its Importance in Fruit Physiology and Pathology. POSTHARVEST PATHOLOGY 2021. [DOI: 10.1007/978-3-030-56530-5_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
There is growing interest in the use of associative, plant growth-promoting bacteria (PGPB) as biofertilizers to serve as a sustainable alternative for agriculture application. While a variety of mechanisms have been proposed to explain bacterial plant growth promotion, the molecular details of this process remain unclear. The plant rhizosphere harbors a diverse population of microorganisms, including beneficial plant growth-promoting bacteria (PGPB), that colonize plant roots and enhance growth and productivity. In order to specifically define bacterial traits that contribute to this beneficial interaction, we used high-throughput transposon mutagenesis sequencing (TnSeq) in two model root-bacterium systems associated with Setaria viridis: Azoarcus olearius DQS4T and Herbaspirillum seropedicae SmR1. This approach identified ∼100 significant genes for each bacterium that appeared to confer a competitive advantage for root colonization. Most of the genes identified specifically in A. olearius encoded metabolism functions, whereas genes identified in H. seropedicae were motility related, suggesting that each strain requires unique functions for competitive root colonization. Genes were experimentally validated by site-directed mutagenesis, followed by inoculation of the mutated bacteria onto S. viridis roots individually, as well as in competition with the wild-type strain. The results identify key bacterial functions involved in iron uptake, polyhydroxybutyrate metabolism, and regulation of aromatic metabolism as important for root colonization. The hope is that by improving our understanding of the molecular mechanisms used by PGPB to colonize plants, we can increase the adoption of these bacteria in agriculture to improve the sustainability of modern cropping systems.
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Meena KK, Bitla UM, Sorty AM, Singh DP, Gupta VK, Wakchaure GC, Kumar S. Mitigation of Salinity Stress in Wheat Seedlings Due to the Application of Phytohormone-Rich Culture Filtrate Extract of Methylotrophic Actinobacterium Nocardioides sp. NIMMe6. Front Microbiol 2020; 11:2091. [PMID: 33071995 PMCID: PMC7531191 DOI: 10.3389/fmicb.2020.02091] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 08/08/2020] [Indexed: 01/02/2023] Open
Abstract
Salinity stress is an important plant growth limiting factor influencing crop productivity negatively. Microbial interventions for salinity stress mitigation have invited significant attention due to the promising impacts of interactive associations on the intrinsic mechanisms of plants. We report the impact of microbial inoculation of a halotolerant methylotrophic actinobacterium (Nocardioides sp. NIMMe6; LC140963) and seed coating of its phytohormone-rich bacterial culture filtrate extract (BCFE) on wheat seedlings grown under saline conditions. Different plant-growth-promoting (PGP) attributes of the bacterium in terms of its growth in N-limiting media and siderophore and phytohormone [indole-3-acetic acid (IAA) and salicylic acid] production influenced plant growth positively. Microbial inoculation and priming with BCFE resulted in improved germination (92% in primed seeds at 10 dS m–1), growth, and biochemical accumulation (total protein 42.01 and 28.75 mg g–1 in shoot and root tissues at 10 dS m–1 in BCFE-primed seeds) and enhanced the activity level of antioxidant enzymes (superoxide dismutase, catalase, peroxidase, and ascorbate peroxidase) to confer stress mitigation. Biopriming with BCFE proved impactful. The BCFE application has further influenced the overexpression of defense-related genes in the seedlings grown under salinity stress condition. Liquid chromatography–mass spectrometry-based characterization of the biomolecules in the BCFE revealed quantification of salicylate and indole-3-acetate (Rt 4.978 min, m/z 138.1 and 6.177 min, 129.1), respectively. The high tolerance limit of the bacterium to 10% NaCl in the culture media suggested its possible survival and growth under high soil salinity condition as microbial inoculant. The production of a high quantity of IAA (45.6 μg ml–1 of culture filtrate) by the bacterium reflected its capability to not only support plant growth under salinity condition but also mitigate stress due to the impact of phytohormone as defense mitigators. The study suggested that although microbial inoculation offers stress mitigation in plants, the phytohormone-rich BCFE from Nocardioides sp. NIMMe6 has potential implications for defense against salinity stress in wheat.
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Affiliation(s)
- Kamlesh K Meena
- ICAR-National Institute of Abiotic Stress Management, Baramati, India
| | - Utkarsh M Bitla
- ICAR-National Institute of Abiotic Stress Management, Baramati, India
| | - Ajay M Sorty
- ICAR-National Institute of Abiotic Stress Management, Baramati, India
| | - Dhananjaya P Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Vijai K Gupta
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - G C Wakchaure
- ICAR-National Institute of Abiotic Stress Management, Baramati, India
| | - Satish Kumar
- ICAR-National Institute of Abiotic Stress Management, Baramati, India
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Sphingopyxis sp. Strain OPL5, an Isoprene-Degrading Bacterium from the Sphingomonadaceae Family Isolated from Oil Palm Leaves. Microorganisms 2020; 8:microorganisms8101557. [PMID: 33050387 PMCID: PMC7600658 DOI: 10.3390/microorganisms8101557] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/30/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022] Open
Abstract
The volatile secondary metabolite, isoprene, is released by trees to the atmosphere in enormous quantities, where it has important effects on air quality and climate. Oil palm trees, one of the highest isoprene emitters, are increasingly dominating agroforestry over large areas of Asia, with associated uncertainties over their effects on climate. Microbes capable of using isoprene as a source of carbon for growth have been identified in soils and in the tree phyllosphere, and most are members of the Actinobacteria. Here, we used DNA stable isotope probing to identify the isoprene-degrading bacteria associated with oil palm leaves and inhabiting the surrounding soil. Among the most abundant isoprene degraders of the leaf-associated community were members of the Sphingomonadales, although no representatives of this order were previously known to degrade isoprene. Informed by these data, we obtained representatives of the most abundant isoprene degraders in enrichments, including Sphingopyxis strain OPL5 (Sphingomonadales), able to grow on isoprene as the sole source of carbon and energy. Sequencing of the genome of strain OPL5, as well as a novel Gordonia strain, confirmed their pathways of isoprene degradation and broadened our knowledge of the genetic and taxonomic diversity of this important bacterial trait.
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Berlanga-Clavero MV, Molina-Santiago C, de Vicente A, Romero D. More than words: the chemistry behind the interactions in the plant holobiont. Environ Microbiol 2020; 22:4532-4544. [PMID: 32794337 DOI: 10.1111/1462-2920.15197] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/09/2020] [Accepted: 08/11/2020] [Indexed: 02/04/2023]
Abstract
Plants and microbes have evolved sophisticated ways to communicate and coexist. The simplest interactions that occur in plant-associated habitats, i.e., those involved in disease detection, depend on the production of microbial pathogenic and virulence factors and the host's evolved immunological response. In contrast, microbes can also be beneficial for their host plants in a number of ways, including fighting pathogens and promoting plant growth. In order to clarify the mechanisms directly involved in these various plant-microbe interactions, we must still deepen our understanding of how these interkingdom communication systems, which are constantly modulated by resident microbial activity, are established and, most importantly, how their effects can span physically separated plant compartments. Efforts in this direction have revealed a complex and interconnected network of molecules and associated metabolic pathways that modulate plant-microbe and microbe-microbe communication pathways to regulate diverse ecological responses. Once sufficiently understood, these pathways will be biotechnologically exploitable, for example, in the use of beneficial microbes in sustainable agriculture. The aim of this review is to present the latest findings on the dazzlingly diverse arsenal of molecules that efficiently mediate specific microbe-microbe and microbe-plant communication pathways during plant development and on different plant organs.
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Affiliation(s)
- María Victoria Berlanga-Clavero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
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40
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Kim S, Lee SH, Seo H, Kim KJ. Biochemical properties and crystal structure of formate-tetrahydrofolate ligase from Methylobacterium extorquens CM4. Biochem Biophys Res Commun 2020; 528:426-431. [PMID: 32505353 DOI: 10.1016/j.bbrc.2020.05.198] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 11/28/2022]
Abstract
Methylobacterium extorquens is a methylotroph model organism that has the ability to assimilate formate using the tetrahydrofolate (THF) pathway. The formate-tetrahydrofolate ligase from M. extorquens (MeFtfL) is an enzyme involved in the THF pathway that catalyzes the conversion of formate, THF, and ATP into formyltetrahydrofolate and ADP. To investigate the biochemical properties of MeFtfL, we evaluated the metal usage and enzyme kinetics of the enzyme. MeFtfL uses the Mg ion for catalytic activity, but also has activity for Mn and Ca ions. The enzyme kinetics analysis revealed that Km value of farmate was much higher than THF and ATP, which shows that the ligation activity of MeFtfL is highly dependent on formation concentration. We also determined the crystal structure of MeFtfL at 2.8 Å resolution. MeFtfL functions as a tetramer, and each monomer consists of three domains. The structural superposition of MeFtfL with FtfL from Moorella thermoacetica allowed us to predict the substrate binding site of the enzyme.
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Affiliation(s)
- Seongmin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seul Hoo Lee
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hogyun Seo
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Aydogan EL, Budich O, Hardt M, Choi YH, Jansen-Willems AB, Moser G, Müller C, Kämpfer P, Glaeser SP. Global warming shifts the composition of the abundant bacterial phyllosphere microbiota as indicated by a cultivation-dependent and -independent study of the grassland phyllosphere of a long-term warming field experiment. FEMS Microbiol Ecol 2020; 96:5835220. [DOI: 10.1093/femsec/fiaa087] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 05/08/2020] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
The leaf-colonizing bacterial microbiota was studied in a long-term warming experiment on a permanent grassland, which had been continuously exposed to increased surface temperature (+2°C) for more than six years. Two abundant plant species, Arrhenatherum elatius and Galium album, were studied. Surface warming reduced stomata opening and changed leaf metabolite profiles. Leaf surface colonization and the concentration of leaf-associated bacterial cells were not affected. However, bacterial 16S ribosomal RNA (rRNA) gene amplicon Illumina sequencing showed significant temperature effects on the plant species-specific phyllosphere microbiota. Warming partially affected the concentrations of cultured bacteria and had a significant effect on the composition of most abundant cultured plant species-specific bacteria. The abundance of Sphingomonas was significantly reduced. Sphingomonas isolates from warmed plots represented different phylotypes, had different physiological traits and were better adapted to higher temperatures. Among Methylobacterium isolates, a novel phylotype with a specific mxaFtype was cultured from plants of warmed plots while the most abundant phylotype cultured from control plots was strongly reduced. This study clearly showed a correlation of long-term surface warming with changes in the plant physiology and the development of a physiologically and genetically adapted phyllosphere microbiota.
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Affiliation(s)
- Ebru L Aydogan
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Olga Budich
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Martin Hardt
- Biomedical Research Center Seltersberg – Imaging Unit, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Anne B Jansen-Willems
- Institute of Plant Ecology (IFZ), Justus Liebig University Giessen, D-39392 Giessen, Germany
| | - Gerald Moser
- Institute of Plant Ecology (IFZ), Justus Liebig University Giessen, D-39392 Giessen, Germany
| | - Christoph Müller
- Institute of Plant Ecology (IFZ), Justus Liebig University Giessen, D-39392 Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, D04V1W8 Dublin, Ireland
| | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Stefanie P Glaeser
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
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Yadav AN, Singh J, Rastegari AA, Yadav N. Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications. ACTA ACUST UNITED AC 2020. [PMCID: PMC7123684 DOI: 10.1007/978-3-030-38453-1_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.
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Affiliation(s)
- Ajar Nath Yadav
- Department of Biotechnology, Eternal University, Baru Sahib, Himachal Pradesh India
| | - Joginder Singh
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab India
| | | | - Neelam Yadav
- Gopi Nath PG College, Veer Bahadur Singh Purvanchal University, Ghazipur, Uttar Pradesh India
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Vadivukkarasi P, Bhai RS. Phyllosphere-associated Methylobacterium: a potential biostimulant for ginger (Zingiber officinale Rosc.) cultivation. Arch Microbiol 2020; 202:369-375. [PMID: 31673721 DOI: 10.1007/s00203-019-01753-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 10/25/2022]
Abstract
Methanol, a by-product associated with plant metabolism, is a substrate for pink pigmented facultative methylotrophs (PPFMs) of phyllosphere. The symbiotic interaction of PPFMs has many desirable effects on plant growth and disease resistance. The present study investigated the potential of native PPFMs for mitigating biotic stress and plant growth promotion in ginger. PPFMs were isolated from ginger phyllosphere by leaf imprint technique and screened against major fungal phytopathogens of ginger viz. Macrophomina phaseolina, Sclerotium rolfsii, Pythium myriotylum, Colletotrichum gloeosporioides and Fusarium oxysporum. Among the 60 PPFMs, IISRGPPFM13 was selected for its highly inhibitory activity against the target pathogens. The isolate was useful for mineral solubility, production of IAA, siderophores and hydrolytic enzymes like cellulase, pectinase, lipase, amylase and chitinase. On in planta experiments revealed that IISRGPPFM13 considerably increased plant growth parameters when the bacterium was applied as soil drenching cum foliar spraying. Methanol utilization potential of the isolate was confirmed by mxaF gene analysis where the sequence showing 95.51% identity towards Methylobacterium platani and M. iners. Further, 16S rRNA gene sequence showing 98.73% identity with M. komagatae 002-079 T (AB252201). This is the first report of its kind that a genus of Methylobacterium with biostimulant potential isolated from the phyllosphere of ginger.
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Affiliation(s)
- Ponnusamy Vadivukkarasi
- Division of Crop Protection, ICAR-Indian Institute of Spices Research (IISR), Marikunnu P.O., Kozhikode, Kerala, 673012, India
| | - R Suseela Bhai
- Division of Crop Protection, ICAR-Indian Institute of Spices Research (IISR), Marikunnu P.O., Kozhikode, Kerala, 673012, India.
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Wang Y, Wang C, Gu Y, Wang P, Song W, Ma J, Yang X. The variability of bacterial communities in both the endosphere and ectosphere of different niches in Chinese chives (Allium tuberosum). PLoS One 2020; 15:e0227671. [PMID: 31945106 PMCID: PMC6964972 DOI: 10.1371/journal.pone.0227671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/24/2019] [Indexed: 12/18/2022] Open
Abstract
Deciphering the various types of interactions between plants and their microbiomes is a hot topic for research in ecology as well as in plant sciences and agronomy. To analyse and compare the differences in microbial communities in different compartments of Chinese chives, high-throughput sequencing technology was employed to amplify and sequence the V5-V6 region of the 16S rDNA of microorganisms in the leaves, phylloplanes, stems, roots and rhizospheres of Chinese chives. The sequences were clustered by operational taxonomic units (OTUs), and the community composition of bacteria between the endosphere (inner tissues) and ectosphere (outer surfaces) of Chinese chives was analysed based on the OTU. Overall, the results indicated that the endophytic bacteria in Chinese chives mainly include Proteobacteria, Actinobacteria, and Actinomycetes. Alpha diversity index analysis and OTU number analysis showed that the bacterial diversity and richness of the underground plant compartments were higher than those of the above-ground parts. PCoA based on the OTU level showed that the vertical stratification structure of plants and compartments had significant effects on the bacterial community structure. The richness of endophytic bacteria also varied greatly among the different varieties of Chinese chive. A considerable number of endophytic bacteria form symbiotic and mutually beneficial relationships with host plants, which play an important role in regulating host growth, metabolism and stress resistance. Further investigations are needed to uncover the evolution of interactions between plants and endophytes.
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Affiliation(s)
- Yuxin Wang
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
- * E-mail:
| | - Chaonan Wang
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
| | - Yizhu Gu
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
| | - Pingzhi Wang
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
| | - Weitang Song
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
| | - Jinhai Ma
- Henan Jiuxing Institute of Biotechnology, Pingdingshan, Henan, China
| | - Xiaofei Yang
- Henan Jiuxing Institute of Biotechnology, Pingdingshan, Henan, China
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Hara S, Matsuda M, Minamisawa K. Growth Stage-dependent Bacterial Communities in Soybean Plant Tissues: Methylorubrum Transiently Dominated in the Flowering Stage of the Soybean Shoot. Microbes Environ 2019; 34:446-450. [PMID: 31413227 PMCID: PMC6934392 DOI: 10.1264/jsme2.me19067] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022] Open
Abstract
Plant-associated bacteria are critical for plant growth and health. However, the effects of plant growth stages on the bacterial community remain unclear. Analyses of the microbiome associated with field-grown soybean revealed a marked shift in the bacterial community during the growth stages. The relative abundance of Methylorubrum in the leaf and stem increased from 0.2% to more than 45%, but decreased to approximately 15%, with a peak at the flowering stage at which nitrogen metabolism changed in the soybean plant. These results suggest the significance of a time-series analysis for understanding the relationship between the microbial community and host plant physiology.
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Affiliation(s)
- Shintaro Hara
- Graduate School of Life Sciences, Tohoku University2–2–1 Katahira, Aoba-ku, Sendai 980–8577Japan
| | - Masatoshi Matsuda
- Genesis Research Institute Inc.4–1–35 Shinmachi, Noritake, Nishi-ku, Nagoya 451–0051Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University2–2–1 Katahira, Aoba-ku, Sendai 980–8577Japan
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Minard G, Tikhonov G, Ovaskainen O, Saastamoinen M. The microbiome of the Melitaea cinxia butterfly shows marked variation but is only little explained by the traits of the butterfly or its host plant. Environ Microbiol 2019; 21:4253-4269. [PMID: 31436012 PMCID: PMC6900084 DOI: 10.1111/1462-2920.14786] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 12/13/2022]
Abstract
Understanding of the ecological factors that shape intraspecific variation of insect microbiota in natural populations is relatively poor. In Lepidopteran caterpillars, microbiota is assumed to be mainly composed of transient bacterial symbionts acquired from the host plant. We sampled Glanville fritillary (Melitaea cinxia) caterpillars from natural populations to describe their gut microbiome and to identify potential ecological factors that determine its structure. Our results demonstrate high variability of microbiota composition even among caterpillars that shared the same host plant individual and most likely the same genetic background. We observed that the caterpillars harboured microbial classes that varied among individuals and alternated between two distinct communities (one composed of mainly Enterobacteriaceae and another with more variable microbiota community). Even though the general structure of the microbiota was not attributed to the measured ecological factors, we found that phylogenetically similar microbiota showed corresponding responses to the sex and the parasitoid infection of the caterpillar and to those of the host plant's microbial and chemical composition. Our results indicate high among-individual variability in the microbiota of the M. cinxia caterpillar and contradict previous findings that the host plant is the major driver of the microbiota communities of insect herbivores.
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Affiliation(s)
- Guillaume Minard
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
- Université de LyonLyonFrance
- Ecologie Microbienne, UMR CNRS 5557, UMR INRA 1418, VetAgro Sup, Université Lyon 1VilleurbanneFrance
| | - Gleb Tikhonov
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and TechnologyN‐7491TrondheimNorway
| | - Marjo Saastamoinen
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life SciencesUniversity of HelsinkiHelsinkiFinland
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Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands. ISME JOURNAL 2019; 14:463-475. [PMID: 31659233 PMCID: PMC6976627 DOI: 10.1038/s41396-019-0543-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 12/25/2022]
Abstract
The active bacterial rhizobiomes and root exudate profiles of phytometers of six plant species growing in central European temperate grassland communities were investigated in three regions located up to 700 km apart, across diverse edaphic conditions and along a strong land use gradient. The recruitment process from bulk soil communities was identified as the major direct driver of the composition of active rhizosphere bacterial communities. Unexpectedly, the effect of soil properties, particularly soil texture, water content, and soil type, strongly dominated over plant properties and the composition of polar root exudates of the primary metabolism. While plant species-specific selection of bacteria was minor, the RNA-based composition of active rhizosphere bacteria substantially differed between rhizosphere and bulk soil. Although other variables could additionally be responsible for the consistent enrichment of particular bacteria in the rhizosphere, distinct bacterial OTUs were linked to the presence of specific polar root exudates independent of individual plant species. Our study also identified numerous previously unknown taxa that are correlated with rhizosphere dynamics and hence represent suitable targets for future manipulations of the plant rhizobiome.
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Wang C, He L, Xing Y, Zhou W, Yang F, Chen X, Zhang Q. Effects of mixing Neolamarckia cadamba leaves on fermentation quality, microbial community of high moisture alfalfa and stylo silage. Microb Biotechnol 2019; 12:869-878. [PMID: 31237418 PMCID: PMC6680604 DOI: 10.1111/1751-7915.13429] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/04/2019] [Accepted: 05/08/2019] [Indexed: 11/28/2022] Open
Abstract
Neolamarckia cadamba is not only a fodder of high nutritional value, but also a source of natural antimicrobial agent. The silage quality of high moisture alfalfa and stylo with or without N. cadamba leaves (NCL) was investigated, and microbial community after ensiling was analysed. Results showed that the silage samples with NCL have lower pH (4.32 versus 4.88, 4.26 versus 4.71 in alfalfa and stylo silage, respectively), ammonia-N content (67.5 versus 146, 42.2 versus 95.1 g kg-1 total N) and higher lactic acid (13.3 versus 10.4, 17.3 versus 13.6 g kg-1 dry matter), true protein N (592 versus 287, 815 versus 589 g kg-1 total N). The addition of NCL also influenced the bacterial community distribution. The relative abundance of Clostridium and Enterobacter decreased, whereas Lactobacillus abundance increased when NCL was added. In conclusion, NCL could inhibit undesirable microorganisms in high moisture alfalfa and stylo silage. Mixing with NCL could be a feasible way to improve the quality of silage.
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Affiliation(s)
- Cheng Wang
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, Guangdong Research and Development Centre of Modern Agriculture (Woody forage) Industrial Technology, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Liwen He
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, Guangdong Research and Development Centre of Modern Agriculture (Woody forage) Industrial Technology, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Yaqi Xing
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, Guangdong Research and Development Centre of Modern Agriculture (Woody forage) Industrial Technology, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Wei Zhou
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, Guangdong Research and Development Centre of Modern Agriculture (Woody forage) Industrial Technology, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Fuyu Yang
- College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Xiaoyang Chen
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, Guangdong Research and Development Centre of Modern Agriculture (Woody forage) Industrial Technology, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Qing Zhang
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, Guangdong Research and Development Centre of Modern Agriculture (Woody forage) Industrial Technology, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
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Defining the Genetic Basis of Plant⁻Endophytic Bacteria Interactions. Int J Mol Sci 2019; 20:ijms20081947. [PMID: 31010043 PMCID: PMC6515357 DOI: 10.3390/ijms20081947] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 01/17/2023] Open
Abstract
Endophytic bacteria, which interact closely with their host, are an essential part of the plant microbiome. These interactions enhance plant tolerance to environmental changes as well as promote plant growth, thus they have become attractive targets for increasing crop production. Numerous studies have aimed to characterise how endophytic bacteria infect and colonise their hosts as well as conferring important traits to the plant. In this review, we summarise the current knowledge regarding endophytic colonisation and focus on the insights that have been obtained from the mutants of bacteria and plants as well as ‘omic analyses. These show how endophytic bacteria produce various molecules and have a range of activities related to chemotaxis, motility, adhesion, bacterial cell wall properties, secretion, regulating transcription and utilising a substrate in order to establish a successful interaction. Colonisation is mediated by plant receptors and is regulated by the signalling that is connected with phytohormones such as auxin and jasmonic (JA) and salicylic acids (SA). We also highlight changes in the expression of small RNAs and modifications of the cell wall properties. Moreover, in order to exploit the beneficial plant-endophytic bacteria interactions in agriculture successfully, we show that the key aspects that govern successful interactions remain to be defined.
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Contrasting in vitro and in vivo methanol oxidation activities of lanthanide-dependent alcohol dehydrogenases XoxF1 and ExaF from Methylobacterium extorquens AM1. Sci Rep 2019; 9:4248. [PMID: 30862918 PMCID: PMC6414531 DOI: 10.1038/s41598-019-41043-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/28/2019] [Indexed: 11/19/2022] Open
Abstract
Lanthanide (Ln) elements are utilized as cofactors for catalysis by XoxF-type methanol dehydrogenases (MDHs). A primary assumption is that XoxF enzymes produce formate from methanol oxidation, which could impact organisms that require formaldehyde for assimilation. We report genetic and phenotypic evidence showing that XoxF1 (MexAM1_1740) from Methylobacterium extorquens AM1 produces formaldehyde, and not formate, during growth with methanol. Enzyme purified with lanthanum or neodymium oxidizes formaldehyde. However, formaldehyde oxidation via 2,6-dichlorophenol-indophenol (DCPIP) reduction is not detected in cell-free extracts from wild-type strain methanol- and lanthanum-grown cultures. Formaldehyde activating enzyme (Fae) is required for Ln methylotrophic growth, demonstrating that XoxF1-mediated production of formaldehyde is essential. Addition of exogenous lanthanum increases growth rate with methanol by 9–12% but does not correlate with changes to methanol consumption or formaldehyde accumulation. Transcriptomics analysis of lanthanum methanol growth shows upregulation of xox1 and downregulation of mxa genes, consistent with the Ln-switch, no differential expression of formaldehyde conversion genes, downregulation of pyrroloquinoline quinone (PQQ) biosynthesis genes, and upregulation of fdh4 formate dehydrogenase (FDH) genes. Additionally, the Ln-dependent ethanol dehydrogenase ExaF reduces methanol sensitivity in the fae mutant strain when lanthanides are present, providing evidence for the capacity of an auxiliary role for ExaF during Ln-dependent methylotrophy.
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