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Govindaraju AM, Friel CA, Good NM, Banks SL, Wayne KS, Martinez-Gomez NC. Lanthanide-dependent isolation of phyllosphere methylotrophs selects for a phylogenetically conserved but metabolically diverse community. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546956. [PMID: 38077020 PMCID: PMC10705262 DOI: 10.1101/2023.06.28.546956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The influence of lanthanide biochemistry during methylotrophy demands a reassessment of how the composition and metabolic potential of methylotrophic phyllosphere communities are affected by the presence of these metals. To investigate this, methylotrophs were isolated from soybean leaves by selecting for bacteria capable of methanol oxidation with lanthanide cofactors. Of the 344 pink-pigmented facultative methylotroph isolates, none were obligately lanthanide-dependent. Phylogenetic analyses revealed that all strains were nearly identical to each other and to model strains from the extorquens clade of Methylobacterium, with rpoB providing higher resolution than 16s rRNA for strain-specific identification. Despite the low species diversity, the metabolic capabilities of the community diverged greatly. Strains encoding identical PQQ-dependent alcohol dehydrogenases displayed significantly different growth from each other on alcohols in the presence and absence of lanthanides. Several strains also lacked well-characterized lanthanide-associated genes thought to be important for phyllosphere colonization. Additionally, 3% of our isolates were capable of growth on sugars and 23% were capable of growth on aromatic acids, substantially expanding the range of multicarbon substrates utilized by members of the extorquens clade in the phyllosphere. Whole genome sequences of eleven novel strains are reported. Our findings suggest that the expansion of metabolic capabilities, as well as differential usage of lanthanides and their influence on metabolism among closely related strains, point to evolution of niche partitioning strategies to promote colonization of the phyllosphere.
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Affiliation(s)
- Alekhya M. Govindaraju
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Colleen A. Friel
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Nathan M. Good
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Sidney L. Banks
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Kenan S. Wayne
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
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Tani A, Masuda S, Fujitani Y, Iga T, Haruna Y, Kikuchi S, Shuaile W, Lv H, Katayama S, Yurimoto H, Sakai Y, Kato J. Metabolism-linked methylotaxis sensors responsible for plant colonization in Methylobacterium aquaticum strain 22A. Front Microbiol 2023; 14:1258452. [PMID: 37901831 PMCID: PMC10613068 DOI: 10.3389/fmicb.2023.1258452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
Motile bacteria take a competitive advantage in colonization of plant surfaces to establish beneficial associations that eventually support plant health. Plant exudates serve not only as primary growth substrates for bacteria but also as bacterial chemotaxis attractants. A number of plant-derived compounds and corresponding chemotaxis sensors have been documented, however, the sensors for methanol, one of the major volatile compounds released by plants, have not been identified. Methylobacterium species are ubiquitous plant surface-symbiotic, methylotrophic bacteria. A plant-growth promoting bacterium, M. aquaticum strain 22A exhibits chemotaxis toward methanol (methylotaxis). Its genome encodes 52 methyl-accepting chemotaxis proteins (MCPs), among which we identified three MCPs (methylotaxis proteins, MtpA, MtpB, and MtpC) responsible for methylotaxis. The triple gene mutant of the MCPs exhibited no methylotaxis, slower gathering to plant tissues, and less efficient colonization on plants than the wild type, suggesting that the methylotaxis mediates initiation of plant-Methylobacterium symbiosis and engages in proliferation on plants. To examine how these MCPs are operating methylotaxis, we generated multiple gene knockouts of the MCPs, and Ca2+-dependent MxaFI and lanthanide (Ln3+)-dependent XoxF methanol dehydrogenases (MDHs), whose expression is regulated by the presence of Ln3+. MtpA was found to be a cytosolic sensor that conducts formaldehyde taxis (formtaxis), as well as methylotaxis when MDHs generate formaldehyde. MtpB contained a dCache domain and exhibited differential cellular localization in response to La3+. MtpB expression was induced by La3+, and its activity required XoxF1. MtpC exhibited typical cell pole localization, required MxaFI activity, and was regulated under MxbDM that is also required for MxaF expression. Strain 22A methylotaxis is realized by three independent MCPs, two of which monitor methanol oxidation by Ln3+-regulated MDHs, and one of which monitors the common methanol oxidation product, formaldehyde. We propose that methanol metabolism-linked chemotaxis is the key factor for the efficient colonization of Methylobacterium on plants.
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Affiliation(s)
- Akio Tani
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Sachiko Masuda
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- Japan Science and Technology Agency, Advanced Low Carbon Technology Research and Development Program (JST ALCA), Kawaguchi, Japan
| | - Yoshiko Fujitani
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Toshiki Iga
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Yuuki Haruna
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Shiho Kikuchi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Wang Shuaile
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Haoxin Lv
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Shiori Katayama
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroya Yurimoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasuyoshi Sakai
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Junichi Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
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Mousavi SA, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria. Minutes of the closed annual meeting: videoconference on 11 October 2022 followed by online discussion until 31 December 2022. Int J Syst Evol Microbiol 2023; 73. [PMID: 37115621 DOI: 10.1099/ijsem.0.005856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Affiliation(s)
- Seyed Abdollah Mousavi
- Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
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Lee HD, Grady CJ, Krell K, Strebeck C, Good NM, Martinez-Gomez NC, Gilad AA. A Novel Protein for the Bioremediation of Gadolinium Waste. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522788. [PMID: 36711778 PMCID: PMC9881998 DOI: 10.1101/2023.01.05.522788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Several hundreds of tons of gadolinium-based contrast agents (GBCAs) are being dumped into the environment every year. Although macrocyclic GBCAs exhibit superior stability compared to their linear counterparts, we have found that the structural integrity of chelates are susceptible to ultraviolet light, regardless of configuration. In this study, we present a synthetic protein termed GLamouR that binds and reports gadolinium in an intensiometric manner. We then explore the extraction of gadolinium from GBCA-spiked artificial urine samples and investigate if the low picomolar concentrations reported in gadolinium-contaminated water sources pose a barrier for bioremediation. Based on promising results, we anticipate GLamouR can be used for detecting and mining REEs beyond gadolinium as well and hope to expand the biological toolbox for such applications.
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Affiliation(s)
- Harvey D. Lee
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
| | - Connor J. Grady
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
| | - Katie Krell
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Cooper Strebeck
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI, United States
| | - Nathan M. Good
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - N. Cecilia Martinez-Gomez
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Assaf A. Gilad
- Department of Radiology, Michigan State University, East Lansing, MI, United States
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, United States
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