start-ver=1.4 cd-journal=joma no-vol=13 cd-vols= no-issue= article-no= start-page=921635 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2022 dt-pub=20220707 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Siderophore for Lanthanide and Iron Uptake for Methylotrophy and Plant Growth Promotion in Methylobacterium aquaticum Strain 22A en-subtitle= kn-subtitle= en-abstract= kn-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. en-copyright= kn-copyright= en-aut-name=JumaPatrick Otieno en-aut-sei=Juma en-aut-mei=Patrick Otieno kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=FujitaniYoshiko en-aut-sei=Fujitani en-aut-mei=Yoshiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=AlessaOla en-aut-sei=Alessa en-aut-mei=Ola kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=OyamaTokitaka en-aut-sei=Oyama en-aut-mei=Tokitaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=YurimotoHiroya en-aut-sei=Yurimoto en-aut-mei=Hiroya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=SakaiYasuyoshi en-aut-sei=Sakai en-aut-mei=Yasuyoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=TaniAkio en-aut-sei=Tani en-aut-mei=Akio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= affil-num=1 en-affil= Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil= Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil= Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=4 en-affil=Graduate School of Science, Kyoto University kn-affil= affil-num=5 en-affil=Graduate School of Agriculture, Kyoto University kn-affil= affil-num=6 en-affil=Graduate School of Agriculture, Kyoto University kn-affil= affil-num=7 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=Methylobacterium species kn-keyword=Methylobacterium species en-keyword=lanthanide kn-keyword=lanthanide en-keyword=lanthanophore kn-keyword=lanthanophore en-keyword=siderophore kn-keyword=siderophore en-keyword=plant growth promoter kn-keyword=plant growth promoter en-keyword=heavy metal sequestration kn-keyword=heavy metal sequestration END start-ver=1.4 cd-journal=joma no-vol=13 cd-vols= no-issue= article-no= start-page=921636 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2022 dt-pub=20220623 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=A Periplasmic Lanthanide Mediator, Lanmodulin, in Methylobacterium aquaticum Strain 22A en-subtitle= kn-subtitle= en-abstract= kn-abstract=Methylobacterium and Methylorubrum species oxidize methanol via pyrroloquinoline quinone-methanol dehydrogenases (MDHs). MDHs can be classified into two major groups, Ca2+-dependent MDH (MxaF) and lanthanide (Ln(3+))-dependent MDH (XoxF), whose expression is regulated by the availability of Ln(3+). A set of a siderophore, TonB-dependent receptor, and an ABC transporter that resembles the machinery for iron uptake is involved in the solubilization and transport of Ln(3+). The transport of Ln(3+) into the cytosol enhances XoxF expression. A unique protein named lanmodulin from Methylorubrum extorquens strain AM1 was identified as a specific Ln(3+)-binding protein, and its biological function was implicated to be an Ln(3+) shuttle in the periplasm. In contrast, it remains unclear how Ln(3+) levels in the cells are maintained, because Ln(3+) is potentially deleterious to cellular systems due to its strong affinity to phosphate ions. In this study, we investigated the function of a lanmodulin homolog in Methylobacterium aquaticum strain 22A. The expression of a gene encoding lanmodulin (lanM) was induced in response to the presence of La3+. A recombinant LanM underwent conformational change upon La3+ binding. Phenotypic analyses on lanM deletion mutant and overexpressing strains showed that LanM is not necessary for the wild-type and XoxF-dependent mutant's methylotrophic growth. We found that lanM expression was regulated by MxcQE (a two-component regulator for MxaF) and TonB_Ln (a TonB-dependent receptor for Ln(3+)). The expression level of mxcQE was altered to be negatively dependent on Ln(3+) concentration in increment lanM, whereas it was constant in the wild type. Furthermore, when exposed to La3+, increment lanM showed an aggregating phenotype, cell membrane impairment, La deposition in the periplasm evidenced by electron microscopy, differential expression of proteins involved in membrane integrity and phosphate starvation, and possibly lower La content in the membrane vesicle (MV) fractions. Taken together, we concluded that lanmodulin is involved in the complex regulation mechanism of MDHs and homeostasis of cellular Ln levels by facilitating transport and MV-mediated excretion. en-copyright= kn-copyright= en-aut-name=FujitaniYoshiko en-aut-sei=Fujitani en-aut-mei=Yoshiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=ShibataTakeshi en-aut-sei=Shibata en-aut-mei=Takeshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TaniAkio en-aut-sei=Tani en-aut-mei=Akio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=K.K. AB SCIEX kn-affil= affil-num=3 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=lanmodulin kn-keyword=lanmodulin en-keyword=lanthanide kn-keyword=lanthanide en-keyword=methanol dehydrogenase kn-keyword=methanol dehydrogenase en-keyword=Methylobacterium species kn-keyword=Methylobacterium species en-keyword=membrane vesicles kn-keyword=membrane vesicles END start-ver=1.4 cd-journal=joma no-vol=12 cd-vols= no-issue= article-no= start-page=740610 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=20211006 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species en-subtitle= kn-subtitle= en-abstract= kn-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. en-copyright= kn-copyright= en-aut-name=AlessaOla en-aut-sei=Alessa en-aut-mei=Ola kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=OguraYoshitoshi en-aut-sei=Ogura en-aut-mei=Yoshitoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=FujitaniYoshiko en-aut-sei=Fujitani en-aut-mei=Yoshiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=TakamiHideto en-aut-sei=Takami en-aut-mei=Hideto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=HayashiTetsuya en-aut-sei=Hayashi en-aut-mei=Tetsuya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=SahinNurettin en-aut-sei=Sahin en-aut-mei=Nurettin kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=TaniAkio en-aut-sei=Tani en-aut-mei=Akio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine kn-affil= affil-num=3 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=4 en-affil=Atmosphere and Ocean Research Institute, The University of Tokyo kn-affil= affil-num=5 en-affil=Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University kn-affil= affil-num=6 en-affil=Egitim Fakultesi, Mugla Sitki Kocman University kn-affil= affil-num=7 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=Methylobacterium kn-keyword=Methylobacterium en-keyword=comparative genomics kn-keyword=comparative genomics en-keyword=methylotroph kn-keyword=methylotroph en-keyword=methanol dehydrogenase kn-keyword=methanol dehydrogenase en-keyword=Methylorubrum kn-keyword=Methylorubrum END start-ver=1.4 cd-journal=joma no-vol=1 cd-vols= no-issue=1 article-no= start-page=15001 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2016 dt-pub=20160111 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=A capsidless ssRNA virus hosted by an unrelated dsRNA virus en-subtitle= kn-subtitle= en-abstract= kn-abstract=Viruses typically encode the capsid that encases their genome, while satellite viruses do not encode a replicase and depend on a helper virus for their replication1. Here, we report interplay between two RNA viruses, yado-nushi virus 1 (YnV1) and yado-kari virus 1 (YkV1), in a phytopathogenic fungus, Rosellinia necatrix2. YkV1 has a close phylogenetic affinity to positive-sense, single-stranded (+)ssRNA viruses such as animal caliciviruses3, while YnV1 has an undivided double-stranded (ds) RNA genome with a resemblance to fungal totiviruses4. Virion transfection and infectious full-length cDNA transformation has shown that YkV1 depends on YnV1 for viability, although it probably encodes functional RNA-dependent RNA polymerase (RdRp). Immunological and molecular analyses have revealed trans-encapsidation of not only YkV1 RNA but also RdRp by the capsid protein of the other virus (YnV1), and enhancement of YnV1 accumulation by YkV1. This study demonstrates interplay in which the capsidless (+)ssRNA virus (YkV1), hijacks the capsid protein of the dsRNA virus (YnV1), and replicates as if it were a dsRNA virus. en-copyright= kn-copyright= en-aut-name=ZhangRui en-aut-sei=Zhang en-aut-mei=Rui kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=HisanoSakae en-aut-sei=Hisano en-aut-mei=Sakae kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TaniAkio en-aut-sei=Tani en-aut-mei=Akio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=KondoHideki en-aut-sei=Kondo en-aut-mei=Hideki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=KanematsuSatoko en-aut-sei=Kanematsu en-aut-mei=Satoko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=SuzukiNobuhiro en-aut-sei=Suzuki en-aut-mei=Nobuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= affil-num=1 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=4 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=5 en-affil=NARO Institute of Fruit Tree Science kn-affil= affil-num=6 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=Molecular evolution kn-keyword=Molecular evolution en-keyword=Viral genetics kn-keyword=Viral genetics END start-ver=1.4 cd-journal=joma no-vol=8 cd-vols= no-issue=6 article-no= start-page=822 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=20200530 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Lanthanide-Dependent Methanol and Formaldehyde Oxidation inMethylobacterium aquaticumStrain 22A en-subtitle= kn-subtitle= en-abstract= kn-abstract=Lanthanides (Ln) are an essential cofactor for XoxF-type methanol dehydrogenases (MDHs) in Gram-negative methylotrophs. The Ln(3+)dependency of XoxF has expanded knowledge and raised new questions in methylotrophy, including the differences in characteristics of XoxF-type MDHs, their regulation, and the methylotrophic metabolism including formaldehyde oxidation. In this study, we genetically identified one set of Ln(3+)- and Ca2+-dependent MDHs (XoxF1 and MxaFI), that are involved in methylotrophy, and an ExaF-type Ln(3+)-dependent ethanol dehydrogenase, among six MDH-like genes inMethylobacterium aquaticumstrain 22A. We also identified the causative mutations in MxbD, a sensor kinase necessary formxaFexpression andxoxF1repression, for suppressive phenotypes inxoxF1mutants defective in methanol growth even in the absence of Ln(3+). Furthermore, we examined the phenotypes of a series of formaldehyde oxidation-pathway mutants (fae1,fae2,mchin the tetrahydromethanopterin (H4MPT) pathway andhgdin the glutathione-dependent formaldehyde dehydrogenase (GSH) pathway). We found that MxaF produces formaldehyde to a toxic level in the absence of the formaldehyde oxidation pathways and that either XoxF1 or ExaF can oxidize formaldehyde to alleviate formaldehyde toxicity in vivo. Furthermore, the GSH pathway has a supportive role for the net formaldehyde oxidation in addition to the H4MPT pathway that has primary importance. Studies on methylotrophy inMethylobacteriumspecies have a long history, and this study provides further insights into genetic and physiological diversity and the differences in methylotrophy within the plant-colonizing methylotrophs. en-copyright= kn-copyright= en-aut-name=YanpiratPatcha en-aut-sei=Yanpirat en-aut-mei=Patcha kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=NakatsujiYukari en-aut-sei=Nakatsuji en-aut-mei=Yukari kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=HiragaShota en-aut-sei=Hiraga en-aut-mei=Shota kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=FujitaniYoshiko en-aut-sei=Fujitani en-aut-mei=Yoshiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=IzumiTerumi en-aut-sei=Izumi en-aut-mei=Terumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=MasudaSachiko en-aut-sei=Masuda en-aut-mei=Sachiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=MitsuiRyoji en-aut-sei=Mitsui en-aut-mei=Ryoji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=NakagawaTomoyuki en-aut-sei=Nakagawa en-aut-mei=Tomoyuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=TaniAkio en-aut-sei=Tani en-aut-mei=Akio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=4 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=5 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=6 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=7 en-affil=Department of Biochemistry, Faculty of Science, Okayama University of Science kn-affil= affil-num=8 en-affil=The United Graduate School of Agricultural Science, Gifu University kn-affil= affil-num=9 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=lanthanide kn-keyword=lanthanide en-keyword=methylotroph kn-keyword=methylotroph en-keyword=XoxF kn-keyword=XoxF en-keyword=methanol dehydrogenase kn-keyword=methanol dehydrogenase en-keyword=Methylobacteriumspecies kn-keyword=Methylobacteriumspecies END start-ver=1.4 cd-journal=joma no-vol=70 cd-vols= no-issue=5 article-no= start-page=1683 end-page=1696 dt-received= dt-revised= dt-accepted= dt-pub-year=2019 dt-pub=20190502 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Honeydew-associated microbes elicit defense responses against brown planthopper in rice en-subtitle= kn-subtitle= en-abstract= kn-abstract=Feeding of sucking insects, such as the rice brown planthopper (Nilaparvata lugens; BPH), causes only limited mechanical damage on plants that is otherwise essential for injury-triggered defense responses against herbivores. In pursuit of complementary BPH elicitors perceived by plants, we examined the potential effects of BPH honeydew secretions on the BPH monocot host, rice (Oryza sativa). We found that BPH honeydew strongly elicits direct and putative indirect defenses in rice, namely accumulation of phytoalexins in the leaves, and release of volatile organic compounds from the leaves that serve to attract natural enemies of herbivores, respectively. We then examined the elicitor active components in the honeydew and found that bacteria in the secretions are responsible for the activation of plant defense. Corroborating the importance of honeydew-associated microbiota for induced plant resistance, BPHs partially devoid of their microbiota via prolonged antibiotics ingestion induced significantly less defense in rice relative to antibiotic-free insects applied to similar groups of plants. Our data suggest that rice plants may additionally perceive herbivores via their honeydew-associated microbes, allowing them to discriminate between incompatible herbivores?that do not produce honeydew?and those that are compatible and therefore dangerous. en-copyright= kn-copyright= en-aut-name=WariDavid en-aut-sei=Wari en-aut-mei=David kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=KabirMd Alamgir en-aut-sei=Kabir en-aut-mei=Md Alamgir kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=MujionoKadis en-aut-sei=Mujiono en-aut-mei=Kadis kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=HojoYuko en-aut-sei=Hojo en-aut-mei=Yuko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=ShinyaTomonori en-aut-sei=Shinya en-aut-mei=Tomonori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=TaniAkio en-aut-sei=Tani en-aut-mei=Akio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=NakataniHiroko en-aut-sei=Nakatani en-aut-mei=Hiroko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=GalisIvan en-aut-sei=Galis en-aut-mei=Ivan kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=4 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=5 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=6 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=7 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=8 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=Honeydew-associated microorganisms kn-keyword=Honeydew-associated microorganisms en-keyword=phytoalexins kn-keyword=phytoalexins en-keyword=plant defense kn-keyword=plant defense en-keyword=rice (Oryza sativa) kn-keyword=rice (Oryza sativa) en-keyword=rice brown planthopper (Nilaparvata lugens) kn-keyword=rice brown planthopper (Nilaparvata lugens) en-keyword=sucking insect kn-keyword=sucking insect END start-ver=1.4 cd-journal=joma no-vol=7 cd-vols= no-issue=3 article-no= start-page=e33800 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2012 dt-pub=20120329 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Practical Application of Methanol-Mediated Mutualistic Symbiosis between Methylobacterium Species and a Roof Greening Moss, Racomitrium japonicum en-subtitle= kn-subtitle= en-abstract= kn-abstract=Bryophytes, or mosses, are considered the most maintenance-free materials for roof greening. Racomitrium species are most often used due to their high tolerance to desiccation. Because they grow slowly, a technology for forcing their growth is desired. We succeeded in the efficient production of R. japonicum in liquid culture. The structure of the microbial community is crucial to stabilize the culture. A culture-independent technique revealed that the cultures contain methylotrophic bacteria. Using yeast cells that fluoresce in the presence of methanol, methanol emission from the moss was confirmed, suggesting that it is an important carbon and energy source for the bacteria. We isolated Methylobacterium species from the liquid culture and studied their characteristics. The isolates were able to strongly promote the growth of some mosses including R. japonicum and seed plants, but the plant-microbe combination was important, since growth promotion was not uniform across species. One of the isolates, strain 22A, was cultivated with R. japonicum in liquid culture and in a field experiment, resulting in strong growth promotion. Mutualistic symbiosis can thus be utilized for industrial moss production. en-copyright= kn-copyright= en-aut-name=TaniAkio en-aut-sei=Tani en-aut-mei=Akio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=TakaiYuichiro en-aut-sei=Takai en-aut-mei=Yuichiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=SuzukawaIkko en-aut-sei=Suzukawa en-aut-mei=Ikko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=AkitaMotomu en-aut-sei=Akita en-aut-mei=Motomu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=MuraseHaruhiko en-aut-sei=Murase en-aut-mei=Haruhiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=KimbaraKazuhide en-aut-sei=Kimbara en-aut-mei=Kazuhide kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= affil-num=1 en-affil= kn-affil=Institute of Plant Science and Resources, Okayama University affil-num=2 en-affil= kn-affil=Research Institute of Environment, Agriculture and Fisheries, Osaka Prefectural Government affil-num=3 en-affil= kn-affil=Meiho-Construction affil-num=4 en-affil= kn-affil=Faculty of Biological Engineering, Kinki University affil-num=5 en-affil= kn-affil=Graduate School of Agriculture and Biological Sciences, Osaka Prefecture University affil-num=6 en-affil= kn-affil=Institute of Plant Science and Resources, Okayama University END start-ver=1.4 cd-journal=joma no-vol=7 cd-vols= no-issue=7 article-no= start-page=e40784 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2012 dt-pub=20120712 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=High-Throughput Identification and Screening of Novel Methylobacterium Species Using Whole-Cell MALDI-TOF/MS Analysis en-subtitle= kn-subtitle= en-abstract= kn-abstract=Methylobacterium species are ubiquitous α-proteobacteria that reside in the phyllosphere and are fed by methanol that is emitted from plants. In this study, we applied whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (WC-MS) to evaluate the diversity of Methylobacterium species collected from a variety of plants. The WC-MS spectrum was reproducible through two weeks of cultivation on different media. WC-MS spectrum peaks of M. extorquens strain AM1 cells were attributed to ribosomal proteins, but those were not were also found. We developed a simple method for rapid identification based on spectra similarity. Using all available type strains of Methylobacterium species, the method provided a certain threshold similarity value for species-level discrimination, although the genus contains some type strains that could not be easily discriminated solely by 16S rRNA gene sequence similarity. Next, we evaluated the WC-MS data of approximately 200 methylotrophs isolated from various plants with MALDI Biotyper software (Bruker Daltonics). Isolates representing each cluster were further identified by 16S rRNA gene sequencing. In most cases, the identification by WC-MS matched that by sequencing, and isolates with unique spectra represented possible novel species. The strains belonging to M. extorquens, M. adhaesivum, M. marchantiae, M. komagatae, M. brachiatum, M. radiotolerans, and novel lineages close to M. adhaesivum, many of which were isolated from bryophytes, were found to be the most frequent phyllospheric colonizers. The WC-MS technique provides emerging high-throughputness in the identification of known/novel species of bacteria, enabling the selection of novel species in a library and identification without 16S rRNA gene sequencing. en-copyright= kn-copyright= en-aut-name=TaniAkio en-aut-sei=Tani en-aut-mei=Akio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=NurettinSahin en-aut-sei=Nurettin en-aut-mei=Sahin kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=MatsuyamaYumiko en-aut-sei=Matsuyama en-aut-mei=Yumiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=EnomotoTakashi en-aut-sei=Enomoto en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=NishimuraNaoki en-aut-sei=Nishimura en-aut-mei=Naoki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=YokotaAkira en-aut-sei=Yokota en-aut-mei=Akira kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=KimbaraKazuhide en-aut-sei=Kimbara en-aut-mei=Kazuhide kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= affil-num=1 en-affil= kn-affil=Institute of Plant Science and Resources, Okayama University affil-num=2 en-affil= kn-affil=Faculty of Education, Mugla Sitki Kocman University affil-num=3 en-affil= kn-affil= affil-num=4 en-affil= kn-affil=Institute of Plant Science and Resources, Okayama University affil-num=5 en-affil= kn-affil=Botanical Garden, Okayama University of Science affil-num=6 en-affil= kn-affil=Faculty of Mathematics and Natural Sciences, University of Indonesia affil-num=7 en-affil= kn-affil=Faculty of Engineering, Shizuoka University END start-ver=1.4 cd-journal=joma no-vol=7 cd-vols= no-issue=11 article-no= start-page=e50480 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2013 dt-pub=20130322 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=A Catalytic Role of XoxF1 as La3+-Dependent Methanol Dehydrogenase in Methylobacterium extorquens Strain AM1 en-subtitle= kn-subtitle= en-abstract= kn-abstract=In the methylotrophic bacterium Methylobacterium extorquens strain AM1, MxaF, a Ca2+-dependent methanol dehydrogenase (MDH), is the main enzyme catalyzing methanol oxidation during growth on methanol. The genome of strain AM1 contains another MDH gene homologue, xoxF1, whose function in methanol metabolism has remained unclear. In this work, we show that XoxF1 also functions as an MDH and is La3+-dependent. Despite the absence of Ca2+ in the medium strain AM1 was able to grow on methanol in the presence of La3+. Addition of La3+ increased MDH activity but the addition had no effect on mxaF or xoxF1 expression level. We purified MDH from strain AM1 grown on methanol in the presence of La3+, and its N-terminal amino acid sequence corresponded to that of XoxF1. The enzyme contained La3+ as a cofactor. The ΔmxaF mutant strain could not grow on methanol in the presence of Ca2+, but was able to grow after supplementation with La3+. Taken together, these results show that XoxF1 participates in methanol metabolism as a La3+-dependent MDH in strain AM1. en-copyright= kn-copyright= en-aut-name=NakagawaTomoyuki en-aut-sei=Nakagawa en-aut-mei=Tomoyuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=MitsuiRyoji en-aut-sei=Mitsui en-aut-mei=Ryoji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TaniAkio en-aut-sei=Tani en-aut-mei=Akio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=SasaKentaro en-aut-sei=Sasa en-aut-mei=Kentaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=TashiroShinya en-aut-sei=Tashiro en-aut-mei=Shinya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=IwamaTomonori en-aut-sei=Iwama en-aut-mei=Tomonori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=HayakawaTakashi en-aut-sei=Hayakawa en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=KawaiKeiichi en-aut-sei=Kawai en-aut-mei=Keiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= affil-num=1 en-affil= kn-affil=Faculty of Applied Biological Science, Gifu University affil-num=2 en-affil= kn-affil=Department of Biochemistry, Faculty of Science, Okayama University of Science affil-num=3 en-affil= kn-affil=Institute of Plant Science and Resources, Okayama University affil-num=4 en-affil= kn-affil=Faculty of Applied Biological Science, Gifu University affil-num=5 en-affil= kn-affil=Faculty of Applied Biological Science, Gifu University affil-num=6 en-affil= kn-affil=Faculty of Applied Biological Science, Gifu University affil-num=7 en-affil= kn-affil=Faculty of Applied Biological Science, Gifu University affil-num=8 en-affil= kn-affil=Tokai Gakuin University END start-ver=1.4 cd-journal=joma no-vol=2 cd-vols= no-issue= article-no= start-page=606 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2013 dt-pub=20131113 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Evaluation of rhizosphere, rhizoplane and phyllosphere bacteria and fungi isolated from rice in Kenya for plant growth promoters en-subtitle= kn-subtitle= en-abstract= kn-abstract=Rice (Oryza sativa L.) is the most important staple food crop in many developing countries, and is ranked third in Kenya after maize and wheat. Continuous cropping without replenishing soil nutrients is a major problem in Kenya resulting to declining soil fertility. The use of chemical fertilizers to avert the problem of low soil fertility is currently limited due to rising costs and environmental concerns. Many soil micro-organisms are able to solubilize the unavailable phosphorus, increase uptake of nitrogen and also synthesize growth promoting hormones including auxin. The aim of this study was to isolate and characterize phyllosphere, rhizoplane and rhizosphere micro-organisms from Kenyan rice with growth promoting habits. In this study whole plant rice samples were collected from different rice growing regions of Kenya. 76.2%, over 80% and 38.5% of the bacterial isolates were positive for phosphate solubilization, nitrogenase activity and IAA production whereas 17.5% and 5% of the fungal isolates were positive for phosphate solubilization and IAA production respectively. Hence these micro-organisms have potential for utilization as bio-fertilizers in rice production. en-copyright= kn-copyright= en-aut-name=Rashid MwajitaMwashasha en-aut-sei=Rashid Mwajita en-aut-mei=Mwashasha kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=MurageHunja en-aut-sei=Murage en-aut-mei=Hunja kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TaniAkio en-aut-sei=Tani en-aut-mei=Akio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=KahangiEsther M en-aut-sei=Kahangi en-aut-mei=Esther M kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= affil-num=1 en-affil= kn-affil=Kenya Agricultural Research Institute affil-num=2 en-affil= kn-affil=Jomo Kenyatta University of Agriculture and Technology affil-num=3 en-affil= kn-affil=Institute of Plant Science and Resources Okayama University affil-num=4 en-affil= kn-affil=Jomo Kenyatta University of Agriculture and Technology en-keyword=Micro-organisms kn-keyword=Micro-organisms en-keyword=Phosphate solubilization kn-keyword=Phosphate solubilization en-keyword=Nitrogen fixation kn-keyword=Nitrogen fixation en-keyword=IAA production kn-keyword=IAA production END start-ver=1.4 cd-journal=joma no-vol=31 cd-vols= no-issue= article-no= start-page=21 end-page=25 dt-received= dt-revised= dt-accepted= dt-pub-year=2009 dt-pub=200912 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=Cooling effect on buildings by the roof greening at Research Institute for Bioresources, Okayama University kn-title=岡山大学資源生物科学研究所における屋上緑化による建物冷却効果 en-subtitle= kn-subtitle= en-abstract= kn-abstract=Roof greening is known to be environmentally friendly technology. Recently developed new roof greening systems, such as the thin-layer/Excel soil? system and the wetland type greening system, were tested at the roof top of buildings of Research Institute for Bioresources, Okayama University. After a multi-year test, these new systems have been established during high-temperature and less-rainfall summer seasons in the south Okayama region. Data indicated that roof greening effectively reduced the temperature of the concrete surface (more than 10°C). The room temperature under the green roof was also reduced both in a stock room (up to 6°C) and in an office room (about 2°C). We also provided the estimation indicating that this roof greening is useful for the decrease in CO(2) emission through the reduction of the electric power for air-conditioning in the summer. en-copyright= kn-copyright= en-aut-name=KatsuharaMaki en-aut-sei=Katsuhara en-aut-mei=Maki kn-aut-name=且原真木 kn-aut-sei=且原 kn-aut-mei=真木 aut-affil-num=1 ORCID= en-aut-name=TanakamaruShigemi en-aut-sei=Tanakamaru en-aut-mei=Shigemi kn-aut-name=田中丸重美 kn-aut-sei=田中丸 kn-aut-mei=重美 aut-affil-num=2 ORCID= en-aut-name=MoriIzumi C. en-aut-sei=Mori en-aut-mei=Izumi C. kn-aut-name=森泉 kn-aut-sei=森 kn-aut-mei=泉 aut-affil-num=3 ORCID= en-aut-name=TaniAkio en-aut-sei=Tani en-aut-mei=Akio kn-aut-name=谷明生 kn-aut-sei=谷 kn-aut-mei=明生 aut-affil-num=4 ORCID= en-aut-name=UtsugiShigeko en-aut-sei=Utsugi en-aut-mei=Shigeko kn-aut-name=宇都木繁子 kn-aut-sei=宇都木 kn-aut-mei=繁子 aut-affil-num=5 ORCID= en-aut-name=EnomotoTakashi en-aut-sei=Enomoto en-aut-mei=Takashi kn-aut-name=榎本敬 kn-aut-sei=榎本 kn-aut-mei=敬 aut-affil-num=6 ORCID= en-aut-name=MaitaniToshihiko en-aut-sei=Maitani en-aut-mei=Toshihiko kn-aut-name=米谷俊彦 kn-aut-sei=米谷 kn-aut-mei=俊彦 aut-affil-num=7 ORCID= affil-num=1 en-affil= kn-affil=岡山大学資源生物科学研究所 affil-num=2 en-affil= kn-affil=岡山大学資源生物科学研究所 affil-num=3 en-affil= kn-affil=岡山大学資源生物科学研究所 affil-num=4 en-affil= kn-affil=岡山大学資源生物科学研究所 affil-num=5 en-affil= kn-affil=岡山大学資源生物科学研究所 affil-num=6 en-affil= kn-affil=岡山大学資源生物科学研究所 affil-num=7 en-affil= kn-affil=岡山大学資源生物科学研究所 en-keyword=Roof greening kn-keyword=Roof greening en-keyword=wetland type greening kn-keyword=wetland type greening en-keyword=thin-Iayer/ Excel soil? system kn-keyword=thin-Iayer/ Excel soil? system en-keyword=cooling effect kn-keyword=cooling effect END