著者

長崎 慶三

出版者

日本微生物生態学会

雑誌

Microbes and environments (ISSN:13426311)

巻号頁・発行日

vol.13, no.2, pp.109-113, 1998-06-30

参考文献数

13

被引用文献数

3

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Three ways of the transformation and degradation of dimethyl sulfide (DMS) by marine microorganisms or by their products are reviewed. DMS is transformed to methyl mercaptan and formaldehyde under oxic conditions by some strains of sulfur oxidizing bacteria and methylotrophs. DMS is transformed to dimethyl sulfoxide (DMSO) under oxic conditions by the bacterium which utilizes DMS as a sulfur source, ammonia oxidizers, methanotrophs, and photosensitizers produced by marine algae. DMS is transformed or degraded under anoxic conditions by some strains of methanogens and phototrophic bacteria.

著者

Takehisa Yano Hiromi Kubota Junya Hanai Jun Hitomi Hajime Tokuda

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.28, no.1, pp.87-95, 2013 (Released:2013-03-12)

参考文献数

53

被引用文献数

11 49

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A comprehensive survey of microbial flora within pink biofilms in bathrooms was performed. Pink biofilms develop relatively rapidly in bathrooms, can be difficult to remove, and are quick to recur. Bacterium-sized cells were found to be predominant in 42 pink biofilms in Japan using a scanning electron microscope. Methylobacterium strains were detected from all samples in bathrooms by an isolation method. To explain this predominance, 14 biofilm samples were analyzed by fluorescence in situ hybridization. Methylobacterium was indicated to be the major genus in all biofilms. The isolated Methylobacterium survived after contact with 1.0% cleaning agents, including benzalkonium chloride for 24 h. Their tolerance did not differ under biofilm-like conditions on fiber reinforced plastics (FRP), a general material of bath tubs, floors, and walls. Also, the strains exhibited higher tolerance to desiccation than other isolated species on FRP. Some Methylobacterium survived and exhibited potential to grow after four weeks of desiccation without any nutrients. These specific characteristics could be a cause of their predominance in bathrooms, an environment with rapid flowing water, drying, low nutrients, and occasional exposure to cleaning agents.

著者

Shun Hashimoto Kohki Goto Pongdet Pyromyou Pongpan Songwattana Teerana Greetatorn Panlada Tittabutr Nantakorn Boonkerd Neung Teaumroong Toshiki Uchiumi

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.35, no.3, pp.ME20041, 2020 (Released:2020-07-02)

参考文献数

20

被引用文献数

2

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The rhizobial type III secretion system secretes effector proteins into host plant cells, which may either promote or inhibit symbiosis with legumes. We herein demonstrated that the type III secretion system of Bradyrhizobium sp. SUTN9-2 obstructed symbiosis with Lotus japonicus Miyakojima, L. japonicus Gifu, and Lotus burttii. A mutant of SUTN9-2 that is unable to secrete effector proteins showed better nodulation and plant growth promotion than wild-type SUTN9-2 when paired with these Lotus spp. We propose that SUTN9-2 is a useful strain for understanding the mechanisms by which effector proteins obstruct symbiosis between Bradyrhizobium and Lotus spp.

著者

Tajul Islam Øivind Larsen Nils-Kåre Birkeland

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.35, no.3, pp.ME20044, 2020 (Released:2020-06-12)

参考文献数

54

被引用文献数

6

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A novel cold-adapted methane-oxidizing bacterium, termed TFB, was isolated from the thermoglacial Arctic karst spring, Trollosen, located in the South Spitsbergen National Park (Norway). The source water is cold and extremely low in phosphate and nitrate. The isolate belongs to the Methylovulum genus of gammaproteobacterial methanotrophs, with the closest phylogenetic affiliation with Methylovulum miyakonense and Methylovulum psychrotolerans (96.2 and 96.1% 16S rRNA gene sequence similarities, respectively). TFB is a strict aerobe that only grows in the presence of methane or methanol. It fixes atmospheric nitrogen and contains Type I intracellular membranes. The growth temperature range was 2–22°C, with an optimum at 13–18°C. The functional genes pmoA, mxaF, and nifH were identified by PCR, whereas mmoX and cbbL were not. C16:1ω5c was identified as the major fatty acid constituent, at an amount (>49%) not previously found in any methanotrophs, and is likely to play a major role in cold adaptation. Strain TFB may be regarded as a new psychrotolerant or psychrophilic species within the genus Methylovulum. The recovery of this cold-adapted bacterium from a neutral Arctic thermal spring increases our knowledge of the diversity and adaptation of extremophilic gammaproteobacterial methanotrophs in the candidate family “Methylomonadaceae”.

著者

吉水 守 絵面 良男

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.14, no.4, pp.269-275, 1999-12-31 (Released:2009-10-05)

参考文献数

25

被引用文献数

7 10

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Many bacteria producing anti-viral substances were isolated from the aquatic environment. Fish intestinal bacteria such as Aeromonas spp. and Vibrio spp. producing anti-viral substances were isolated from intestinal contents of masu salmon (Oncorhynchus masou), Japanese flounder (Paralichthys olivaceus) and barfin flounder (Verasper moseri). These Aeromonas strains produced anti-infectious hematopoietic necrosis virus (IHNV) substances and Vibrio strains showed anti-IHNV, Oncorhynchus masou virus (OMV) and barfin flounder nervous necrosis virus (BF-NNV) activities. When Aeromonas spp. strains M-26 and M-38 were mixed with food pellets and fed to rainbow trout (O. mykiss) and masu salmon, both bacteria became dominant in the intestinal microflora and anti-IHNV activity was observed in homogenates of intestinal contents. These rainbow trout and masu salmon fed the Aeromonas spp. showed more resistance to the artificial IHNV challenge test. Barfin flounder fed Vibrio sp. strain 2IF6a with Altemia salina showed the anti-OMV and BF-NNV activities in the intestinal contents. Larvae fed the Vibrio sp. showed a higher survival rate than the fish cultured using the virus free sea water.

著者

Shohei Kusakabe Nahoko Higasitani Takakazu Kaneko Michiko Yasuda Hiroki Miwa Shin Okazaki Kazuhiko Saeki Atsushi Higashitani Shusei Sato

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.35, no.1, pp.ME19141, 2020 (Released:2020-02-20)

参考文献数

65

被引用文献数

21

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Bradyrhizobium elkanii, a rhizobium with a relatively wide host range, possesses a functional type III secretion system (T3SS) that is involved in symbiotic incompatibility against Rj4-genotype soybean (Glycine max) and some accessions of mung bean (Vigna radiata). To expand our knowledge on the T3SS-mediated partner selection mechanism in the symbiotic legume-rhizobia association, we inoculated three Lotus experimental accessions with wild-type and T3SS-mutant strains of B. elkanii USDA61. Different responses were induced by T3SS in a host genotype-dependent manner. Lotus japonicus Gifu inhibited infection; L. burttii allowed infection, but inhibited nodule maturation at the post-infection stage; and L. burttii and L. japonicus MG-20 both displayed a nodule early senescence-like response. By conducting inoculation tests with mutants of previously reported and newly identified effector protein genes of B. elkanii USDA61, we identified NopF as the effector protein triggering the inhibition of infection, and NopM as the effector protein triggering the nodule early senescence–like response. Consistent with these results, the B. elkanii USDA61 gene for NopF introduced into the Lotus symbiont Mesorhizobium japonicum induced infection inhibition in L. japonicus Gifu, but did not induce any response in L. burttii or L. japonicus MG-20. These results suggest that Lotus accessions possess at least three checkpoints to eliminate unfavorable symbionts, including the post-infection stage, by recognizing different T3SS effector proteins at each checkpoint.

著者

Akira Hashimoto-Gotoh Koichi Kitao Takayuki Miyazawa

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.35, no.1, pp.ME19130, 2020 (Released:2020-01-23)

参考文献数

62

被引用文献数

5

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MicroRNAs (miRNAs) are a group of small non-coding RNAs that suppress the expression of target mRNAs. The seed sequence of miRNA plays a crucial role in recognizing the 3′-untranslated region of the target mRNA. Cells infected with a simian foamy virus (SFV) isolated from an African green monkey (Chlorocebus aethiops) (SFVcae) showed high expression levels of viral miRNAs encoded in the long terminal repeat of SFVcae. In the present study, we investigated the roles and expression of miRNAs derived from an SFV isolated from a Japanese macaque (Macaca fuscata) (SFVmfu) using next-generation sequencing technologies. The results obtained showed that SFVmfu also expressed viral miRNAs; however, the seed sequences of most miRNAs derived from SFVmfu differed from those reported previously from SFVcae. Cells persistently infected with SFVmfu strongly expressed an miRNA with the same seed sequence as the miR-1 microRNA precursor family. Luciferase reporter assays indicated that this miRNA down-regulates the expression of adenylyl cyclase-associated protein 1, which is up-regulated in several solid tumors. The present results suggest that SFVmfu utilizes viral miRNAs to establish long-term co-existence with the Japanese macaque.

著者

Fumio Inagaki Yoshinobu Motomura Katsumi Doi Sachihiro Taguchi Eiji Izawa Donald R. Lowe Seiya Ogata

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.16, no.2, pp.125-130, 2001 (Released:2001-07-16)

参考文献数

32

被引用文献数

16 29

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At Steep Cone hot spring, Lower Geyser Basin, Yellowstone National Park, a mound of siliceous deposits called "siliceous sinter" forms from discharged boiling geothermal water that is supersaturated with amorphous silica. Electron-probe microanalyzer (EPMA) observations suggested that silica is deposited on the surface of the cells and that microorganisms affect the formation of the siliceous sinter. EPMA signals and backscattered electron images of sinter samples taken at the inner wall of the boiling pool revealed framboidal pyrite structures associated with a network of silicified microbial structures. The structure of bacterial community in a beige-colored sinter sediment (75.8°C, pH 8.6) was studied by molecular clone type phylogenetic analysis of PCR-mediated 16S rDNA fragments. The bacterial rDNA clones found indicated the presence of a complex community in the sinter sediment. Sequences closely related to the genera Thermus and Saccharomonospora were dominated; evidence of indigenous microbial components.

著者

Shun Kobayashi Daisuke Hira Keitaro Yoshida Masanori Toyofuku Yosuke Shida Wataru Ogasawara Takashi Yamaguchi Nobuo Araki Mamoru Oshiki

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.33, no.4, pp.428-434, 2018 (Released:2018-12-28)

参考文献数

47

被引用文献数

1 35

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Aerobic ammonia-oxidizing archaea (AOA) play a crucial role in the global nitrogen cycle by oxidizing ammonia to nitrite, and nitric oxide (NO) is a key intermediate in AOA for sustaining aerobic ammonia oxidation activity. We herein heterologously expressed the NO-forming, copper-containing, dissimilatory nitrite reductase (NirK) from Nitrososphaera viennensis and investigated its enzymatic properties. The recombinant protein catalyzed the reduction of 15NO2− to 15NO, the oxidation of hydroxylamine (15NH2OH) to 15NO, and the production of 14–15N2O from 15NH2OH and 14NO2−. To the best of our knowledge, the present study is the first to document the enzymatic properties of AOA NirK.

著者

Keishi Kameyama Kikuji Itoh

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.29, no.4, pp.427-430, 2014 (Released:2014-12-19)

参考文献数

23

被引用文献数

77 288

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The aim of the present study was to identify bacteria that may contribute to the onset of metabolic dysfunctions. We isolated and identified a candidate bacterium belonging to Lachnospiraceae (strain AJ110941) in the feces of hyperglycemic obese mice. The colonization of germ-free ob/ob mice by AJ110941 induced significant increases in fasting blood glucose levels as well as liver and mesenteric adipose tissue weights, and decreases in plasma insulin levels and HOMA-β values. These results indicated that the specific gut commensal bacterium AJ110941 influenced the development of obesity and diabetes in ob/ob mice with genetic susceptibility for obesity.

著者

Arisa Nishihara Shin Haruta Shawn E. McGlynn Vera Thiel Katsumi Matsuura

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.33, no.1, pp.10-18, 2018 (Released:2018-03-29)

参考文献数

77

被引用文献数

21

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The activity of nitrogen fixation measured by acetylene reduction was examined in chemosynthetic microbial mats at 72–75°C in slightly-alkaline sulfidic hot springs in Nakabusa, Japan. Nitrogenase activity markedly varied from sampling to sampling. Nitrogenase activity did not correlate with methane production, but was detected in samples showing methane production levels less than the maximum amount, indicating a possible redox dependency of nitrogenase activity. Nitrogenase activity was not affected by 2-bromo-ethane sulfonate, an inhibitor of methanogenesis. However, it was inhibited by the addition of molybdate, an inhibitor of sulfate reduction and sulfur disproportionation, suggesting the involvement of sulfate-reducing or sulfur-disproportionating organisms. Nitrogenase activity was affected by different O2 concentrations in the gas phase, again supporting the hypothesis of a redox potential dependency, and was decreased by the dispersion of mats with a homogenizer. The loss of activity that occurred from dispersion was partially recovered by the addition of H2, sulfate, and carbon dioxide. These results suggested that the observed activity of nitrogen fixation was related to chemoautotrophic sulfate reducers, and fixation may be active in a limited range of ambient redox potential. Since thermophilic chemosynthetic communities may resemble ancient microbial communities before the appearance of photosynthesis, the present results may be useful when considering the ancient nitrogen cycle on earth.

著者

Arisa Nishihara Vera Thiel Katsumi Matsuura Shawn E. McGlynn Shin Haruta

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.33, no.4, pp.357-365, 2018 (Released:2018-12-28)

参考文献数

79

被引用文献数

1 23

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Chemosynthetic microbial communities develop and form dense cell aggregates in slightly alkaline sulfidic hot springs in the temperature range of 70–86°C at Nakabusa, Japan. Nitrogenase activity has recently been detected in the microbial communities collected. To identify possible members capable of nitrogen fixation, we examined the diversities of 16S rRNA and nitrogenase reductase (NifH) gene sequences in four types of chemosynthetic communities with visually different colors and thicknesses. The results of a 16S rRNA gene analysis indicated that all four microbial communities had similar bacterial constituents; the phylum Aquificae was the dominant member, followed in abundance by Thermodesulfobacteria, Firmicutes, and Thermotogae. Most of the NifH sequences were related to sequences reported in hydrothermal vents and terrestrial hot springs. The results of a phylogenetic analysis of NifH sequences revealed diversity in this gene among the communities collected, distributed within 7 phylogenetic groups. NifH sequences affiliated with Aquificae (Hydrogenobacter/Thermocrinis) and Firmicutes (Caldicellulosiruptor) were abundant. At least two different energy metabolic pathways appeared to be related to nitrogen fixation in the communities analyzed; aerobic sulfur/hydrogen-oxidizing bacteria in Aquificae and fermentative bacteria in Firmicutes. The metabolic characteristics of these two dominant phyla differed from those previously inferred from nitrogenase activity assays on chemosynthetic communities, which were associated with hydrogen-dependent autotrophic sulfate reduction. These assays may correspond to the observed NifH sequences that are distantly related to the known species of Thermodesulfovibrio sp. (Nitrospirae) detected in the present study. The activities of nitrogen-fixing organisms in communities may depend on redox states as well as the availability of electron donors, acceptors, and carbon sources.

著者

Nahoko Uchi Mitsutaka Fukudome Narumi Nozaki Miyuzu Suzuki Ken-ichi Osuki Shuji Shigenobu Toshiki Uchiumi

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.34, no.2, pp.155-160, 2019 (Released:2019-06-27)

参考文献数

37

被引用文献数

18

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Aphids have a mutualistic relationship with the bacterial endosymbiont Buchnera aphidicola. We previously reported seven cysteine-rich peptides in the pea aphid Acyrthosiphon pisum and named them Bacteriocyte-specific Cysteine-Rich (BCR) peptides; these peptides are exclusively expressed in bacteriocytes, special aphid cells that harbor symbionts. Similar symbiotic organ-specific cysteine-rich peptides identified in the root nodules of leguminous plants are named Nodule-specific Cysteine-Rich (NCR) peptides. NCR peptides target rhizobia in the nodules and are essential for symbiotic nitrogen fixation. A BacA (membrane protein) mutant of Sinorhizobium is sensitive to NCR peptides and is unable to establish symbiosis. Based on the structural and expressional similarities between BCR peptides and NCR peptides, we hypothesized that aphid BCR peptides exhibit antimicrobial activity, similar to some NCR peptides. We herein synthesized BCR peptides and investigated their antimicrobial activities and effects on the bacterial membrane of Escherichia coli. The peptides BCR1, BCR3, BCR5, and BCR8 exhibited antimicrobial activities with increased membrane permeability. An sbmA mutant of E. coli, a homolog of bacA of S. meliloti, was more sensitive to BCR peptides than the wild type. Our results suggest that BCR peptides have properties that may be required to control the endosymbiont, similar to NCR peptides in legumes.

著者

石田 昭夫 上野 友美

出版者

日本微生物生態学会

雑誌

Microbes and environments (ISSN:13426311)

巻号頁・発行日

vol.11, no.3, pp.67-72, 1996-12-31

参考文献数

10

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非好塩性細菌である大腸菌(<i>Escherichia coli</i> ATCC-9637)を用いて,海水環境下での菌の増殖及び耐塩性誘導とその保持について,天然海水の代わりに組成成分の明確な人工海水を使用し検討した。<br>2.5倍濃度の人工海水に酵母エキスを加えた培地では,この大腸菌株はほとんど増殖できないが,通常濃度の人工海水であれば十分に増殖できることが分かった。さらに,通常濃度の人工海水に酵母エキス(1%)を添加した培地で,30分間前振盪処理をすることによって,無処理では増殖の観察できない2.5倍濃度の人工海水中でも菌増殖が可能となる耐塩性が誘導された。このような耐塩性の誘導には,培地の人工海水濃度が通常の1/2~1付近が最も効果的であること,さらに酵母エキスを必要とすることが分かった。このことは,淡水性の大腸菌が河口周辺または海水環境下で酵母エキスのような有機物の存在があれば,耐塩性が誘導され,より高濃度の塩分環境に適応出来ることを示唆している。<br>誘導された耐塩性は,有機物なしでも人工海水中に低温下で菌体が保存された場合は,少なくとも2週間はほぼ完全に保持されそれ以降次第に消失することが分かった。耐塩性の保持に有効な人工海水の成分を検討したところ,浸透圧を維持するNaClとMgイオン及びCaイオンの共存が必要であることが分かった。一方,純水中で菌体を保存した場合は,耐塩性は1週間でほぼ消失したが,平板培養法で観察した生菌数はわずかの減少しか見られないことから,耐塩性の消失と菌の死滅は別個の機構によると考えられる。

著者

Annisa N. Lathifah Yong Guo Nobuo Sakagami Wataru Suda Masanobu Higuchi Tomoyasu Nishizawa Irfan D. Prijambada Hiroyuki Ohta

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME19041, (Released:2019-07-20)

被引用文献数

9

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Microbial colonization, followed by succession, on newly exposed volcanic substrates represents the beginning of the development of an early ecosystem. During early succession, colonization by mosses or plants significantly alters the pioneer microbial community composition through the photosynthetic carbon input. To provide further insights into this process, we investigated the three-year-old volcanic deposits of Mount Merapi, Indonesia. Samples were collected from unvegetated (BRD) and moss-covered (BRUD) sites. Forest site soil (FRS) near the volcanic deposit-covered area was also collected for reference. An analysis of BRD and BRUD revealed high culturable cell densities (1.7–8.5×105 CFU g–1) despite their low total C (<0.01%). FRS possessed high CFU (3×106 g–1); however, its relative value per unit of total C (2.6%) was lower than that of the deposit samples. Based on the tag pyrosequencing of 16S rRNA genes, the BRD bacterial community was characterized by a higher number of betaproteobacterial families (or genus), represented by chemolithotrophic Methylophilaceae, Leptothrix, and Sulfuricellaceae. In contrast, BRUD was predominated by different betaproteobacterial families, such as Oxalobacteraceae, Comamonadaceae, and Rhodocyclaceae. Some bacterial (Oxalobacteraceae) sequences were phylogenetically related to those of known moss-associated bacteria. Within the FRS community, Proteobacteria was the most abundant phylum, followed by Acidobacteria, whereas Burkholderiaceae was the most dominant bacterial family within FRS. These results suggest that an inter-family succession of Betaproteobacteria occurred in response to colonization by mosses, followed by plants.

著者

Nengfei Wang Yudong Guo Gaoyang Li Yan Xia Mingyang Ma Jiaye Zang Yue Ma Xiaofei Yin Wenbing Han Jinjiang Lv Huansheng Cao

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME18091, (Released:2019-06-07)

被引用文献数

6

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Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3–V4 region. Dominant phyla in sediments and soils included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae; sediments contained a unique phylum, Euryarchaeota, with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.

著者

Tatsuya Kuranishi Jun-ichiro Sekiguchi Izumi Yanagisawa Makoto Akiwa Yuko Tokuno

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME18128, (Released:2019-03-28)

被引用文献数

2

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Although Pantoea species are widely distributed among plants, water, soils, humans, and animals, due to a lack of efficient isolation methods, the clonality of Pantoea species is poorly characterized. Therefore, we developed a new semi-selective medium designated ‘lysine-ornithine-mannitol-arginine-charcoal’ (LOMAC) to isolate these species. In an inclusive and exclusive study examining 94 bacterial strains, all Pantoea strains exhibited yellow colonies on LOMAC medium. The performance of the medium was assessed using Pantoea-spiked soils. Percent average agreement relative to the Api20E biochemical test was 97%. A total of 24 soil spot samples and 19 plant types were subjected to practical trials. Of the 91 yellow colonies selected on LOMAC medium, 81 were correctly identified as Pantoea species using the biochemical test. The sequencing of 16S rRNA (rrs) and gyrB from these isolates confirmed that Pantoea agglomerans, P. vagans, P. ananatis, and P. deleyi were present in Japanese fields. A phylogenetic analysis using rrs enabled only the limited separation of strains within each Pantoea spp., whereas an analysis using gyrB revealed higher variability and enabled the finer resolution of distinct branches. P. agglomerans isolates were divided into 3 groups, 2 of which were new clades, with the other comprising a large group including biocontrol strains. P. vagans was also in one of the new clades. The present results indicate that LOMAC medium is useful for screening Pantoea species. The use of LOMAC medium will provide new opportunities for identifying the beneficial properties of Japanese Pantoea isolates.

著者

Analhuda Abdullah Tahir Nor Farhana Mohd Barnoh Nurtasbiyah Yusof Nuurul Nadrah Mohd Said Motoo Utsumi Ang May Yen Hazni Hashim Megat Johari Megat Mohd Noor Fazrena Nadia MD Akhir Shaza Eva Mohamad Norio Sugiura Nor’azizi Othman Zuriati Zakaria Hirofumi Hara

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME18117, (Released:2019-04-23)

被引用文献数

17

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Oil palm empty fruit bunches (OPEFB) are the most abundant, inexpensive, and environmentally friendly lignocellulosic biomass in Malaysia. Investigations on the microbial diversity of decaying OPEFB may reveal microbes with complex enzymes that have the potential to enhance the conversion of lignocellulose into second-generation biofuels as well as the production of other value-added products. In the present study, fungal and bacterial diversities in decaying OPEFB were identified using Illumina MiSeq sequencing of the V3 region of the 16S rRNA gene and V4 region of the 18S rRNA gene. Fungal diversity in decaying OPEFB was dominated by the phylum Ascomycota (14.43%), while most of the bacterial sequences retrieved belonged to Proteobacteria (76.71%). Three bacterial strains isolated from decaying OPEFB, designated as S18, S20, and S36, appeared to grow with extracted OPEFB-lignin and Kraft lignin (KL) as the sole carbon source. 16S rRNA gene sequencing identified the 3 isolates as Paenibacillus sp.. The molecular weight distribution of KL before and after degradation showed significant depolymerization when treated with bacterial strains S18, S20, and S36. The presence of low-molecular-weight lignin-related compounds, such as vanillin and 2-methoxyphenol derivatives, which were detected by a GC-MS analysis, confirmed the KL-degrading activities of isolated Paenibacillus strains.

著者

Sayed Ziauddin Hashami Hiroyuki Nakamura Naoko Ohkama-Ohtsu Katsuhiro Kojima Salem Djedidi Izumi Fukuhara Mohammad Daud Haidari Hitoshi Sekimoto Tadashi Yokoyama

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.34, no.1, pp.64-75, 2019 (Released:2019-03-30)

参考文献数

35

被引用文献数

9

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Legumes form root nodules and fix atmospheric nitrogen by establishing symbiosis with rhizobia. However, excessive root nodules are harmful to plants because of the resulting overconsumption of energy from photosynthates. The delay of an inoculation of the soybean super-nodulation mutant NOD1–3 with Bradyrhizobium diazoefficiens USDA110T by 5 d after an inoculation with several soil bacteria confirmed that one bacterial group significantly decreased root nodules throughout the study period. Moreover, no significant changes were observed in nitrogen fixation by root nodules between an inoculation with USDA 110T only and co-inoculation treatments. To clarify the potential involvement of PR proteins in the restriction of nodule formation in the plants tested, the relative expression levels of PR-1, PR-2, PR-5, and PDF1.2 in NOD1–3 roots were measured using real-time PCR. One group of soil bacteria (Gr.3), which markedly reduced nodule numbers, significantly induced the expression of PR-1, PR-5 and PDF1.2 genes by day 5 after the inoculation. By days 7, 10, and 20 after the inoculation, the expression levels of PR-2 and PR-5 were lower than those with the uninoculated treatment. Inoculations with this group of soil bacteria resulted in lower root nodule numbers than with other tested soil bacteria exerting weak inhibitory effects on nodulation, and were accompanied by the induction of plant defense-related genes. Thus, PR genes appear to play important roles in the mechanisms that suppresses nodule formation on soybean roots.

著者

Yuga Hirakata Mamoru Oshiki Kyohei Kuroda Masashi Hatamoto Kengo Kubota Takashi Yamaguchi Hideki Harada Nobuo Araki

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.30, no.4, pp.335-338, 2015 (Released:2015-12-22)

参考文献数

22

被引用文献数

11 23

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The aim of the present study was to investigate the prokaryotic community structure of the anaerobic ciliate, Metopus sp. using rRNA sequencing, fluorescence in situ hybridization (FISH), and transmission electron microscopy (TEM). Metopus sp. was physically separated from anaerobic granular sludge in a domestic wastewater treatment plant and anoxically cultivated for 7 d. 16S rRNA gene sequences from the prokaryotes Methanoregula boonei and Clostridium aminobutyricum were abundantly detected in Metopus ciliates. The FISH analysis using the oligonucleotide probes Mg1200b and Cla568 demonstrated that these prokaryotes were localized within Metopus cells. These results identify M. boonei- and C. aminobutyricum-like prokaryotes as novel endosymbionts of Metopus ciliates.