著者
石田 昭夫 上野 友美
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.11, no.3, pp.67-72, 1996-12-31 (Released:2009-10-05)
参考文献数
10

非好塩性細菌である大腸菌(Escherichia coli 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。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。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
Tomoko Mihara Hitoshi Koyano Pascal Hingamp Nigel Grimsley Susumu Goto Hiroyuki 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
pp.ME17203, (Released:2018-05-25)
被引用文献数
26

Since the discovery of the giant mimivirus, evolutionarily related viruses have been isolated or identified from various environments. Phylogenetic analyses of this group of viruses, tentatively referred to as the family “Megaviridae”, suggest that it has an ancient origin that may predate the emergence of major eukaryotic lineages. Environmental genomics has since revealed that Megaviridae represents one of the most abundant and diverse groups of viruses in the ocean. In the present study, we compared the taxon richness and phylogenetic diversity of Megaviridae, Bacteria, and Archaea using DNA-dependent RNA polymerase as a common marker gene. By leveraging existing microbial metagenomic data, we found higher richness and phylogenetic diversity in this single viral family than in the two prokaryotic domains. We also obtained results showing that the evolutionary rate alone cannot account for the observed high diversity of Megaviridae lineages. These results suggest that the Megaviridae family has a deep co-evolutionary history with diverse marine protists since the early “Big-Bang” radiation of the eukaryotic tree of life.
著者
Shawn E. McGlynn
出版者
日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会
雑誌
Microbes and Environments (ISSN:13426311)
巻号頁・発行日
pp.ME16166, (Released:2017-03-17)
被引用文献数
47

Anaerobic methane oxidation in archaea is often presented to operate via a pathway of “reverse methanogenesis”. However, if the cumulative reactions of a methanogen are run in reverse there is no apparent way to conserve energy. Recent findings suggest that chemiosmotic coupling enzymes known from their use in methylotrophic and acetoclastic methanogens—in addition to unique terminal reductases—biochemically facilitate energy conservation during complete CH4 oxidation to CO2. The apparent enzyme modularity of these organisms highlights how microbes can arrange their energy metabolisms to accommodate diverse chemical potentials in various ecological niches, even in the extreme case of utilizing “reverse” thermodynamic potentials.
著者
Yu Nakajima Takashi Tsukamoto Yohei Kumagai Yoshitoshi Ogura Tetsuya Hayashi Jaeho Song Takashi Kikukawa Makoto Demura Kazuhiro Kogure Yuki Sudo Susumu Yoshizawa
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.ME17197, (Released:2018-03-16)
被引用文献数
1

Light-driven ion-pumping rhodopsins are widely distributed among bacteria, archaea, and eukaryotes in the euphotic zone of the aquatic environment. H+-pumping rhodopsin (proteorhodopsin: PR), Na+-pumping rhodopsin (NaR), and Cl–-pumping rhodopsin (ClR) have been found in marine bacteria, which suggests that these genes evolved independently in the ocean. Putative microbial rhodopsin genes were identified in the genome sequences of marine Cytophagia. In the present study, one of these genes was heterologously expressed in Escherichia coli cells and the rhodopsin protein named Rubricoccus marinus halorhodopsin (RmHR) was identified as a light-driven inward Cl– pump. Spectroscopic assays showed that the estimated dissociation constant (Kd,int.) of this rhodopsin was similar to that of haloarchaeal halorhodopsin (HR), while the Cl–-transporting photoreaction mechanism of this rhodopsin was similar to that of HR, but different to that of the already-known marine bacterial ClR. This amino acid sequence similarity also suggested that this rhodopsin is similar to haloarchaeal HR and cyanobacterial HRs (e.g., SyHR and MrHR). Additionally, a phylogenetic analysis revealed that retinal biosynthesis pathway genes (blh and crtY) belong to a phylogenetic lineage of haloarchaea, indicating that these marine Cytophagia acquired rhodopsin-related genes from haloarchaea by lateral gene transfer. Based on these results, we concluded that inward Cl–-pumping rhodopsin is present in genera of the class Cytophagia and may have the same evolutionary origins as haloarchaeal HR.
著者
Satoshi Hiraoka Ching-chia Yang Wataru Iwasaki
出版者
日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会
雑誌
Microbes and Environments (ISSN:13426311)
巻号頁・発行日
pp.ME16024, (Released:2016-07-05)
被引用文献数
2 43

Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.
著者
Hideaki Sasaki Susumu Shirato Tomoya Tahara Kenji Sato Hiroyuki Takenaka
出版者
日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会
雑誌
Microbes and Environments (ISSN:13426311)
巻号頁・発行日
pp.ME13035, (Released:2013-11-19)
被引用文献数
2 10

The Fukushima Daiichi Nuclear Power Plant accident released large amounts of radioactive substances into the environment and contaminated the soil of Tohoku and Kanto districts in Japan. Removal of radioactive material from the environment is an urgent problem, and soil purification using plants is being considered. In this study, we investigated the ability of 12 seed plant species and a cyanobacterium to accumulate radioactive material. The plants did not accumulate radioactive material at high levels, but high accumulation was observed in the terrestrial cyanobacterium Nostoc commune. In Nihonmatsu City, Fukushima Prefecture, N. commune accumulated 415,000 Bq/kg dry weight 134Cs and 607,000 Bq kg-1 dry weight 137Cs. The concentration of cesium in N. commune tended to be high in areas where soil radioactivity was high. A cultivation experiment confirmed that N. commune absorbed radioactive cesium from polluted soil. These data demonstrated that radiological absorption using N. commune might be suitable for decontaminating polluted soil.
著者
Arisa Nishihara Katsumi Matsuura Marcus Tank Shawn E. McGlynn Vera Thiel 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
pp.ME18041, (Released:2018-11-23)
被引用文献数
3

The phylum Aquificae comprises chemolithoautotrophic thermophilic to hyperthermophilic bacteria, in which the nitrogenase reductase gene (nifH) has been reported. However, nitrogen-fixing activity has not yet been demonstrated in members of this deeply branching bacterial phylum. We isolated two thermophilic diazotrophic strains from chemosynthetic microbial communities in slightly alkaline hot springs (≥70°C) in Nakabusa, Nagano Prefecture, Japan. A phylogenetic analysis based on 16S rRNA genes identified these strains as members of the genus Hydrogenobacter within Aquificae. Their NifH sequences showed 96.5 and 97.4% amino acid sequence identities to that from Hydrogenobacter thermophilus TK-6. Nitrogenase activity, measured by acetylene reduction, was confirmed in both strains at 70°C. These novel strains grew under semi-aerobic conditions by using CO2 as the sole carbon source and N2 as the sole nitrogen source in media containing hydrogen and/or thiosulfate. To the best of our knowledge, this is the first demonstration of active nitrogen fixation in thermophilic bacteria at 70°C and in the phylum Aquificae.
著者
Yu Nakajima Takashi Tsukamoto Yohei Kumagai Yoshitoshi Ogura Tetsuya Hayashi Jaeho Song Takashi Kikukawa Makoto Demura Kazuhiro Kogure Yuki Sudo Susumu Yoshizawa
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.89-97, 2018 (Released:2018-03-29)
参考文献数
43
被引用文献数
1

Light-driven ion-pumping rhodopsins are widely distributed among bacteria, archaea, and eukaryotes in the euphotic zone of the aquatic environment. H+-pumping rhodopsin (proteorhodopsin: PR), Na+-pumping rhodopsin (NaR), and Cl−-pumping rhodopsin (ClR) have been found in marine bacteria, which suggests that these genes evolved independently in the ocean. Putative microbial rhodopsin genes were identified in the genome sequences of marine Cytophagia. In the present study, one of these genes was heterologously expressed in Escherichia coli cells and the rhodopsin protein named Rubricoccus marinus halorhodopsin (RmHR) was identified as a light-driven inward Cl− pump. Spectroscopic assays showed that the estimated dissociation constant (Kd,int.) of this rhodopsin was similar to that of haloarchaeal halorhodopsin (HR), while the Cl−-transporting photoreaction mechanism of this rhodopsin was similar to that of HR, but different to that of the already-known marine bacterial ClR. This amino acid sequence similarity also suggested that this rhodopsin is similar to haloarchaeal HR and cyanobacterial HRs (e.g., SyHR and MrHR). Additionally, a phylogenetic analysis revealed that retinal biosynthesis pathway genes (blh and crtY) belong to a phylogenetic lineage of haloarchaea, indicating that these marine Cytophagia acquired rhodopsin-related genes from haloarchaea by lateral gene transfer. Based on these results, we concluded that inward Cl−-pumping rhodopsin is present in genera of the class Cytophagia and may have the same evolutionary origins as haloarchaeal HR.
著者
Katharina Lührig Björn Canbäck Catherine J. Paul Tomas Johansson Kenneth M. Persson Peter Rådström
出版者
日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会
雑誌
Microbes and Environments (ISSN:13426311)
巻号頁・発行日
vol.30, no.1, pp.99-107, 2015 (Released:2015-03-24)
参考文献数
44
被引用文献数
8 24

Next-generation sequencing of the V1–V2 and V3 variable regions of the 16S rRNA gene generated a total of 674,116 reads that described six distinct bacterial biofilm communities from both water meters and pipes. A high degree of reproducibility was demonstrated for the experimental and analytical work-flow by analyzing the communities present in parallel water meters, the rare occurrence of biological replicates within a working drinking water distribution system. The communities observed in water meters from households that did not complain about their drinking water were defined by sequences representing Proteobacteria (82–87%), with 22–40% of all sequences being classified as Sphingomonadaceae. However, a water meter biofilm community from a household with consumer reports of red water and flowing water containing elevated levels of iron and manganese had fewer sequences representing Proteobacteria (44%); only 0.6% of all sequences were classified as Sphingomonadaceae; and, in contrast to the other water meter communities, markedly more sequences represented Nitrospira and Pedomicrobium. The biofilm communities in pipes were distinct from those in water meters, and contained sequences that were identified as Mycobacterium, Nocardia, Desulfovibrio, and Sulfuricurvum. The approach employed in the present study resolved the bacterial diversity present in these biofilm communities as well as the differences that occurred in biofilms within a single distribution system, and suggests that next-generation sequencing of 16S rRNA amplicons can show changes in bacterial biofilm communities associated with different water qualities.
著者
Yusuke Takashima Kensuke Seto Yousuke Degawa Yong Guo Tomoyasu Nishizawa Hiroyuki Ohta Kazuhiko Narisawa
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.ME18081, (Released:2018-12-08)
被引用文献数
4

Endofungal bacteria are widespread within the phylum Mucoromycota, and these include Burkholderiaceae-related endobacteria (BRE). However, the prevalence of BRE in Mortierellomycotinan fungi and their phylogenetic divergence remain unclear. Therefore, we examined the prevalence of BRE in diverse species of Mortierella. We surveyed 238 isolates of Mortierella spp. mainly obtained in Japan that were phylogenetically classified into 59 species. BRE were found in 53 isolates consisting of 22 species of Mortierella. Among them, 20 species of Mortierella were newly reported as the fungal hosts of BRE. BRE in a Glomeribacter-Mycoavidus clade in the family Burkholderiaceae were separated phylogenetically into three groups. These groups consisted of a group containing Mycoavidus cysteinexigens, which is known to be associated with M. elongata, and two other newly distinguishable groups. Our results demonstrated that BRE were harbored by many species of Mortierella and those that associated with isolates of Mortierella spp. were more phylogenetically divergent than previously reported.
著者
Takuro Nunoura Manabu Nishizawa Miho Hirai Shigeru Shimamura Phurt Harnvoravongchai Osamu Koide Yuki Morono Toshiaki Fukui Fumio Inagaki Junichi Miyazaki Yoshihiro Takaki Ken Takai
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.2, pp.186-194, 2018 (Released:2018-07-04)
参考文献数
72
被引用文献数
21

The Challenger Deep is the deepest ocean on Earth. The present study investigated microbial community structures and geochemical cycles associated with the trench bottom sediments of the Challenger Deep, the Mariana Trench. The SSU rRNA gene communities found in trench bottom sediments were dominated by the bacteria Chloroflexi (SAR202 and other lineages), Bacteroidetes, Planctomycetes, “Ca. Marinimicrobia” (SAR406), and Gemmatimonadetes and by the archaeal α subgroup of MGI Thaumarchaeota and “Ca. Woesearchaeota” (Deep-sea Hydrothermal Vent Euryarchaeotic Group 6). The SSU rRNA gene sequencing analysis indicated that the dominant populations of the thaumarchaeal α group in hadal water and sediments were similar to each other at the species or genus level. In addition, the co-occurrence of nitrification and denitrification was revealed by the combination of pore water geochemical analyses and quantitative PCR for nitrifiers.
著者
Yanze Li Hisashi Endo Yasuhiro Gotoh Hiroyasu Watai Nana Ogawa Romain Blanc-Mathieu Takashi Yoshida Hiroyuki 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
pp.ME19037, (Released:2019-08-03)
被引用文献数
1

Giant viruses of ‘Megaviridae’ have the ability to widely disperse around the globe. We herein examined ‘Megaviridae’ communities in four distinct aquatic environments (coastal and offshore seawater, brackish water, and hot spring freshwater), which are distantly located from each other (between 74 and 1,765 km), using a meta-barcoding method. We identified between 593 and 3,627 OTUs in each sample. Some OTUs were detected in all five samples tested as well as in many of the Tara Oceans metagenomes, suggesting the existence of viruses of this family in a wide range of habitats and the ability to circulate on the planet.
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
pp.ME18058, (Released:2018-10-12)
被引用文献数
7

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
Miho Hirai Shinro Nishi Miwako Tsuda Michinari Sunamura Yoshihiro Takaki Takuro Nunoura
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.32, no.4, pp.336-343, 2017 (Released:2017-12-27)
参考文献数
34
被引用文献数
3 15

Shotgun metagenomics is a low biased technology for assessing environmental microbial diversity and function. However, the requirement for a sufficient amount of DNA and the contamination of inhibitors in environmental DNA leads to difficulties in constructing a shotgun metagenomic library. We herein examined metagenomic library construction from subnanogram amounts of input environmental DNA from subarctic surface water and deep-sea sediments using two library construction kits: the KAPA Hyper Prep Kit and Nextera XT DNA Library Preparation Kit, with several modifications. The influence of chemical contaminants associated with these environmental DNA samples on library construction was also investigated. Overall, shotgun metagenomic libraries were constructed from 1 pg to 1 ng of input DNA using both kits without harsh library microbial contamination. However, the libraries constructed from 1 pg of input DNA exhibited larger biases in GC contents, k-mers, or small subunit (SSU) rRNA gene compositions than those constructed from 10 pg to 1 ng DNA. The lower limit of input DNA for low biased library construction in this study was 10 pg. Moreover, we revealed that technology-dependent biases (physical fragmentation and linker ligation vs. tagmentation) were larger than those due to the amount of input DNA.
著者
Régis Rouzé Anne Moné Frédéric Delbac Luc Belzunces Nicolas Blot
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.3, pp.226-233, 2019 (Released:2019-09-25)
参考文献数
86
被引用文献数
1

The gut of the European honeybee Apis mellifera is the site of exposure to multiple stressors, such as pathogens and ingested chemicals. Therefore, the gut microbiota, which contributes to host homeostasis, may be altered by these stressors. The abundance of major bacterial taxa in the gut was evaluated in response to infection with the intestinal parasite Nosema ceranae or chronic exposure to low doses of the neurotoxic insecticides coumaphos, fipronil, thiamethoxam, and imidacloprid. Experiments were performed under laboratory conditions on adult workers collected from hives in February (winter bees) and July (summer bees) and revealed season-dependent changes in the bacterial community composition. N. ceranae and a lethal fipronil treatment increased the relative abundance of both Gilliamella apicola and Snodgrassella alvi in surviving winter honeybees. The parasite and a sublethal exposure to all insecticides decreased the abundance of Bifidobacterium spp. and Lactobacillus spp. regardless of the season. The similar effects induced by insecticides belonging to distinct molecular families suggested a shared and indirect mode of action on the gut microbiota, possibly through aspecific alterations in gut homeostasis. These results demonstrate that infection and chronic exposure to low concentrations of insecticides may affect the honeybee holobiont.
著者
今中 忠行
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.13, no.3, pp.171-175, 1998-09-30 (Released:2009-10-05)
参考文献数
11

It has been understood as a common sense that petroleum can be oxidized by the microorganisms in the presence of molecular oxygen. In contrast, we isolated an extremely interesting bacterium strain HD-1 which could assimilate petroleum under anaerobic condition. The bacterium could grow on CO2 as a sole carbon source, and produced n-alkane/alkene, major components of petroleum.
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
pp.ME18030, (Released:2018-11-07)
被引用文献数
5

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.