Microbes and Environments
Online ISSN : 1347-4405
Print ISSN : 1342-6311
ISSN-L : 1342-6311
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Showing 1-13 articles out of 13 articles from the selected issue
Minireview
  • Jiayue Yang, Yongshou Yang, Manami Ishii, Mayuko Nagata, Wanping Aw, N ...
    Type: Minireview
    2020 Volume 35 Issue 3 ME20037
    Published: 2020
    Released: July 04, 2020
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    Microbes inhabit various environments, such as soil, water environments, plants, and animals. Humans harbor a complex commensal microbial community in the gastrointestinal tract, which is known as the gut microbiota. The gut microbiota participates not only in various metabolic processes in the human body, it also plays a critical role in host immune responses. Gut microbes that inhabit the intestinal epithelial surface form polymicrobial biofilms. In the last decade, it has been widely reported that gut microbial biofilms and gut microbiota-derived products, such as metabolites and bacterial membrane vesicles, not only directly affect the host intestinal environment, but also indirectly influence the health of the host. In this review, we discuss the most recent findings from human and animal studies on the interactions between the gut microbiota and hosts, and their associations with various disorders, including inflammatory diseases, atopic dermatitis, metabolic disorders, and psychiatric and neurological diseases. The integrated approach of metabologenomics together with biofilm imaging may provide valuable insights into the gut microbiota and suggest remedies that may lead to a healthier society.

Short Communication
Regular Paper
  • Teerana Greetatorn, Shun Hashimoto, Taro Maeda, Mitsutaka Fukudome, Po ...
    Type: Regular Paper
    2020 Volume 35 Issue 3 ME20049
    Published: 2020
    Released: July 29, 2020
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    Supplementary material

    Bradyrhizobium sp. strain SUTN9-2 is a symbiotic and endophytic diazotrophic bacterium found in legume and rice plants and has the potential to promote growth. The present results revealed that SUTN9-2 underwent cell enlargement, increased its DNA content, and efficiently performed nitrogen fixation in response to rice extract. Some factors in rice extract induced the expression of cell cycle and nitrogen fixation genes. According to differentially expressed genes (DEGs) from the transcriptomic analysis, SUTN9-2 was affected by rice extract and the deletion of the bclA gene. The up-regulated DEGs encoding a class of oxidoreductases, which act with oxygen atoms and may have a role in controlling oxygen at an appropriate level for nitrogenase activity, followed by GroESL chaperonins are required for the function of nitrogenase. These results indicate that following its exposure to rice extract, nitrogen fixation by SUTN9-2 is induced by the collective effects of GroESL and oxidoreductases. The expression of the sensitivity to antimicrobial peptides transporter (sapDF) was also up-regulated, resulting in cell differentiation, even when bclA (sapDF) was mutated. This result implies similarities in the production of defensin-like antimicrobial peptides (DEFs) by rice and nodule-specific cysteine-rich (NCR) peptides in legume plants, which affect bacterial cell differentiation.

Short Communication
  • Yu Sato, Kenji Okano, Hiroyuki Kimura, Kohsuke Honda
    Type: Short Communication
    2020 Volume 35 Issue 3 ME20074
    Published: 2020
    Released: July 29, 2020
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    Supplementary material

    Growth temperature is one of the most representative biological parameters for characterizing living organisms. Prokaryotes have been isolated from various temperature environments and show wide diversity in their growth temperatures. We herein constructed a database of growth TEMPeratures of Usual and RAre prokaryotes (TEMPURA, http://togodb.org/db/tempura), which contains the minimum, optimum, and maximum growth temperatures of 8,639 prokaryotic strains. Growth temperature information is linked with taxonomy IDs, phylogenies, and genomic information. TEMPURA provides useful information to researchers working on biotechnological applications of extremophiles and their biomolecules as well as those performing fundamental studies on the physiological diversity of prokaryotes.

Short Communication
Short Communication
Short Communication
  • Shun Hashimoto, Kohki Goto, Pongdet Pyromyou, Pongpan Songwattana, Tee ...
    Type: Short Communication
    2020 Volume 35 Issue 3 ME20041
    Published: 2020
    Released: July 02, 2020
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    Supplementary material

    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.

Short Communication
Regular Paper
  • Yuto Chiba, Yuji Tomaru, Hiromori Shimabukuro, Kei Kimura, Miho Hirai, ...
    Type: Regular Paper
    2020 Volume 35 Issue 3 ME20016
    Published: 2020
    Released: June 17, 2020
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    Supplementary material

    Protists provide insights into the diversity and function of RNA viruses in marine systems. Among them, marine macroalgae are good targets for RNA virome analyses because they have a sufficient biomass in nature. However, RNA viruses in macroalgae have not yet been examined in detail, and only partial genome sequences have been reported for the majority of RNA viruses. Therefore, to obtain further insights into the distribution and diversity of RNA viruses associated with marine protists, we herein examined RNA viruses in macroalgae and a diatom. We report the putative complete genome sequences of six novel RNA viruses from two marine macroalgae and one diatom holobiont. Four viruses were not classified into established viral genera or families. Furthermore, a virus classified into Totiviridae showed a genome structure that has not yet been reported in this family. These results suggest that a number of distinct RNA viruses are widespread in a broad range of protists.

Regular Paper
  • Hiroaki Takebe, Kento Tominaga, Kentaro Fujiwara, Keigo Yamamoto, Taka ...
    Type: Regular Paper
    2020 Volume 35 Issue 3 ME20033
    Published: 2020
    Released: June 17, 2020
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    Supplementary material

    The phytoplanktonic production and prokaryotic consumption of organic matter significantly contribute to marine carbon cycling. Organic matter released from phytoplankton via three processes (exudation of living cells, cell disruption through grazing, and viral lysis) shows distinct chemical properties. We herein investigated the effects of phytoplanktonic whole-cell fractions (WF) (representing cell disruption by grazing) and extracellular fractions (EF) (representing exudates) prepared from Heterosigma akashiwo, a bloom-forming Raphidophyceae, on prokaryotic communities using culture-based experiments. We analyzed prokaryotic community changes for two weeks. The shift in cell abundance by both treatments showed similar dynamics, reaching the first peak (~4.1×106‍ ‍cells‍ ‍mL–1) on day 3 and second peak (~1.1×106‍ ‍cells‍ ‍mL–1) on day 13. We classified the sequences obtained into operational taxonomic units (OTUs). A Bray-Curtis dissimilarity analysis revealed that the OTU-level community structure changed distinctively with the two treatments. Ten and 13 OTUs were specifically abundant in the WF and EF treatments, respectively. These OTUs were assigned as heterotrophic bacteria mainly belonging to the Alteromonadales (Gammaproteobacteria) and Bacteroidetes clades and showed successive dynamics following the addition of organic matter. We also analyzed the dynamics of these OTUs in the ocean using publicly available metagenomic data from a natural coastal bloom in Monterey Bay, USA. At least two WF treatment OTUs showed co-occurrence with H. akashiwo, indicating that the blooms of H. akashiwo also affect these OTUs in the ocean. The present results strongly suggest that the thriving and dead cells of uninfected phytoplankton differentially influence the marine prokaryotic community.

Regular Paper
  • Sukanlaya Sarapat, Pongpan Songwattana, Aphakorn Longtonglang, Kamolch ...
    Type: Regular Paper
    2020 Volume 35 Issue 3 ME20024
    Published: 2020
    Released: June 16, 2020
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    Supplementary material

    Bacteria exhibiting 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, which inhibits the biosynthesis of ethylene in higher plants, promote plant growth through the degradation of ethylene precursors, such as ACC. ACC deaminase activity in Bradyrhizobium sp. SUTN9-2 was enhanced by genetic engineering and adaptive laboratory evolution (ALE)-based methods. The transferal of a plasmid containing the acdR and acdS genes into SUTN9-2 was genetic engineering improved, while the ALE method was performed based on the accumulation of an adaptive bacterial population that continuously grew under specified growth conditions for a long time. ACC deaminase enzyme activity was 8.9–fold higher in SUTN9-2:pMG103::acdRS and 1.4–fold higher in SUTN9-2 (ACCDadap) than in the wild-type strain. The effects of increased activity were examined in the host plant (Vigna radiata (L.) R.Wilczek SUT1). The improved strains enhanced nodulation in early stage of plant growth. SUTN9-2:pMG103::acdRS also maintained nitrogen fixation under water deficit conditions and increased the plant biomass after rehydration. Changes in nucleotides and amino acids in the AcdS protein of SUTN9-2 (ACCDadap) were then investigated. Some nucleotides predicted to be located in the ACC-binding site were mutated. These mutations may have increased ACC deaminase activity, which enhanced both symbiotic interactions and drought tolerance and promoted recovery after rehydration more than lower ACC deaminase activity. Adaptive evolution represents a promising strategy for further applications in the field.

Short Communication
Regular Paper
  • Tajul Islam, Øivind Larsen, Nils-Kåre Birkeland
    Type: Regular Paper
    2020 Volume 35 Issue 3 ME20044
    Published: 2020
    Released: June 12, 2020
    JOURNALS OPEN ACCESS FULL-TEXT HTML
    Supplementary material

    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”.

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