DOI： 10.1007/s10532-023-10014-9

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Society for Microbiology  

Comprehensive investigation of multiple genomic data sets from targeted microbial taxa deposited in databases may provide substantial information to predict metabolic capabilities and ecological roles in different environments. This study is the first report that details the functional profiling of Thalassospira spp. that have repeatedly been found in polycyclic aromatic hydrocarbon (PAH)-exposed marine bacterial communities by using genomic data from a new isolate, Thalassospira strain GO-4, and other strains in databases.

File： spectrum.03149-22-1.pdf

DOI： 10.1128/spectrum.03149-22

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.ibiod.2022.105500

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Society for Microbiology  

The genus Thalassospira has often been studied as a potential major contributing member of aromatic hydrocarbon-exposed microbial communities. Here, the complete genome sequence of a new isolate of Thalassospira , strain GO-4, was obtained and was confirmed to possess functional genes that are responsible for its metabolism of phthalic acid.

File： Kayama MRA 2022.pdf

DOI： 10.1128/mra.00532-22

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File： microorganisms-10-00510.pdf

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Society for Microbiology  

A bacterial chromosome that was naturally fused with the secondary chromosome, or “chromid,” and presented as an unexpectedly large single replicon was discovered in the genome of
<named-content content-type="genus-species">Cupriavidus necator</named-content>
strain KK10, a biotechnologically useful member of the family
<italic>Burkholderiaceae</italic>
. Although
<italic>Burkholderiaceae</italic>
is a well-documented group that conserves chromids in their genomes, this chromosomal fusion event has not been previously reported for this family.

File： Mori & Kanaly Microbiol Spectr 2022.pdf

DOI： 10.1128/spectrum.02225-21

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

File： 1-s2.0-S2772416621000188-main.pdf

DOI： 10.1016/j.hazadv.2021.100018

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Society for Microbiology  

<named-content content-type="genus-species">Cupriavidus necator</named-content>
KK10 has been investigated in azaarene and diesel fuel biodegradation studies and is capable of polyhydroxyalkanoate production. Its complete genome sequence revealed two closed circular sequences, the chromosome (6.68 Mb) and plasmid (1.67 Mb). The KK10 genome carries functional genes potentially responsible for azaarene biodegradation and polyhydroxyalkanoate (PHA) biosynthesis.

File： Mori MRA KK10.pdf

DOI： 10.1128/mra.00423-21

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.petrol.2021.108870

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Society for Microbiology  

<title>ABSTRACT</title>
<named-content content-type="genus-species">Sphingobium barthaii</named-content> KK22^T is a high-molecular-weight polycyclic aromatic hydrocarbon-degrading soil bacterium that has been investigated in biotransformation, microbial ecology, and DNA damage studies. The complete genome sequence of <named-content content-type="genus-species">S. barthaii</named-content> revealed four closed circular sequences, including two chromosomes, a megaplasmid, and a smaller plasmid, by hybrid assembly using short- and long-read sequencing technologies.

File： Mori & Kanaly 2021 MRA.pdf

DOI： 10.1128/mra.01250-20

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Society for Microbiology  

A soil bacterial consortium that was grown on diesel fuel and consisted of more than 10 members from different genera was maintained through repetitive sub-culturing and was utilized as a practical model to investigate a bacterial community that was continuously exposed to petroleum hydrocarbons. Through metagenomics analyses, consortium member isolation, growth assays and metabolite identification which supported the linkage of genomic data and functionality, two pioneering genera, <italic>Sphingobium</italic> and <italic>Pseudomonas</italic>, whose catabolic capabilities were differentiated, were found to be responsible for the creation of specialized ecological niches that were apparently occupied by other bacterial members for survival within the consortium. Co-existing genera, <italic>Achromobacter</italic> and <italic>Cupriavidus</italic>, maintained their existence in the consortium through metabolic dependencies by utilizing hydrocarbon biotransformation products of pioneer metabolism which was confirmed through growth tests and identification of biotransformation products of the isolated strains. Pioneering <italic>Sphingobium</italic> and <italic>Pseudomona</italic>s spp. utilized relatively water insoluble hydrocarbon parent compounds and facilitated the development of a consortium community structure that resulted in creation of niches in response to diesel fuel exposure which were created through the production of more water soluble biotransformation products available to co-colonizers. That these and other organisms were still present in the consortium after multiple transfers spanning 15 years, provided evidence for these ecological niches. Member survival through occupation of these niches led to robustness of each group within the multispecies bacterial community. Overall, these results contribute to our understanding of the complex ecological relationships that may evolve during prokaryotic hydrocarbon pollutant biodegradation.


<bold>Importance</bold> There are few metagenome studies that have explored soil consortia maintained on a complex hydrocarbon substrate after the community interrelationships were formed. A soil bacterial consortium maintained on diesel fuel was utilized as a practical model to investigate bacterial community relationships through metagenomics analyses, consortium member isolation, growth assays and metabolite identification which supported the linkage of genomic data and functionality. Two pioneering genera were responsible for biodegradation of aromatics and alkanes by initiating biotransformation and thereby created specialized niches that were populated by other members. A model that represents these relationships was constructed which contributes to our understanding of the complex ecological relationships that evolve during prokaryotic hydrocarbon pollutant biodegradation.

DOI： 10.1128/aem.02268-20

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Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

DOI： 10.1007/s10230-020-00711-9

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Other Link： http://link.springer.com/article/10.1007/s10230-020-00711-9/fulltext.html

Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.ibiod.2020.104993

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File： fmicb-10-02435(2).pdf

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File： mSystems-2019-Chen-e00410-19.full(1).pdf

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File： fmicb-10-00297(1).pdf

DOI： 10.3389/fmicb.2019.00297

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

Chemosynthetic Fe-oxidizing communities are common at diffuse-flow hydrothermal vents throughout the world's oceans. The foundational members of these communities are the Zetaproteobacteria, a class of Proteobacteria that is primarily associated with ecosystems fueled by ferrous iron, Fe(II). We report here the discovery of two new isolates of Zetaproteobacteria isolated from the Mid-Atlantic Ridge (TAG-1), and the Mariana back-arc (SV-108), that are unique in that they can utilize either Fe(II) or molecular hydrogen (H-2) as sole electron donor and oxygen as terminal electron acceptor for growth. Both strains precipitated Fe-oxyhydroxides as amorphous particulates. The cell doubling time on H-2 vs Fe(II) for TAG-1 was 14.1 vs 21.8 h, and for SV-108 it was 16.3 vs 20 h, and it appeared both strains could use either H-2 or Fe(II) simultaneously. The strains were close relatives, based on genomic analysis, and both possessed genes for the uptake NiFe-hydrogenase required for growth on H-2. These two strains belong to Zetaproteobacteria operational taxonomic unit 9 (ZetaOTU9). A meta-analysis of public databases found ZetaOTU9 was only associated with Fe(II)-rich habitats, and not in other environments where known H-2-oxidizers exist. These results expand the metabolic repertoire of the Zetaproteobacteria, yet confirm that Fe(II) metabolism is the primary driver of their physiology and ecology.

File： ismej2017132a(1).pdf

DOI： 10.1038/ismej.2017.132

Web of Science

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Language：English   Publishing type：Research paper (scientific journal)  

File： ismej2016186a.pdf

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：MICROBIOLOGY SOC  

A new acidophilic iron-oxidizing strain (C25) belonging to the novel genus Acidithrix was isolated from pelagic iron-rich aggregates ('iron snow') collected below the redoxcline of an acidic lignite mine lake. Strain C25 catalysed the oxidation of ferrous iron [Fe(II)] under oxic conditions at 25 degrees C at a rate of 3.8 mM Fe(II) day(-1) in synthetic medium and 3.0 mM Fe(II) day(-1) in sterilized lake water in the presence of yeast extract, producing the rust-coloured, poorly crystalline mineral schwertmannite [Fe(III) oxyhydroxylsulfate]. During growth, rod-shaped cells of strain C25 formed long filaments, and then aggregated and degraded into shorter fragments, building large cell mineral aggregates in the late stationary phase. Scanning electron microscopy analysis of cells during the early growth phase revealed that Fe(III)-minerals were formed as single needles on the cell surface, whereas the typical pincushion-like schwertmannite was observed during later growth phases at junctions between the cells, leaving major parts of the cell not encrusted. This directed mechanism of biomineralization at specific locations on the cell surface has not been reported from other acidophilic iron-oxidizing bacteria. Strain C25 was also capable of reducing Fe(III) under micro-oxic conditions which led to a dissolution of the Fe(III)-minerals. Thus, strain C25 appeared to have ecological relevance for both the formation and transformation of the pelagic iron-rich aggregates at oxic/anoxic transition zones in the acidic lignite mine lake.

DOI： 10.1099/mic.0.000205

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：COPERNICUS GESELLSCHAFT MBH  

Filamentous macroscopic algae were observed in slightly acidic to circumneutral (pH 5.9-6.5), metal-rich stream water that leaked out from a former uranium mining district (Ronneburg, Germany). These algae differed in color and morphology and were encrusted with Fedeposits. To elucidate their potential interaction with Fe(II)-oxidizing bacteria (FeOB), we collected algal samples at three time points during summer 2013 and studied the algae-bacteria-mineral compositions via confocal laser scanning microscopy (CLSM), scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectra, and a 16S and 18S rRNA gene-based bacterial and algae community analysis. Surprisingly, sequencing analysis of 18S rRNA gene regions of green and brown algae revealed high homologies with the freshwater algae Tribonema (99.9-100 %). CLSM imaging indicated a loss of active chloroplasts in the algae cells, which may be responsible for the change in color in Tribonema. Fe(III)-precipitates on algal cells identified as ferrihydrite and schwertmannite by FTIR were associated with microbes and extracellular polymeric substances (EPS)-like glycoconjugates. SEM imaging revealed that while the green algae were fully encrusted with Fe-precipitates, the brown algae often exhibited discontinuous series of precipitates. This pattern was likely due to the intercalary growth of algal filaments which allowed them to avoid detrimental encrustation. 16S rRNA gene-targeted studies revealed that Gallionella-related FeOB dominated the bacterial RNA and DNA communities (70-97 and 63-96 %, respectively), suggesting their capacity to compete with the abiotic Feoxidation under the putative oxygen-saturated conditions that occur in association with photosynthetic algae. Quantitative PCR (polymerase chain reaction) revealed even higher Gallionella-related 16S rRNA gene copy numbers on the surface of green algae compared to the brown algae. The latter harbored a higher microbial diversity, including some putative predators of algae. A loss of chloroplasts in the brown algae could have led to lower photosynthetic activities and reduced EPS production, which is known to affect predator colonization. Collectively, our results suggest the coexistence of oxygen-generating algae Tribonema sp. and strictly microaerophilic neutrophilic FeOB in a heavy metal-rich environment.

File： bg-12-5277-2015.pdf

DOI： 10.5194/bg-12-5277-2015

Web of Science

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Presentation type：Oral presentation (general)  

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Language：English   Presentation type：Poster presentation  

File： ISME 2018 poster JM_final.pdf

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Presentation type：Oral presentation (general)  

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Presentation type：Poster presentation  

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Presentation type：Poster presentation  

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Presentation type：Poster presentation  

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Language：English   Presentation type：Oral presentation (general)  

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Language：English   Presentation type：Poster presentation  

File： Mori ISME16 Final.pdf

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Language：English   Presentation type：Poster presentation  

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Presentation type：Poster presentation  

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Presentation type：Oral presentation (general)  

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Language：English   Presentation type：Poster presentation  

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Presentation type：Oral presentation (general)  

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Presentation type：Poster presentation  

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