Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.margen.2023.101070

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

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File： fmicb-10-02435(2).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)  

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)  

DOI： 10.1099/mic.0.000205

Web of Science

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

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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