Complete Genome Sequence of an Anaerobic Benzene-Degrading Bacterium,
            <i>Azoarcus</i>
            sp. Strain DN11

Devanadera, Allan; Vejarano, Felipe; Zhai, Yu Feng; Suzuki-Minakuchi, Chiho; Ohtsubo, Yoshiyuki; Tsuda, Masashi; Kasai, Yuki; Takahata, Yoh; Okada, Kazunori; Nojiri, Hideaki

doi:10.1128/mra.01699-18

Cited by 7 publications

(4 citation statements)

References 11 publications

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“…toluolicum, and Ar. toluvorans, together with the “Azoarcus” strains CIB and DN11 [ 20 , 37 ]. Aromatoleum diolicum sits just outside Group 2, and the strain KH32C appears not to belong to either group, but is slightly closer to the Aromatoleum Group 2 than to Group 1.…”

Section: Resultsmentioning

confidence: 99%

Comparative Genomics Provides Insights into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera

Raittz

Pierri

Maluk

et al. 2021

Genes

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Among other attributes, the Betaproteobacterial genus Azoarcus has biotechnological importance for plant growth-promotion and remediation of petroleum waste-polluted water and soils. It comprises at least two phylogenetically distinct groups. The “plant-associated” group includes strains that are isolated from the rhizosphere or root interior of the C4 plant Kallar Grass, but also strains from soil and/or water; all are considered to be obligate aerobes and all are diazotrophic. The other group (now partly incorporated into the new genus Aromatoleum) comprises a diverse range of species and strains that live in water or soil that is contaminated with petroleum and/or aromatic compounds; all are facultative or obligate anaerobes. Some are diazotrophs. A comparative genome analysis of 32 genomes from 30 Azoarcus-Aromatoleum strains was performed in order to delineate generic boundaries more precisely than the single gene, 16S rRNA, that has been commonly used in bacterial taxonomy. The origin of diazotrophy in Azoarcus-Aromatoleum was also investigated by comparing full-length sequences of nif genes, and by physiological measurements of nitrogenase activity using the acetylene reduction assay. Based on average nucleotide identity (ANI) and whole genome analyses, three major groups could be discerned: (i) Azoarcus comprising Az. communis, Az. indigens and Az. olearius, and two unnamed species complexes, (ii) Aromatoleum Group 1 comprising Ar. anaerobium, Ar. aromaticum, Ar. bremense, and Ar. buckelii, and (iii) Aromatoleum Group 2 comprising Ar. diolicum, Ar. evansii, Ar. petrolei, Ar. toluclasticum, Ar. tolulyticum, Ar. toluolicum, and Ar. toluvorans. Single strain lineages such as Azoarcus sp. KH32C, Az. pumilus, and Az. taiwanensis were also revealed. Full length sequences of nif-cluster genes revealed two groups of diazotrophs in Azoarcus-Aromatoleum with nif being derived from Dechloromonas in Azoarcus sensu stricto (and two Thauera strains) and from Azospira in Aromatoleum Group 2. Diazotrophy was confirmed in several strains, and for the first time in Az. communis LMG5514, Azoarcus sp. TTM-91 and Ar. toluolicum TT. In terms of ecology, with the exception of a few plant-associated strains in Azoarcus (s.s.), across the group, most strains/species are found in soil and water (often contaminated with petroleum or related aromatic compounds), sewage sludge, and seawater. The possession of nar, nap, nir, nor, and nos genes by most Azoarcus-Aromatoleum strains suggests that they have the potential to derive energy through anaerobic nitrate respiration, so this ability cannot be usefully used as a phenotypic marker to distinguish genera. However, the possession of bzd genes indicating the ability to degrade benzoate anaerobically plus the type of diazotrophy (aerobic vs. anaerobic) could, after confirmation of their functionality, be considered as distinguishing phenotypes in any new generic delineations. The taxonomy of the Azoarcus-Aromatoleum group should be revisited; retaining the generic name Azoarcus for its entirety, or creating additional genera are both possible outcomes.

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Section: Resultsmentioning

confidence: 99%

Comparative Genomics Provides Insights into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera

Raittz

Pierri

Maluk

et al. 2021

Genes

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“…Other bacteria belonging to Betaproteobacteria , Azoarcus sp. strain KH32C [ 52 ], DN11 [ 53 ], and CIB [ 54 ] isolated from agricultural fields of paddy rice and soybean, gasoline-contaminated groundwater, and culture medium of another Azoarcus strain, respectively, have similar genes to the MHCR gene cluster in the MAG ISEC-1. Although these Azoarcus strains have not been identified as EAMs, previous studies have shown that Azoarcus members are the predominant components of electroactive microbial communities in several bioelectrochemical enrichments [ 55 , 56 ].…”

Section: Discussionmentioning

confidence: 99%

In situ electrosynthetic bacterial growth using electricity generated by a deep-sea hydrothermal vent

et al. 2022

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Electroautotrophic microorganisms have attracted great attention since they exhibit a new type of primary production. Here, in situ electrochemical cultivation was conducted using the naturally occurring electromotive forces at a deep-sea hydrothermal vent. The voltage and current generation originating from the resulting microbial activity was observed for 12 days of deployment, with fluctuation in response to tidal cycles. A novel bacterium belonging to the genus Thiomicrorhabdus dominated the microbial community specifically enriched on the cathode. Metagenomic analysis provided the draft genome of the bacterium and the gene repertoire indicated that the bacterium has the potential for thio-autotrophic growth, which is a typical physiological feature of the members of the genus, while the bacterium had a unique gene cluster encoding multi-heme cytochrome c proteins responsible for extracellular electron transfer. Herein, we propose this bacterium as a new species, specifically enriched during electricity generation, as ‘Candidatus Thiomicrorhabdus electrophagus’. This finding suggests the natural occurrence of electrosynthetic microbial populations using the geoelectricity in deep-sea hydrothermal environments.

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“…Successful isolates using nitrate as an electron acceptor and capable of benzene degradation include Azoarcus species isolated from gasoline-contaminated groundwater in Kumamoto, Japan (Kasai et al, 2006). The genome of the benzene-degrading Azoarcus strain DN11 was later published by Devanadera et al (2019). In addition, a strain of the species Bacillus cereus growing on benzene under nitrate-reducing was isolated by screening procedure from gasoline-contaminated soil (Dou et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Anaerobe isolation from denitrifying benzene-degrading enrichment culture and their capacity to mineralize benzene

Eziuzor

Vogt

2023

Preprint

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Only a few benzene-mineralizing anaerobes have been isolated to date. In an attempt using classical isolation techniques to isolate benzene-mineralizing pure cultures from a benzene-mineralizing nitrate-reducing microbial community, two putative isolates were gained under nitrate-reducing conditions spiked separately with acetate and benzene as sole sources of carbon and energy with media containing ammonium or without ammonium. Both putative isolates; Bz4 (with ammonium) and Bz7 (without ammonium) - mineralized 13C-labelled acetate under anoxic conditions at 3.3 and 2.7 micromole per day, respectively, revealed by analysis of evolved 13CO2. However, only Bz4 mineralized [13C6]-labelled benzene (0.298 micromole benzene mineralized per day) generated up to 960.2 plusmn 0.3 per mille ẟ13C-CO2 during 184 days while producing only slight amounts of nitrite (4.60 plusmn 0.004 micromole); no benzene was mineralized by Bz7 during 184 d, and no nitrite was detected. The 16S rRNA gene amplicon sequencing of the acetate-grown bacteria revealed consortia enriched in Nocardioides (8.9%), Pseudomonas (18.2%), Rhizobiaceae (21.0%), Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium (51.4%) for Bz4 and Simplicispira (96.7%) for Bz7. The gained Bz4 consortium that mineralized benzene under anoxic condition can be further purified and explored for their metabolic potentials.

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Complete Genome Sequence of an Anaerobic Benzene-Degrading Bacterium, Azoarcus sp. Strain DN11

Abstract: Here, we present the complete genome sequence of Azoarcus sp. strain DN11, a denitrifying bacterium capable of anaerobic benzene degradation.

Cited by 7 publications

References 11 publications

Comparative Genomics Provides Insights into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera

Comparative Genomics Provides Insights into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera

In situ electrosynthetic bacterial growth using electricity generated by a deep-sea hydrothermal vent

Anaerobe isolation from denitrifying benzene-degrading enrichment culture and their capacity to mineralize benzene

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