Complete genome sequence and comparative genome analysis of Alcanivorax sp. IO_7, a marine alkane-degrading bacterium isolated from hydrothermally-influenced deep seawater of southwest Indian ridge

Sinha, Rupesh Kumar; Krishnan, K. P.; Kurian, P. John

doi:10.1016/j.ygeno.2020.10.020

Cited by 15 publications

(10 citation statements)

References 36 publications

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“…The Alcanivorax genus is known to be widely distributed in marine environments, e.g., hydrothermal vent plumes ( Wang W. et al, 2020 ), hydrothermal fluids ( Bertrand et al, 2013 ), and crustal fluids ( Orcutt et al, 2020 ). They have previously been deemed to obligate marine hydrocarbon decomposers that can degrade a wide spectrum of straight and branched alkanes ( Yakimov et al, 1998 , 2019 ; Dong et al, 2021 ; Sinha et al, 2021 ). Recently, they have also been detected in Fe(II)-bearing minerals incubated at oceanic crust boreholes that are influenced by ambient water flow and crustal fluids ( Smith et al, 2011 ; Orcutt et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

“…The genus Alcanivorax belonging to the class Gammaproteobacteria was proposed by Yakimov et al (1998) and was gradually recovered and isolated from deep-sea hydrothermal fields ( Vetriani et al, 2005 ; Bertrand et al, 2013 ; Ramasamy et al, 2020 ; Dong et al, 2021 ; Sinha et al, 2021 ), such as sulfide minerals and hydrothermal vent plume. As far as we know, there are 16 valid types of species in this genus, 1 15 of which are isolated from deep sea sediments and seawater ( Dong et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…As far as we know, there are 16 valid types of species in this genus, 1 15 of which are isolated from deep sea sediments and seawater ( Dong et al, 2021 ). They have previously been recognized as obligate hydrocarbon decomposers that can utilize alkanes as carbon sources that facilitate the removal of alkanes from marine environments ( Yakimov et al, 1998 , 2019 ; Dong et al, 2021 ; Sinha et al, 2021 ). Recently, the strain 3B.1 was isolated from a long-term in situ enrichment basalt slice at the oceanic crust on Juan de Fuca Ridge and was first classified as an iron oxidizer in the genus Alcanivorax ( Smith et al, 2011 ).…”

Section: Introductionmentioning

confidence: 99%

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Potential autotrophic carbon-fixer and Fe(II)-oxidizer Alcanivorax sp. MM125-6 isolated from Wocan hydrothermal field

et al. 2022

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The genus Alcanivorax is common in various marine environments, including in hydrothermal fields. They were previously recognized as obligate hydrocarbonoclastic bacteria, but their potential for autotrophic carbon fixation and Fe(II)-oxidation remains largely elusive. In this study, an in situ enrichment experiment was performed using a hydrothermal massive sulfide slab deployed 300 m away from the Wocan hydrothermal vent. Furthermore, the biofilms on the surface of the slab were used as an inoculum, with hydrothermal massive sulfide powder from the same vent as an energy source, to enrich the potential iron oxidizer in the laboratory. Three dominant bacterial families, Alcanivoraceae, Pseudomonadaceae, and Rhizobiaceae, were enriched in the medium with hydrothermal massive sulfides. Subsequently, strain Alcanivorax sp. MM125-6 was isolated from the enrichment culture. It belongs to the genus Alcanivorax and is closely related to Alcanivorax profundimaris ST75FaO-1T (98.9% sequence similarity) indicated by a phylogenetic analysis based on 16S rRNA gene sequences. Autotrophic growth experiments on strain MM125-6 revealed that the cell concentrations were increased from an initial 7.5 × 105 cells/ml to 3.13 × 108 cells/ml after 10 days, and that the δ13CVPDB in the cell biomass was also increased from 234.25‰ on day 2 to gradually 345.66 ‰ on day 10. The gradient tube incubation showed that bands of iron oxides and cells formed approximately 1 and 1.5 cm, respectively, below the air-agarose medium interface. In addition, the SEM-EDS data demonstrated that it can also secrete acidic exopolysaccharides and adhere to the surface of sulfide minerals to oxidize Fe(II) with NaHCO3 as the sole carbon source, which accelerates hydrothermal massive sulfide dissolution. These results support the conclusion that strain MM125-6 is capable of autotrophic carbon fixation and Fe(II) oxidization chemoautotrophically. This study expands our understanding of the metabolic versatility of the Alcanivorax genus as well as their important role(s) in coupling hydrothermal massive sulfide weathering and iron and carbon cycles in hydrothermal fields.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Potential autotrophic carbon-fixer and Fe(II)-oxidizer Alcanivorax sp. MM125-6 isolated from Wocan hydrothermal field

et al. 2022

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“…Oil contamination enhances the exo-polysaccharide production of phytoplankton [ 55 ], and its amphiphilicity promoted the dissolution of oil in sea water [ 56 , 57 ]. These results may be the reasons that many alkane-degrading bacteria have been isolated from deep-sea environments [ 58 , 59 , 60 ]. Furthermore, some excellent characteristics were maintained by strain sw-1, and it was able to grow under conditions of 1%–3% NaCl and utilize alkanes at a low temperature of 15 °C ( Figure 6 c,e), indicating strain sw-1 is promising for application in high salt and low temperature environments.…”

Section: Discussionmentioning

confidence: 99%

Characterization and Transcriptome Analysis of a Long-Chain n-Alkane-Degrading Strain Acinetobacter pittii SW-1

Kong

Zhao

Gào

et al. 2021

IJERPH

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Strain sw-1, isolated from 7619-m seawater of the Mariana Trench, was identified as Acinetobacter pittii by 16S rRNA gene and whole-genome sequencing. A. pittii sw-1 was able to efficiently utilize long-chain n-alkanes (C18–C36), but not short- and medium-chain n-alkanes (C8–C16). The degradation rate of C20 was 91.25%, followed by C18, C22, C24, C32, and C36 with the degradation rates of 89.30%, 84.03%, 80.29%, 30.29%, and 13.37%, respectively. To investigate the degradation mechanisms of n-alkanes for this strain, the genome and the transcriptome analyses were performed. Four key alkane hydroxylase genes (alkB, almA, ladA1, and ladA2) were identified in the genome. Transcriptomes of strain sw-1 grown in C20 or CH3COONa (NaAc) as the sole carbon source were compared. The transcriptional levels of alkB and almA, respectively, increased 78.28- and 3.51-fold in C20 compared with NaAc, while ladA1 and ladA2 did not show obvious change. The expression levels of other genes involved in the synthesis of unsaturated fatty acids, permeases, membrane proteins, and sulfur metabolism were also upregulated, and they might be involved in n-alkane uptake. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) confirmed that alkB expression was significantly induced by C20, C24, and C32, and almA induction extent by C24 and C32 was higher than that with C20. Furthermore, ladA2 expression was only induced by C32, and ladA1 expression was not induced by any of n-alkanes. In addition, A. pittii sw-1 could grow with 0%–3% NaCl or 8 out of 10 kinds of the tested heavy metals and degrade n-alkanes at 15 °C. Taken together, these results provide comprehensive insights into the degradation of long-chain n-alkanes by Acinetobacter isolated from the deep ocean environment.

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“…Strains that phylogenetically close to EBL0706 in the 16S rRNA tree were selected for the comparative analysis. These strains were L. azotoformans ATCC 17025, L. azotoformans KA25, and L. sphaeroides 2.4.1 [ 32 , 33 ]. L. azotoformans ATCC 17025 is formerly L. sphaeroides ATCC 17025 in the NCBI database and Rhodobacter azotoformans ATCC 17025 in the American Type Culture Collection.…”

Section: Methodsmentioning

confidence: 99%

Comparative Genome Analysis Provides Molecular Evidence for Reclassification of the Photosynthetic Bacterium Rhodobacter sphaeroides EBL0706 as a Strain of Luteovulum azotoformans

Wang

Sha

et al. 2021

Microorganisms

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In this study, we conducted a genome-wide comparative analysis of a former Rhodobacter sphaeroides strain EBL0706, which is now recorded as Luteovulum sphaeroides EBL0706. The genome of EBL0706 was compared with that of Luteovulum azotoformans ATCC 17025, Luteovulum azotoformans KA25, and Luteovulum sphaeroides 2.4.1. The average nucleotide identity (ANI), tetra nucleotide signatures (Tetra), digital DNA–DNA hybridization (dDDH) values, comparative genome, and phylogenetic analysis proposed that EBL0706 is a strain of Luteovulum azotoformans. Functional annotations identified a total of 4034 protein-coding genes in the genome of EBL0706, including a complete photosynthetic gene cluster. This study provides genomic molecular verification for the strain EBL0706 to be reclassified to Luteovulum azotoformans.

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Complete genome sequence and comparative genome analysis of Alcanivorax sp. IO_7, a marine alkane-degrading bacterium isolated from hydrothermally-influenced deep seawater of southwest Indian ridge

Cited by 15 publications

References 36 publications

Potential autotrophic carbon-fixer and Fe(II)-oxidizer Alcanivorax sp. MM125-6 isolated from Wocan hydrothermal field

Potential autotrophic carbon-fixer and Fe(II)-oxidizer Alcanivorax sp. MM125-6 isolated from Wocan hydrothermal field

Characterization and Transcriptome Analysis of a Long-Chain n-Alkane-Degrading Strain Acinetobacter pittii SW-1

Comparative Genome Analysis Provides Molecular Evidence for Reclassification of the Photosynthetic Bacterium Rhodobacter sphaeroides EBL0706 as a Strain of Luteovulum azotoformans

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