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Physiological and genomic characterization of Arcobacter anaerophilus IR-1 reveals new metabolic features in Epsilonproteobacteria.

Roalkvam I, Drønen K, Stokke R, Daae FL, Dahle H, Steen IH - Front Microbiol (2015)

Bottom Line: Electron acceptors utilized by most Epsilonproteobacteria, such as oxygen, nitrate, and sulfur, were also used by A. anaerophilus IR-1.The presence of genes for NAD(+)-reducing hydrogenase (hox) and dissimilatory iron reduction (fre) were unique for A. anaerophilus IR-1 among Epsilonproteobacteria.Altogether, our study shows that traditional characterization in combination with a modern genomics approach can expand our knowledge on free-living Arcobacter, and that this complementary approach could also provide invaluable knowledge about the physiology and metabolic pathways in other Epsilonproteobacteria from various environments.

View Article: PubMed Central - PubMed

Affiliation: Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway.

ABSTRACT
In this study we characterized and sequenced the genome of Arcobacter anaerophilus strain IR-1 isolated from enrichment cultures used in nitrate-amended corrosion experiments. A. anaerophilus IR-1 could grow lithoautotrophically on hydrogen and hydrogen sulfide and lithoheterothrophically on thiosulfate and elemental sulfur. In addition, the strain grew organoheterotrophically on yeast extract, peptone, and various organic acids. We show for the first time that Arcobacter could grow on the complex organic substrate tryptone and oxidize acetate with elemental sulfur as electron acceptor. Electron acceptors utilized by most Epsilonproteobacteria, such as oxygen, nitrate, and sulfur, were also used by A. anaerophilus IR-1. Strain IR-1 was also uniquely able to use iron citrate as electron acceptor. Comparative genomics of the Arcobacter strains A. butzleri RM4018, A. nitrofigilis CI and A. anaerophilus IR-1 revealed that the free-living strains had a wider metabolic range and more genes in common compared to the pathogen strain. The presence of genes for NAD(+)-reducing hydrogenase (hox) and dissimilatory iron reduction (fre) were unique for A. anaerophilus IR-1 among Epsilonproteobacteria. Finally, the new strain had an incomplete denitrification pathway where the end product was nitrite, which is different from other Arcobacter strains where the end product is ammonia. Altogether, our study shows that traditional characterization in combination with a modern genomics approach can expand our knowledge on free-living Arcobacter, and that this complementary approach could also provide invaluable knowledge about the physiology and metabolic pathways in other Epsilonproteobacteria from various environments.

No MeSH data available.


Related in: MedlinePlus

Comparative genomics. Unique genes from A. anaerophilus IR-1 (1008), A. nitrofigilis CI (1069), and A. butzleri RM4018 (837) annotated in RAST was extracted and compared.
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Figure 2: Comparative genomics. Unique genes from A. anaerophilus IR-1 (1008), A. nitrofigilis CI (1069), and A. butzleri RM4018 (837) annotated in RAST was extracted and compared.

Mentions: The genome of A. anaerophilus IR-1 was compared to the free-living A. nitrofigilis CI (DSM 7299; Pati et al., 2010) and the pathogen A. butzleri RM4018 (DSM 8739; Miller et al., 2007). Genomes of A. nitrofigilis (NC_014166) and A. butzleri (NC_009850) were obtained from NCBI and uploaded in RAST for comparison with A. anaerophilus IR-1. The genome analyses of A. anaerophilus (3.26 Mbp) resulted in 1432 annotated genes in RAST, while 1542, and 1244 annotated genes, respectively, were identified in A. nitrofigilis (3.22 Mbp) and A. butzleri (2.33 Mbp). Duplicate genes in each genome were removed from the dataset; leaving A. anaerophilus, A. nitrofigilis, and A. butzleri with 1008, 1069, and 837 unique genes, respectively; of which 633 genes were common for all three genomes (Figure 2). The genomes of free-living A. anaerophilus and A. nitrofigilis showed highest similarity, with 221 shared genes, while the pathogen A. butzleri had around 60 genes in common with the two free-living species (Figure 2). The genomes also comprised genes that were unique for each specimen: A. anaerophilus (93), A. nitrofigilis (157), and A. butzleri (85).


Physiological and genomic characterization of Arcobacter anaerophilus IR-1 reveals new metabolic features in Epsilonproteobacteria.

Roalkvam I, Drønen K, Stokke R, Daae FL, Dahle H, Steen IH - Front Microbiol (2015)

Comparative genomics. Unique genes from A. anaerophilus IR-1 (1008), A. nitrofigilis CI (1069), and A. butzleri RM4018 (837) annotated in RAST was extracted and compared.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4584990&req=5

Figure 2: Comparative genomics. Unique genes from A. anaerophilus IR-1 (1008), A. nitrofigilis CI (1069), and A. butzleri RM4018 (837) annotated in RAST was extracted and compared.
Mentions: The genome of A. anaerophilus IR-1 was compared to the free-living A. nitrofigilis CI (DSM 7299; Pati et al., 2010) and the pathogen A. butzleri RM4018 (DSM 8739; Miller et al., 2007). Genomes of A. nitrofigilis (NC_014166) and A. butzleri (NC_009850) were obtained from NCBI and uploaded in RAST for comparison with A. anaerophilus IR-1. The genome analyses of A. anaerophilus (3.26 Mbp) resulted in 1432 annotated genes in RAST, while 1542, and 1244 annotated genes, respectively, were identified in A. nitrofigilis (3.22 Mbp) and A. butzleri (2.33 Mbp). Duplicate genes in each genome were removed from the dataset; leaving A. anaerophilus, A. nitrofigilis, and A. butzleri with 1008, 1069, and 837 unique genes, respectively; of which 633 genes were common for all three genomes (Figure 2). The genomes of free-living A. anaerophilus and A. nitrofigilis showed highest similarity, with 221 shared genes, while the pathogen A. butzleri had around 60 genes in common with the two free-living species (Figure 2). The genomes also comprised genes that were unique for each specimen: A. anaerophilus (93), A. nitrofigilis (157), and A. butzleri (85).

Bottom Line: Electron acceptors utilized by most Epsilonproteobacteria, such as oxygen, nitrate, and sulfur, were also used by A. anaerophilus IR-1.The presence of genes for NAD(+)-reducing hydrogenase (hox) and dissimilatory iron reduction (fre) were unique for A. anaerophilus IR-1 among Epsilonproteobacteria.Altogether, our study shows that traditional characterization in combination with a modern genomics approach can expand our knowledge on free-living Arcobacter, and that this complementary approach could also provide invaluable knowledge about the physiology and metabolic pathways in other Epsilonproteobacteria from various environments.

View Article: PubMed Central - PubMed

Affiliation: Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway.

ABSTRACT
In this study we characterized and sequenced the genome of Arcobacter anaerophilus strain IR-1 isolated from enrichment cultures used in nitrate-amended corrosion experiments. A. anaerophilus IR-1 could grow lithoautotrophically on hydrogen and hydrogen sulfide and lithoheterothrophically on thiosulfate and elemental sulfur. In addition, the strain grew organoheterotrophically on yeast extract, peptone, and various organic acids. We show for the first time that Arcobacter could grow on the complex organic substrate tryptone and oxidize acetate with elemental sulfur as electron acceptor. Electron acceptors utilized by most Epsilonproteobacteria, such as oxygen, nitrate, and sulfur, were also used by A. anaerophilus IR-1. Strain IR-1 was also uniquely able to use iron citrate as electron acceptor. Comparative genomics of the Arcobacter strains A. butzleri RM4018, A. nitrofigilis CI and A. anaerophilus IR-1 revealed that the free-living strains had a wider metabolic range and more genes in common compared to the pathogen strain. The presence of genes for NAD(+)-reducing hydrogenase (hox) and dissimilatory iron reduction (fre) were unique for A. anaerophilus IR-1 among Epsilonproteobacteria. Finally, the new strain had an incomplete denitrification pathway where the end product was nitrite, which is different from other Arcobacter strains where the end product is ammonia. Altogether, our study shows that traditional characterization in combination with a modern genomics approach can expand our knowledge on free-living Arcobacter, and that this complementary approach could also provide invaluable knowledge about the physiology and metabolic pathways in other Epsilonproteobacteria from various environments.

No MeSH data available.


Related in: MedlinePlus