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Genome sequence of a native-feather degrading extremely thermophilic Eubacterium, Fervidobacterium islandicum AW-1.

Lee YJ, Jeong H, Park GS, Kwak Y, Lee SJ, Lee SJ, Park MK, Kim JY, Kang HK, Shin JH, Lee DW - Stand Genomic Sci (2015)

Bottom Line: However, its genomic and phylogenetic analysis remains unclear.The genome consists of 2,359,755 bp, which encodes 2,184 protein-coding genes and 64 RNA-encoding genes.This may reveal insights into anaerobic metabolism for keratin degradation and also provide a biological option for poultry waste treatments.

View Article: PubMed Central - PubMed

Affiliation: School of Applied Biosciences, Kyungpook National University, Daegu, Korea.

ABSTRACT
Fervidobacterium islandicum AW-1 (KCTC 4680) is an extremely thermophilic anaerobe isolated from a hot spring in Indonesia. This bacterium could degrade native chicken feathers completely at 70 °C within 48 h, which is of potential importance on the basis of relevant environmental and agricultural issues in bioremediation and development of eco-friendly bioprocesses for the treatment of native feathers. However, its genomic and phylogenetic analysis remains unclear. Here, we report the high-quality draft genome sequence of an extremely thermophilic anaerobe, F. islandicum AW-1. The genome consists of 2,359,755 bp, which encodes 2,184 protein-coding genes and 64 RNA-encoding genes. This may reveal insights into anaerobic metabolism for keratin degradation and also provide a biological option for poultry waste treatments.

No MeSH data available.


Phylogenetic tree based on 16S rRNA gene sequences showing the relationship of F. islandicum AW-1 (in bold) to members of the family Thermotogaceae. The evolutionary history was inferred using the Neighbor-Joining method. The analysis involved 36 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 1,235 positions in the final dataset. Bootstrap values (percentages of 1,000 replications) are shown next to the branches. The sequences used in the analysis were obtained from the GenBank database. Bar, 2 nt substitution per 100 nt. Evolutionary analyses were conducted in MEGA6
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Fig2: Phylogenetic tree based on 16S rRNA gene sequences showing the relationship of F. islandicum AW-1 (in bold) to members of the family Thermotogaceae. The evolutionary history was inferred using the Neighbor-Joining method. The analysis involved 36 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 1,235 positions in the final dataset. Bootstrap values (percentages of 1,000 replications) are shown next to the branches. The sequences used in the analysis were obtained from the GenBank database. Bar, 2 nt substitution per 100 nt. Evolutionary analyses were conducted in MEGA6

Mentions: Out of 37 native chicken feather-degrading anaerobic strains grown at 70 °C enriched in EM-1 medium supplemented with native chicken feathers as a carbon source, we chose the strain AW-1 showing the highest keratinolytic activity [9]. Subsequently, we identified the strictly anaerobic, rod shaped (0.6 × 1 ~ 3.5 μm), motile, non-sporulating, Gram-negative extremophilic bacterium as Fervidobacterium islandicum AW-1 based on cell morphology, physiological characteristics, common DNA characteristics, 16S rRNA gene sequence, and cellular fatty acid profile as described previously (Fig. 1a, b) [9]. This bacterium belongs to the order of Thermotogales, of which all members are Gram-negative rod-shaped anaerobic extremophiles containing unique lipids [10]. After the first isolate F. nodosum had been reported, several Fervidobacterium strains including F. islandicum [11], F. gondwanense [12], F. pennivorans [13], F. changbaicum [14], and F. riparium [15] were isolated and characterized. All of them grew on glucose, mainly producing H2, CO2, and acetate, and also fermented a wide range of nutrients such as peptone, yeast extract, pyruvate, glucose, maltose, raffinose, and starch. Such organotrophs can also reduce S0 to H2S during the course of fermentation. In particular, F. islandicum AW-1 showed the highest keratinolytic activity, resulting in the complete degradation of native chicken feathers (8 g/L) within 48 h (Fig. 1b), and its optimal growth temperature and pH on the native feathers were 70 °C and pH 7.0, respectively [9]. Among the genus Fervidobacterium, F. islandicum AW-1 together with F. pennivorans have been found as native-feather degrading bacteria [9, 13]. Fig. 2 shows the phylogenetic neighborhood of F. islandicum AW-1 in a 16S rRNA gene sequence-based tree. This strain clusters closest to the genus of Fervidobacterium, the Thermotogales order. The 16S rRNA gene sequence (1456 bp) of F. islandicum AW-1 obtained from its genome sequence showed high levels of sequence similarity with members of the genus Fervidobacterium, such as F. changbaicum (99.3 %) [14], F. pennivorans (98.1 %) [13], F. islandicum (97.3 %) [11], F. riparium (96.1 %) [15], F. gondwanense (94.7 %) [12] and F. nodosum (95.4 %) [16] (Fig. 2). RAST analysis to rapidly call and annotate the genes of a complete or essentially complete prokaryotic genome [17] also suggested that F. nodosum Rt17-B1 was actually F. islandicum AW-1's closest neighbor. ANI analysis using BLAST [18] showed that, among the completely sequenced Fervidobacterium and Thermotoga species, F. pennivorans was closest to F. islandicum AW-1 (77.4 % sequence identity and 78.9 % alignment). As shown in Fig. 1, this strain was rod-shaped, occurring singly, in pairs or short chains with a single polar spheroid, a sheath-like outer membrane structure, a so called “toga”, which is a typical morphological feature belonging to the order of Thermotogales. Together with the previous phenotypic and biochemical characterization [9], our sequence analysis suggested that this AW-1 strain could be assigned as a native feathers degradable strain of F. islandicum. This was also supported by the previous DNA-DNA hybridization analysis with F. islandicum (92.4 %) [11] and F. pennivorans (42 %) [13].Fig. 1


Genome sequence of a native-feather degrading extremely thermophilic Eubacterium, Fervidobacterium islandicum AW-1.

Lee YJ, Jeong H, Park GS, Kwak Y, Lee SJ, Lee SJ, Park MK, Kim JY, Kang HK, Shin JH, Lee DW - Stand Genomic Sci (2015)

Phylogenetic tree based on 16S rRNA gene sequences showing the relationship of F. islandicum AW-1 (in bold) to members of the family Thermotogaceae. The evolutionary history was inferred using the Neighbor-Joining method. The analysis involved 36 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 1,235 positions in the final dataset. Bootstrap values (percentages of 1,000 replications) are shown next to the branches. The sequences used in the analysis were obtained from the GenBank database. Bar, 2 nt substitution per 100 nt. Evolutionary analyses were conducted in MEGA6
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4587914&req=5

Fig2: Phylogenetic tree based on 16S rRNA gene sequences showing the relationship of F. islandicum AW-1 (in bold) to members of the family Thermotogaceae. The evolutionary history was inferred using the Neighbor-Joining method. The analysis involved 36 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 1,235 positions in the final dataset. Bootstrap values (percentages of 1,000 replications) are shown next to the branches. The sequences used in the analysis were obtained from the GenBank database. Bar, 2 nt substitution per 100 nt. Evolutionary analyses were conducted in MEGA6
Mentions: Out of 37 native chicken feather-degrading anaerobic strains grown at 70 °C enriched in EM-1 medium supplemented with native chicken feathers as a carbon source, we chose the strain AW-1 showing the highest keratinolytic activity [9]. Subsequently, we identified the strictly anaerobic, rod shaped (0.6 × 1 ~ 3.5 μm), motile, non-sporulating, Gram-negative extremophilic bacterium as Fervidobacterium islandicum AW-1 based on cell morphology, physiological characteristics, common DNA characteristics, 16S rRNA gene sequence, and cellular fatty acid profile as described previously (Fig. 1a, b) [9]. This bacterium belongs to the order of Thermotogales, of which all members are Gram-negative rod-shaped anaerobic extremophiles containing unique lipids [10]. After the first isolate F. nodosum had been reported, several Fervidobacterium strains including F. islandicum [11], F. gondwanense [12], F. pennivorans [13], F. changbaicum [14], and F. riparium [15] were isolated and characterized. All of them grew on glucose, mainly producing H2, CO2, and acetate, and also fermented a wide range of nutrients such as peptone, yeast extract, pyruvate, glucose, maltose, raffinose, and starch. Such organotrophs can also reduce S0 to H2S during the course of fermentation. In particular, F. islandicum AW-1 showed the highest keratinolytic activity, resulting in the complete degradation of native chicken feathers (8 g/L) within 48 h (Fig. 1b), and its optimal growth temperature and pH on the native feathers were 70 °C and pH 7.0, respectively [9]. Among the genus Fervidobacterium, F. islandicum AW-1 together with F. pennivorans have been found as native-feather degrading bacteria [9, 13]. Fig. 2 shows the phylogenetic neighborhood of F. islandicum AW-1 in a 16S rRNA gene sequence-based tree. This strain clusters closest to the genus of Fervidobacterium, the Thermotogales order. The 16S rRNA gene sequence (1456 bp) of F. islandicum AW-1 obtained from its genome sequence showed high levels of sequence similarity with members of the genus Fervidobacterium, such as F. changbaicum (99.3 %) [14], F. pennivorans (98.1 %) [13], F. islandicum (97.3 %) [11], F. riparium (96.1 %) [15], F. gondwanense (94.7 %) [12] and F. nodosum (95.4 %) [16] (Fig. 2). RAST analysis to rapidly call and annotate the genes of a complete or essentially complete prokaryotic genome [17] also suggested that F. nodosum Rt17-B1 was actually F. islandicum AW-1's closest neighbor. ANI analysis using BLAST [18] showed that, among the completely sequenced Fervidobacterium and Thermotoga species, F. pennivorans was closest to F. islandicum AW-1 (77.4 % sequence identity and 78.9 % alignment). As shown in Fig. 1, this strain was rod-shaped, occurring singly, in pairs or short chains with a single polar spheroid, a sheath-like outer membrane structure, a so called “toga”, which is a typical morphological feature belonging to the order of Thermotogales. Together with the previous phenotypic and biochemical characterization [9], our sequence analysis suggested that this AW-1 strain could be assigned as a native feathers degradable strain of F. islandicum. This was also supported by the previous DNA-DNA hybridization analysis with F. islandicum (92.4 %) [11] and F. pennivorans (42 %) [13].Fig. 1

Bottom Line: However, its genomic and phylogenetic analysis remains unclear.The genome consists of 2,359,755 bp, which encodes 2,184 protein-coding genes and 64 RNA-encoding genes.This may reveal insights into anaerobic metabolism for keratin degradation and also provide a biological option for poultry waste treatments.

View Article: PubMed Central - PubMed

Affiliation: School of Applied Biosciences, Kyungpook National University, Daegu, Korea.

ABSTRACT
Fervidobacterium islandicum AW-1 (KCTC 4680) is an extremely thermophilic anaerobe isolated from a hot spring in Indonesia. This bacterium could degrade native chicken feathers completely at 70 °C within 48 h, which is of potential importance on the basis of relevant environmental and agricultural issues in bioremediation and development of eco-friendly bioprocesses for the treatment of native feathers. However, its genomic and phylogenetic analysis remains unclear. Here, we report the high-quality draft genome sequence of an extremely thermophilic anaerobe, F. islandicum AW-1. The genome consists of 2,359,755 bp, which encodes 2,184 protein-coding genes and 64 RNA-encoding genes. This may reveal insights into anaerobic metabolism for keratin degradation and also provide a biological option for poultry waste treatments.

No MeSH data available.