Phylogenetic analysis based on 16S rRNA gene sequences of deep-sea bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone

Nakayama, Akihiko; Saito, Rie; Matsuzaki, Mitsuhiro; Yano, Yutaka; Yoshida, Katsuhiko

doi:10.2323/jgam.51.385

Cited by 10 publications

(27 citation statements)

References 51 publications

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“…Deep-sea bacteria isolated from intestinal contents of deep-sea fishes (Coryphaenoides yaquinae, C. armatus, and Ilyophis sp.) retrieved from depths of 3,100 to 6,100 m in the Northwest Pacific Ocean (Nakayama et al, 1994(Nakayama et al, , 2005Yano,1996;Yano et al,1995Yano et al, , 1997 and Moritella sp. strain 5710 from a deep-sea sediment at a depth of 2,220 m (Hamamoto et al, 1995) which had been maintained as glycerol stock cultures at Ϫ80°C (Sambrook and Russell, 2001) were used.…”

Section: Methodsmentioning

confidence: 99%

“…To harvest cell pellets for extraction of chromosomal DNAs, all the strains shown in Table 1 were incubated as described previously (Nakayama et al, 1994(Nakayama et al, , 2005Yano,1996;Yano et al,1995Yano et al, , 1997. However, the growth pressure used for strains 5710 and T4609 was 0.1 MPa (1 atm).…”

Section: Methodsmentioning

confidence: 99%

“…Sequencing of the PCR products was determined by Macrogen, Inc. as described above. Four primers, (Yano, 1996), 2 (Nakayama et al, 2005), 3 (Yano et al, 1995), and 4 (Nakayama et al, 1994). a This column shows sample nos.…”

Section: Methodsmentioning

confidence: 99%

“…c Genus names were determined by a phylogenetic method based on 16S rRNA gene sequences (Nakayama et al, 2005). Urakawa et al, ShewanellaMDHEXN, ShewanellaMDHEXC, ShewanellaMDH476F (5Ј-CGTTCTGAGACCTTTATCGC-3Ј), and ShewanellaMDH457R (5Ј-GCGATAAAGGTC-TCAGAACG-3Ј) were used for sequencing the PCR products.…”

Section: Methodsmentioning

confidence: 99%

“…Although the fourteen strains used in this study and Moritella sp. strain 2D2 (Saito and Nakayama, 2004) are different strains based on 16S rRNA gene analysis (Nakayama et al, 2005;Saito and Nakayama, 2004), ten kinds of MDH amino acid sequences were obtained. The MDHs of strains 16F1 and 16H2 that were isolated from sample no.…”

Section: Deduced Mdh Amino Acid Sequences Of Deep-sea Bacterial Strainsmentioning

confidence: 99%

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Amino acid substitutions in malate dehydrogenases of piezophilic bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone

Saito

Kato

Nakayama

2006

J. Gen. Appl. Microbiol.

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IntroductionIn a previous paper (Saito and Nakayama, 2004), to elucidate the molecular basis for malate dehydrogenase (MDH) functions at high pressure and low temperature, we cloned, sequenced, and overexpressed the gene encoding MDH from the obligately piezophilic deep-sea bacterium Moritella sp. strain 2D2 isolated Key Words--amino acid substitutions; Coryphaenoides yaquinae; deep-sea piezophilic bacteria; intestinal contents of deep-sea fishes; malate dehydrogenase (MDH); Moritella sp.; Shewanella sp.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Deduced Mdh Amino Acid Sequences Of Deep-sea Bacterial Strainsmentioning

confidence: 99%

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Amino acid substitutions in malate dehydrogenases of piezophilic bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone

Saito

Kato

Nakayama

2006

J. Gen. Appl. Microbiol.

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The Family Moritellaceae

Urakawa

2014

The Prokaryotes

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Distinctive Gene and Protein Characteristics of Extremely PiezophilicColwellia

Peoples

Kyaw

Ugalde

et al. 2020

Preprint

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Background 24The deep ocean is characterized by low temperatures, high hydrostatic pressures, and low 25 concentrations of organic matter. While these conditions likely select for distinct genomic 26 characteristics within prokaryotes, the attributes facilitating adaptation to the deep ocean are 27 relatively unexplored. In this study, we compared the genomes of seven strains within the genus 28Colwellia, including some of the most piezophilic microbes known, to identify genomic features 29 that enable life in the deep sea. 30 31 Results 32 Significant differences were found to exist between piezophilic and non-piezophilic strains of 33 Colwellia. Piezophilic Colwellia have a more basic and hydrophobic proteome. The piezophilic 34 abyssal and hadal isolates have more genes involved in replication/recombination/repair, cell 35 wall/membrane biogenesis, and cell motility. The characteristics of respiration, pilus generation, 36 and membrane fluidity adjustment vary between the strains, with operons for a nuo 37 dehydrogenase and a tad pilus only present in the piezophiles. In contrast, the piezosensitive 38 members are unique in having the capacity for dissimilatory nitrite and TMAO reduction. A 39 number of genes exist only within deep-sea adapted species, such as those encoding d-alanine-d-40 alanine ligase for peptidoglycan formation, alanine dehydrogenase for NADH/NAD + 41 homeostasis, and archaeal methyltransferase for tRNA modification. Many of these piezophile-42 specific genes are in variable regions of the genome near genomic islands, transposases, and 43 toxin-antitoxin systems. 44 45 Conclusions 46We identified a number of adaptations that may facilitate deep-sea radiation in members of the 47 genus Colwellia, as well as in other piezophilic bacteria. An enrichment in more basic and 48 hydrophobic amino acids could help piezophiles stabilize and limit water intrusion into proteins 49 as a result of high pressure. Variations in genes associated with the membrane, including those 50 involved in unsaturated fatty acid production and respiration, indicate that membrane-based 51 adaptations are critical for coping with high pressure. The presence of many piezophile-specific 52 genes near genomic islands highlights that adaptation to the deep ocean may be facilitated by 53 horizontal gene transfer through transposases or other mobile elements. Some of these genes are 54 amenable to further study in genetically tractable piezophilic and piezotolerant deep-sea 55 microorganisms.

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Phylogenetic analysis based on 16S rRNA gene sequences of deep-sea bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone

Cited by 10 publications

References 51 publications

Amino acid substitutions in malate dehydrogenases of piezophilic bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone

Amino acid substitutions in malate dehydrogenases of piezophilic bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone

The Family Moritellaceae

Distinctive Gene and Protein Characteristics of Extremely PiezophilicColwellia

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