• Title, Summary, Keyword: Gammaproteobacteria

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Phylogenetic Analysis of Bacterial Diversity in the Marine Sponge, Asteropus simplex, Collected from Jeju Island (제주도에서 채집한 해양 해면, Asteropus simplex의 공생세균에 관한 계통학적 분석)

  • Jeong, In-Hye;Park, Jin-Sook
    • Korean Journal of Microbiology
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    • v.48 no.4
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    • pp.275-283
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    • 2012
  • Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Asteropus simplex collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and MA media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 94% similarities compared with known bacterial species, and the isolates belonged to five phyla, Alphaproteobacteria, Gammaproteobacteria Actinobacteria, Bacteroidetes, and Firmicutes, of which Gammaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge-derived total gDNA showed 12 DGGE bands, and their sequences showed more than 90% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven phyla, including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteira, Chloroflexi, and Nitrospira. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with A. simplex by both RFLP and DGGE methods, however, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture-independent method than in culture-dependent method.

Seasonal Differences of Bacterial Communities Associated with the Marine Sponge, Hymeniacidon sinapium (주황해변해면(Hymeniacidon sinapium) 공생세균 군집의 계절적 차이)

  • Jeong, Jong-Bin;Park, Jin-Sook
    • Korean Journal of Microbiology
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    • v.48 no.4
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    • pp.262-269
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    • 2012
  • Seasonal differences of the cultivable bacterial communities associated with the marine sponge, Hymeniacidon sinapium, between spring and summer were analyzed through the Amplified Ribosomal DNA Restriction Analysis (ARDRA). For the cultivation of the bacterial isolates, modified Zobell and MA media were used. The 16S rDNA of individual strains were amplified and fragmented by using two restriction enzymes, HaeIII and MspI. As a result, 23 ARDRA types from the spring sponge and 28 types from the summer sponge were obtained. The partial sequencing result of 1 to 3 selected strains from each types showed over 94% similarities with the known species from the public database. The bacterial communities from the sponge, captured on spring, contained 4 phyla: Actinobacteria, Alphaproteobacteria, Gammaproteobacteria, and Firmicutes. There were 5 phyla observed from the bacterial communities associated with the sponge, captured on summer: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Bacteroidetes. Gammaproteobacteria was predominant group in both spring and summer, accounted for 33.8% of total in spring and 67.4% in summer, showed increase pattern on summer. Because Firmicutes and Actinobacteria participated in 30.2% and 8.3% of the spring sponge while they represented only 6.9% and 0% of the summer sponge, both bacterial groups showed decrease drift on summer. Betaproteobacteria (4.7%) and Bacteroidetes (4.7%) were only observed on the sponge captured on summer. On the sponge, Hymeniacidon sinapium, more diverse bacterial communities were shown on summer than on spring, and even from the same sponge, there were seasonal differences.

Succession of bacterial community structure during the early stage of biofilm development in the Antarctic marine environment (남극 해양에서 생물막 생성 초기 단계의 세균 군집 구조 변화)

  • Lee, Yung Mi;Cho, Kyung Hee;Hwang, Kyuin;Kim, Eun Hye;Kim, Mincheol;Hong, Soon Gyu;Lee, Hong Kum
    • Korean Journal of Microbiology
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    • v.52 no.1
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    • pp.49-58
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    • 2016
  • Compared to planktonic bacterial populations, biofilms have distinct bacterial community structures and play important ecological roles in various aquatic environments. Despite their ecological importance in nature, bacterial community structure and its succession during biofilm development in the Antarctic marine environment have not been elucidated. In this study, the succession of bacterial community, particularly during the early stage of biofilm development, in the Antarctic marine environment was investigated by pyrosequencing of the 16S rRNA gene. Overall bacterial distribution in biofilms differed considerably from surrounding seawater. Relative abundance of Gammaproteobacteria and Bacteroidetes which accounted for 78.9-88.3% of bacterial community changed drastically during biofilm succession. Gammaproteobacteria became more abundant with proceeding succession (75.7% on day 4) and decreased to 46.1% on day 7. The relative abundance of Bacteroidetes showed opposite trend to Gammaproteobacteria, decreasing from the early days to the intermediate days and becoming more abundant in the later days. There were striking differences in the composition of major OTUs (${\geq}1%$) among samples during the early stages of biofilm formation. Gammaproteobacterial species increased until day 4, while members of Bacteroidetes, the most dominant group on day 1, decreased until day 4 and then increased again. Interestingly, Pseudoalteromonas prydzensis was predominant, accounting for up to 67.4% of the biofilm bacterial community and indicating its important roles in the biofilm development.

Marine Prokaryotic Diversity of the Deep Sea Waters at the Depth of 1500 m Off the Coast of the Ulleung Island in the East Sea (Korea) (울릉도 연안 수심 1500 m에 서식하는 해양미생물군집의 분포)

  • Kim, Mi-Kyung;Khang, Yongho
    • Korean Journal of Microbiology
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    • v.48 no.4
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    • pp.328-331
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    • 2012
  • Microbial diversity in the 1500 m depth sea waters off the coast of Ulleung island of the East Sea, Korea, was investigated. Genomic DNAs were extracted directly from the marine microbes filtered through ultramembrane filters. Pyrosequencing of 16S rDNAs of these microbes resulted in 13,029 reads, of which uncultured bacteria consisted of 54.1%, alphaproteobacteria 23.4%, and gammaproteobacteria 22.3%. Other classes such as flavobacteria, actinobacteria, and epsilonproteobacteria were distributed within 0.2% of total reads. Among the cultivable bacteria, it was found that Rhodobacteraceae family of alphaproteobacteria, Alteromonadaceae, Halomonadaceae, and Piscirickettsiaceae families of gammaproteobacteria were mostly distributed in the deep-sea waters.

Comparison of Bacterial Diversity in the Water Columns of Goseong Deep Seawaters (고성 심해에서 수심에 따른 해양미생물의 다양성 비교)

  • Khang, Yongho
    • Korean Journal of Microbiology
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    • v.49 no.3
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    • pp.282-285
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    • 2013
  • Microbial diversities in the 300 m and 500 m deep seawaters near Goseong, Gangwon Province (South Korea), were investigated. Pyrosequencing of 16S rRNA genes of marine microbes resulted in 19,474 reads from the 300 m deep seawaters, which consisted of Alphaproteobacteria (57.41%) and Gammaproteobacteria (38.85%), and 82,806 reads from the 500 m deep seawaters, which consisted of Gammaproteobacteria (99.64%) mostly. Rhodobacterales (57.31%) were dominant in the 300 m deep seawaters, but Alteromonadales (45.65%) and Oceanospirillales (34.61%) were dominant in the 500 m deep seawaters. On the bases of operational taxonomic units and diversity indexes (Shannon and Simpson), biodiversity of marine bacteria in the 500 m deep seawaters was shown to be higher than that in the 300 m deep seawaters.

A report on 33 unrecorded bacterial species of Korea isolated in 2014, belonging to the class Gammaproteobacteria

  • Lim, Yeonjung;Joung, Yochan;Nam, Gi Gyun;Jahng, Kwang-Yeop;Kim, Seung-Bum;Joh, Ki-seong;Cha, Chang-Jun;Seong, Chi-Nam;Bae, Jin-Woo;Im, Wan-Taek;Cho, Jang-Cheon
    • Journal of Species Research
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    • v.5 no.2
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    • pp.241-253
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    • 2016
  • In 2014, as a subset study to discover indigenous prokaryotic species in Korea, a total of 33 bacterial strains assigned to the class Gammaproteobacteria were isolated from diverse environmental samples collected from soil, tidal flat, freshwater, seawater, oil-contaminated soil, and guts of animal. From the high 16S rRNA gene sequence similarity (>98.5%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 33 species have been described in Korea; therefore, 1 strain of the Aeromonadales, 6 strains of the Alteromonadales, 3 strains of the Chromatiales, 5 strains of the Enterobacteriales, 4 strains of the Oceanospirillales, 11 strains of the Pseudomonadales, and 3 strains of the Xanthomonadales within the Gammaproteobacteria are described for unreported bacterial species in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, and isolation sources are also described in the species description section.

A Comparison of Bacterial Diversity Associated with the Sponge Spirastrella abata Depending on RFLP and DGGE (RFLP와 DGGE에 따른 해면 Spirastrella abata 공생세균의 다양성 비교)

  • Jeong, Eun-Ji;Im, Choon-Soo;Park, Jin-Sook
    • Korean Journal of Microbiology
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    • v.46 no.4
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    • pp.366-374
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    • 2010
  • Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Spirastrella abata. A total of 164 bacterial strains associated with the sponge were cultivated using Zobell and Natural sea salt media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 95% similarities compared with known bacterial species, and the isolates belonged to four phyla, Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteriodetes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge- derived total gDNA showed five major DGGE bands, and their sequences showed more than 96% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of four phyla, including Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Spirochetes, and Chloroflexi. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with S. abata by both RFLP and DGGE methods; however, overall bacterial community in the sponge differed depending on the analysis methods.

Comparative Analysis of the Community of Culturable Bacteria Associated with Sponges, Spirastrella abata and Spirastrella panis by 16S rDNA-RFLP (16S rDNA-RFLP에 의한 Spirastrella abata와 Spirastrella panis 해면에 서식하는 배양가능한 공생세균 군집의 비교)

  • Cho, Hyun-Hee;Park, Jin-Sook
    • Korean Journal of Microbiology
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    • v.45 no.2
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    • pp.155-162
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    • 2009
  • A cultivation-based approach was employed to compare the culturable bacterial diversity associated with two phylogenetically closely related marine sponges, Spirastrella abata and Spirastrella panis, which have geologically overlapping distribution patterns. The bacteria associated with sponge were cultivated using MA medium supplemented with 3% sponge extracts. Community structures of the culturable bacteria of the two sponge species were analyzed with PCR-RFLP (restriction fragment length polymorphism) based on 16S rDNA sequences. The RFLP fingerprinting of 16S rDNA digested with HaeIII and MspI, revealed 24 independent RFLP types, in which 1-5 representative strains from each type were partially sequenced. The sequence analysis showed >98.4% similarity to known bacterial species in public databases. Overall, the microbial populations of two sponges investigated were found to be the members of the classes; Alphaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria. The Alphaproteobacteria were predominant in the bacterial communities of the two sponges. Gammaproteobacteria represented 38.5% of bacterial community in S. abata. Whereas only 1.6% of this class was present in S. panis. Bacillus species were dominat in S. panis. Bacillus species were found to be 44.3% of bacterial species in S. panis, while they were only 9.7% in S. abata. It is interesting to note that Planococcus maritimus (8.1%, phylum Firmicutes) and Psychrobacter nivimaris (28.9%, phylum Gammaproteobacteria) were found only in S. abata. This result revealed that profiles of bacterial communities from the sponges with a close phylogenetic relationship were highly species-specific.

Bacterial diversity of the Marine Sponge, Halichondria panicea by ARDRA and DGGE (ARDRA와 DGGE를 이용한 Halichondria panicea 해면의 공생세균 다양성)

  • Park, Jin-Sook
    • Korean Journal of Microbiology
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    • v.51 no.4
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    • pp.398-406
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    • 2015
  • Culture-dependent ARDRA and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Halichondria panicea collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and Marine agar media. PCR amplicons of the 16S rRNA gene from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rRNA gene sequences derived from ARDRA patterns showed more than 96% similarities compared with known bacterial species, and the isolates belonged to four classes, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Firmicutes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rRNA genes amplified from the sponge-derived total gDNA showed 14 DGGE bands, and their sequences showed 100% similarities compared with the sequences available in GenBank. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven classes, including Alphaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteira, Bacteroidetes, Cyanobacteria, and Chloroflexi. According to both the ARDRA and DGGE methods, three classes, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, were commonly found in H. panicea. However, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture independent method than in culture-dependent method.

A report on 53 unrecorded bacteria species in Korea in the class Gammaproteobacteria

  • Kanjanasuntree, Rungravee;Cha, Chang-Jun;Cho, Jang-Cheon;Im, Wan-Taek;Kim, Myung Kyum;Jeon, Che-Ok;Joh, Kiseong;Kim, Seung-Bum;Seong, Chi-Nam;Yi, Hana;Lee, Soon Dong;Bae, Jin-Woo;Kim, Wonyong
    • Journal of Species Research
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    • v.8 no.4
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    • pp.319-336
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    • 2019
  • During an investigation of unrecorded prokaryotic species in Republic of Korea, a total of 53 bacterial strains belonging to the class Gammaproteobacteria were isolated from soil, seawater, tidal flats, rhizosphere, salt ponds, beach sand, urine, manure, sediment, and animal intestine (Russian grayling butterfly [Hipparchia autonoe], mouse [Mus musculus], and sea bass [Lateolabrax japonicus]). Strains were identified to species using the 16S rRNA gene sequence, showing high similarity (>98.7%) with the closest bacterial species and forming a robust clade in the neighbor-joining phylogenetic tree. The 53 strains of Gammaproteobacteria in this study have not been report previously in Korea. Therefore, we describe 27 genera of 16 families in 7 orders: 13 strains in the order Alteromonadales, 1 strain in the order Chromatiales, 11 strains in the order Enterobacterales, 7 strains in the order Oceanospirillales, 10 strains in the order Pseudomonadales, 8 strains in the order Vibrionales, and 3 strains in the order Xanthomonadales. Gram reaction, strain ID, isolation source, and morphological and basic biochemical characteristics are described for each species.