1
|
Liu R, Xu H, Zhao S, Dong C, Li J, Wei G, Li G, Gong L, Yan P, Shao Z. Polyethylene terephthalate (PET)-degrading bacteria in the pelagic deep-sea sediments of the Pacific Ocean. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 352:124131. [PMID: 38734049 DOI: 10.1016/j.envpol.2024.124131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Polyethylene terephthalate (PET) plastic pollution is widely found in deep-sea sediments. Despite being an international environmental issue, it remains unclear whether PET can be degraded through bioremediation in the deep sea. Pelagic sediments obtained from 19 sites across a wide geographic range in the Pacific Ocean were used to screen for bacteria with PET degrading potential. Bacterial consortia that could grow on PET as the sole carbon and energy source were found in 10 of the 19 sites. These bacterial consortia showed PET removal rate of 1.8%-16.2% within two months, which was further confirmed by the decrease of carbonyl and aliphatic hydrocarbon groups using attenuated total reflectance-Fourier-transform infrared analysis (ATR-FTIR). Analysis of microbial diversity revealed that Alcanivorax and Pseudomonas were predominant in all 10 PET degrading consortia. Meanwhile, Thalassospira, Nitratireductor, Nocardioides, Muricauda, and Owenweeksia were also found to possess PET degradation potential. Metabolomic analysis showed that Alcanivorax sp. A02-7 and Pseudomonas sp. A09-2 could turn PET into mono-(2-hydroxyethyl) terephthalate (MHET) even in situ stimulation (40 MPa, 10 °C) conditions. These findings widen the currently knowledge of deep-sea PET biodegrading process with bacteria isolates and degrading mechanisms, and indicating that the marine environment is a source of biotechnologically promising bacterial isolates and enzymes.
Collapse
Affiliation(s)
- Renju Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; School of Environmental Science, Harbin Institute of Technology, Harbin 150090, China
| | - Haiming Xu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Sufang Zhao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Jianyang Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Guangshan Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Guangyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Peisheng Yan
- School of Environmental Science, Harbin Institute of Technology, Harbin 150090, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; School of Environmental Science, Harbin Institute of Technology, Harbin 150090, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), China.
| |
Collapse
|
2
|
Li Y, Wang X, Deng T, Zheng G, Tu Z, Zhang L, Yuan L. Flavobacterium poyangense sp. nov., an ammonifying bacterium isolated from a freshwater lake. Int J Syst Evol Microbiol 2024; 74. [PMID: 38865183 DOI: 10.1099/ijsem.0.006416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024] Open
Abstract
A Gram-stain-negative, aerobic, non-spore-forming, nonmotile, rod-shaped, and yellow-pigmented bacterium, designated strain JXAS1T, was isolated from a freshwater sample collected from Poyang Lake in China. Phylogenetic analysis based on 16S rRNA gene sequence revealed that the isolate belonged to the genus Flavobacterium, being closest to Flavobacterium pectinovorum DSM 6368T (98.61 %). The genome size of strain JXAS1T was 4.66 Mb with DNA G+C content 35.7 mol%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain JXAS1T and its closest relatives were below the threshold values of 95 and 70 %, respectively. The strain contained menaquinone 6 (MK-6) as the predominant menaquinone and the major polar lipids were phosphatidylethanolamine, one unidentified glycolipid, and one unidentified polar lipid. The major fatty acids (>5 %) were iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C15 : 0, iso-C17 : 0 3OH, iso-C15 : 0 3OH, and summed feature 9 (iso-C17 : 1 ω9c and/or 10-methyl C16 : 0). Based on phylogenetic, genotypic, and phenotypic evidence, the isolated strain represents a new species in the genus Flavobacterium, and the name Flavobacterium poyangense is proposed. The type strain is JXAS1T (=GDMCC 1.1378T=KCTC 62719T).
Collapse
Affiliation(s)
- Ya Li
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
| | - Xiyang Wang
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
| | - Tao Deng
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
| | - Guohua Zheng
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
| | - Zuxin Tu
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
| | - Lili Zhang
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
| | - Lin Yuan
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, PR China
| |
Collapse
|
3
|
Raman J, Ko YJ, Kim JS, Kim DH, Kim SJ. Overproduction of Xanthophyll Pigment in Flavobacterium sp. JSWR-1 under Optimized Culture Conditions. J Microbiol Biotechnol 2024; 34:710-724. [PMID: 38044702 PMCID: PMC11016774 DOI: 10.4014/jmb.2310.10034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023]
Abstract
Flavobacterium can synthesize xanthophyll, particularly the pigment zeaxanthin, which has significant economic value in nutrition and pharmaceuticals. Recently, the use of carotenoid biosynthesis by bacteria and yeast fermentation technology has shown to be very efficient and offers significant advantages in large-scale production, cost-effectiveness, and safety. In the present study, JSWR-1 strain capable of producing xanthophyll pigment was isolated from a freshwater reservoir in Wanju-gun, Republic of Korea. Based on the morphological, physiological, and molecular characteristics, JSWR-1 classified as belonging to the Flavobacterium species. The bacterium is strictly aerobic, Gram-negative, rod-shaped, and psychrophilic. The completed genome sequence of the strain Flavobacterium sp. JSWR-1 is predicted to be a single circular 3,425,829-bp chromosome with a G+C content of 35.2% and 2,941 protein-coding genes. The optimization of carotenoid production was achieved by small-scale cultivation, resulting in zeaxanthin being identified as the predominant carotenoid pigment. The enhancement of zeaxanthin biosynthesis by applying different light-irradiation, variations in pH and temperature, and adding carbon and nitrogen supplies to the growth medium. A significant increase in intracellular zeaxanthin concentrations was also recorded during fed-batch fermentation achieving a maximum of 16.69 ± 0.71 mg/l, corresponding to a product yield of 4.05 ± 0.15 mg zeaxanthin per gram cell dry weight. Batch and fed-batch culture extracts exhibit significant antioxidant activity. The results demonstrated that the JSWR-1 strain can potentially serve as a source for zeaxanthin biosynthesis.
Collapse
Affiliation(s)
- Jegadeesh Raman
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Young-Joon Ko
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jeong-Seon Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Da-Hye Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| |
Collapse
|
4
|
Kim J, Cha IT, Lee KE, Son YK, Yu J, Seol D. Characteristics and adaptability of Flavobacterium panici BSSL-CR3 in tidal flat revealed by comparative genomic and enzymatic analysis. Arch Microbiol 2022; 205:22. [PMID: 36495352 DOI: 10.1007/s00203-022-03359-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/22/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
Tidal flat microbes play an important ecological role by removing organic pollutants and providing an energy source. However, bacteria isolated from tidal flats and their genomes have been scarcely reported, making it difficult to elucidate which genes and pathways are potentially involved in the above roles. In this study, strain BSSL-CR3, the third reported species among the tidal flat Flavobacterium was analyzed using whole-genome sequencing to investigate its adaptability and functionality in tidal flats. BSSL-CR3 is comprised of a circular chromosome of 5,972,859 bp with a GC content of 33.84%. Genome annotation and API ZYM results showed that BSSL-CR3 has a variety of secondary metabolic gene clusters and enzyme activities including α-galactosidase. BSSL-CR3 had more proteins with a low isoelectric point (pI) than terrestrial Flavobacterium strains, and several genes related to osmotic regulation were found in the genomic island (GI). Comparative genomic analysis with other tidal flat bacteria also revealed that BSSL-CR3 had the largest number of genes encoding Carbohydrate Active EnZymes (CAZymes) which are related to algae degradation. This study will provide insight into the adaptability of BSSL-CR3 to the tidal flats and contribute to facilitating future comparative analysis of bacteria in tidal flats.
Collapse
Affiliation(s)
- Jina Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
| | - In-Tae Cha
- Microorganism Resources Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Youn Kyoung Son
- Microorganism Resources Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Jaewoong Yu
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea.
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea.
| |
Collapse
|
5
|
Lyu L, Li J, Chen Y, Mai Z, Wang L, Li Q, Zhang S. Degradation potential of alkanes by diverse oil-degrading bacteria from deep-sea sediments of Haima cold seep areas, South China Sea. Front Microbiol 2022; 13:920067. [PMID: 36338091 PMCID: PMC9626528 DOI: 10.3389/fmicb.2022.920067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Marine oil spills are a significant concern worldwide, destroying the ecological environment and threatening the survival of marine life. Various oil-degrading bacteria have been widely reported in marine environments in response to marine oil pollution. However, little information is known about culturable oil-degrading bacteria in cold seep of the deep-sea environments, which are rich in hydrocarbons. This study enriched five oil-degrading consortia from sediments collected from the Haima cold seep areas of the South China Sea. Parvibaculum, Erythrobacter, Acinetobacter, Alcanivorax, Pseudomonas, Marinobacter, Halomonas, and Idiomarina were the dominant genera. Further results of bacterial growth and degradation ability tests indicated seven efficient alkane-degrading bacteria belonging to Acinetobacter, Alcanivorax, Kangiella, Limimaricola, Marinobacter, Flavobacterium, and Paracoccus, whose degradation rates were higher in crude oil (70.3–78.0%) than that in diesel oil (62.7–66.3%). From the view of carbon chain length, alkane degradation rates were medium chains > long chains > short chains. In addition, Kangiella aquimarina F7, Acinetobacter venetianus F1, Limimaricola variabilis F8, Marinobacter nauticus J5, Flavobacterium sediminis N3, and Paracoccus sediminilitoris N6 were first identified as oil-degrading bacteria from deep-sea environments. This study will provide insight into the bacterial community structures and oil-degrading bacterial diversity in the Haima cold seep areas, South China Sea, and offer bacterial resources to oil bioremediation applications.
Collapse
Affiliation(s)
- Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Lina Lyu,
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- *Correspondence: Si Zhang,
| |
Collapse
|
6
|
Zhou J, Kong Y, Zhao W, Wei G, Wang Q, Ma L, Wang T, Shu F, Sha W. Comparison of bacterial and archaeal communities in two fertilizer doses and soil compartments under continuous cultivation system of garlic. PLoS One 2021; 16:e0250571. [PMID: 33989289 PMCID: PMC8121308 DOI: 10.1371/journal.pone.0250571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 04/12/2021] [Indexed: 01/10/2023] Open
Abstract
Soil microbial communities are affected by interactions between agricultural management (e.g., fertilizer) and soil compartment, but few studies have considered combinations of these factors. We compared the microbial abundance, diversity and community structure in two fertilizer dose (high vs. low NPK) and soil compartment (rhizosphere vs. bulk soils) under 6-year fertilization regimes in a continuous garlic cropping system in China. The soil contents of NO3- and available K were significantly higher in bulk soil in the high-NPK. The 16S rRNA gene-based bacterial and archaeal abundances were positively affected by both the fertilizer dose and soil compartment, and were higher in the high-NPK fertilization and rhizosphere samples. High-NPK fertilization increased the Shannon index and decreased bacterial and archaeal richness, whereas the evenness was marginally positively affected by both the fertilizer dose and soil compartment. Soil compartment exerted a greater effect on the bacterial and archaeal community structure than did the fertilization dose, as demonstrated by both the nonmetric multidimensional scaling and redundancy analysis results. We found that rhizosphere effects significantly distinguished 12 dominant classes of bacterial and archaeal communities, whereas the fertilizer dose significantly identified four dominant classes. In particular, a Linear Effect Size analysis showed that some taxa, including Alphaproteobacteria, Rhizobiales, Xanthomonadaceae and Flavobacterium, were enriched in the garlic rhizosphere of the high-NPK fertilizer samples. Overall, the fertilizer dose interacted with soil compartment to shape the bacterial and archaeal community composition, abundance, and biodiversity in the garlic rhizosphere. These results provide an important basis for further understanding adaptive garlic-microbe feedback, reframing roots as a significant moderating influence in agricultural management and shaping the microbial community.
Collapse
Affiliation(s)
- Jing Zhou
- School of Life Sciences, Qufu Normal University, Jining, PR China
| | - Yong Kong
- School of Life Sciences, Qufu Normal University, Jining, PR China
| | - Wangfeng Zhao
- College of Biological and Environmental Engineering, Binzhou University, Binzhou, PR China
| | - Guangshan Wei
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC) / School of Marine Sciences, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources of the PR China, Third Institute of Oceanography, Xiamen, China
| | - Qingfeng Wang
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Longchuan Ma
- Shandong Engineering and Technology Research Center for Garlic, Jining, PR China
| | - Taotao Wang
- Shandong Engineering and Technology Research Center for Garlic, Jining, PR China
| | - Fengyue Shu
- School of Life Sciences, Qufu Normal University, Jining, PR China
| | - Weilai Sha
- School of Life Sciences, Qufu Normal University, Jining, PR China
| |
Collapse
|
7
|
Flavobacterium alkalisoli sp. nov., isolated from rhizosphere soil of Suaeda salsa. Int J Syst Evol Microbiol 2020; 70:3888-3898. [DOI: 10.1099/ijsem.0.004255] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A Gram-negative, strictly aerobic, gliding motility, none-spore forming, yellow, rods bacterial strain, designated XS-5T, was isolated from rhizosphere soil of Suaeda salsa, in Tumd Right Banner, Inner Mongolia, PR China. A phylogenetic tree based on the 16S rRNA gene sequences and the phylogenomic tree both showed that strain XS-5T clustered with
Flavobacterium beibuense
F44-8T (shared 97.2 % of 16S rRNA gene similarity) and
Flavobacterium rakeshii
FCS-5T (97.6 %), and shared <96.0 % of 16S rRNA gene similarities with all other type strains. Strain XS-5T contained MK-6 as the major respiratory quinone. Its major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified lipid; and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0, iso-C15 : 0 3-OH, Summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1
ω7c), and Summed feature 9 (iso-C17 : 1
ω9c and/or C16 : 0 10-methyl). The genome consisted of a 3 985 855 bp circular chromosome, with a G+C content of 37.9 mol%, predicting 3616 coding sequences genes, 45 tRNA genes and three rRNA operons. The average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values of strain XS-5T to
F. beibuense
F44-8T and
F. rakeshii
FCS-5T were 79.2 and 79.2 %, 81.7 and 81.6 %, 22.3 and 22.2 %, respectively. The results of phylogenetic, physiological and biochemical tests allowed the discrimination of strain XS-5T from its phylogenetic relatives. Flavobacterium alkalisoli sp. nov. is therefore proposed with strain XS-5T (=CGMCC 1.17077T=KCTC 72459T) as the type strain.
Collapse
|
8
|
Kumru S, Tekedar HC, Blom J, Lawrence ML, Karsi A. Genomic diversity in flavobacterial pathogens of aquatic origin. Microb Pathog 2020; 142:104053. [PMID: 32058022 DOI: 10.1016/j.micpath.2020.104053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 12/15/2022]
Abstract
Flavobacterium species are considered important fish pathogens in wild and cultured fish throughout the world. They can cause acute, subacute, and chronic infections, which are mainly characterized by gill damage, skin lesions, and deep necrotic ulcerations. Primarily, three Flavobacterium species, F. branchiophilum, F. columnare, and F. psychrophilum, have been reported to cause substantial losses to freshwater fish. In this study, we evaluated genomes of 86 Flavobacterium species isolated from aquatic hosts (mainly fish) to identify their unique and shared genome features. Our results showed that F. columnare genomes cluster into four different genetic groups. In silico secretion system analysis identified that all genomes carry type I (T1SS) and type IX (T9SS) secretion systems, but the number of type I secretion system genes shows diversity between species. F. branchiophilum, F. araucananum, F. chilense, F. spartansii, and F. tructae genomes have full type VI secretion system (T6SS). F. columnare, F. hydatis, and F. plurextorum carry partial T6SS with some of the T6SS genes missing. F. columnare, F. araucananum, F. chilense, F. spartansii, F. araucananum, F. tructae, Flavobacterium sp., F. crassostreae, F. succinicans, F. hydatis, and F. plurextorum carry most of the type IV secretion system genes (T4SS). F. columnare genetic groups 1 and 2, Flavobacterium sp., and F. crassostreae encode the least number of antibiotic resistance elements. F. hydatis, F. chilense, and F. plurextorum encode the greatest number of antibiotic resistance genes. Additionally, F. spartansii, F. araucananum, and chilense encode the greatest number of virulence genes while Flavobacterium sp. and F. crassostreae encode the least number of virulence genes. In conclusion, comparative genomics of Flavobacterium species of aquatic origin will help our understanding of Flavobacterium pathogenesis.
Collapse
Affiliation(s)
- Salih Kumru
- Faculty of Fisheries, Recep Tayyip Erdogan University, Rize, Turkey
| | - Hasan C Tekedar
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Hesse, Germany
| | - Mark L Lawrence
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States
| | - Attila Karsi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States.
| |
Collapse
|
9
|
Kim I, Kim J, Chhetri G, Seo T. Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil. J Microbiol 2019; 57:1079-1085. [DOI: 10.1007/s12275-019-9350-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/10/2019] [Accepted: 10/28/2019] [Indexed: 01/02/2023]
|
10
|
Flavobacterium zhairuonensis sp. nov., a gliding bacterium isolated from marine sediment of the East China Sea. J Microbiol 2019; 57:1065-1072. [DOI: 10.1007/s12275-019-9194-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/19/2019] [Accepted: 09/03/2019] [Indexed: 10/25/2022]
|
11
|
Flavobacterium aquariorum sp. nov., isolated from freshwater of the North Han River. J Microbiol 2019; 57:343-349. [DOI: 10.1007/s12275-019-8436-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/02/2018] [Accepted: 11/13/2018] [Indexed: 10/27/2022]
|
12
|
Chhetri G, Yang D, Choi J, Kim H, Seo T. Flavobacterium edaphi sp. nov., isolated from soil from Jeju Island, Korea. Arch Microbiol 2018; 201:539-545. [DOI: 10.1007/s00203-018-1593-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/16/2018] [Accepted: 11/01/2018] [Indexed: 01/02/2023]
|
13
|
Kim SY, Ten LN, Lee SY, Kim SH, Kang IK, Jung HY. Flavobacterium knui sp. nov., a novel member of the family Flavobacteriaceae. Antonie van Leeuwenhoek 2018; 111:2393-2402. [PMID: 30022265 DOI: 10.1007/s10482-018-1128-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/09/2018] [Indexed: 11/25/2022]
Abstract
A Gram-stain negative, non-motile, rod-shaped bacterial strain, designated 2-56T, was isolated from water and characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 2-56T belongs to the family Flavobacteriaceae in the phylum Bacteroidetes and is closely related to Flavobacterium paronense KNUS1T (98.4%) and Flavobacterium collinsense 4-T-2T (96.7%). The G + C content of the genomic DNA of strain 2-56T was 33.4 mol%. The isolate contained MK-6 as the predominant respiratory quinone, and iso-C15:1 G (15.9%), iso-C15:0 (15.8%), iso-C17:0 3-OH (10.7%), and iso-C15:0 3-OH (9.6%) were the major fatty acids. The major polar lipids were phosphatidylethanolamine and an unidentified lipid. The phenotypic and chemotaxonomic data support the affiliation of strain 2-56T with the genus Flavobacterium. However, the DNA-DNA relatedness between the isolate and F. paronense and F. collinsense were 35.7 and 21.5%, respectively, clearly showing that strain 2-56T is not related to them at the species level. Strain 2-56T could be clearly differentiated from its close neighbours on the basis of its phenotypic, genotypic and chemotaxonomic features. Therefore, strain 2-56T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium knui sp. nov. is proposed. The type strain is 2-56T (= KCTC 62061T = JCM 32247T).
Collapse
Affiliation(s)
- Seo-Yeong Kim
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Leonid N Ten
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung-Yeol Lee
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung-Han Kim
- Ginseng Experiment Station, Gyeongsangbuk-do Agricultural Research and Extension Services, Yeongju, 36052, Republic of Korea
| | - In-Kyu Kang
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hee-Young Jung
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea. .,Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.
| |
Collapse
|
14
|
Chen Q, Wang HM, Zhuang W, Sun ZG, Chen J, Ge Y, Qiu JG, He J. Flavobacterium zaozhuangense sp. nov., a new member of the family Flavobacteriaceae, isolated from metolachlor-contaminated soil. Antonie van Leeuwenhoek 2018; 111:1977-1984. [PMID: 29713912 DOI: 10.1007/s10482-018-1090-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/23/2018] [Indexed: 11/28/2022]
Abstract
Strain ZZ-8T, a Gram-negative, aerobic, non-spore-forming, non-motile, yellow-pigmented, rod-shaped bacterium, was isolated from metolachlor-contaminated soil in China. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZZ-8T is a member of the genus Flavobacterium and shows high sequence similarity to Flavobacterium humicola UCM-46T (97.2%) and Flavobacterium pedocola UCM-R36T (97.1%), and lower (< 97%) sequence similarity to other known Flavobacterium species. Chemotaxonomic analysis revealed that strain ZZ-8T possessed MK-6 as the major respiratory quinone; and iso-C15:0 (28.5%), summed feature 9 (iso-C17:1 w9c/C16:0 10-methyl, 22.9%), iso-C17:0 3-OH (17.0%), iso-C15:0 3-OH (8.9%), iso-C15:1 G (8.6%) and summed feature 3 (C16:1 w7c/C16:1 w6c, 5.7%) as the predominant fatty acids. The polar lipids of strain ZZ-8T were determined to be lipids, a glycolipid, aminolipids and phosphatidylethanolamine. Strain ZZ-8T showed low DNA-DNA relatedness with F. pedocola UCM-R36T (43.23 ± 4.1%) and F. humicola UCM-46T (29.17 ± 3.8%). The DNA G+C content was 43.3 mol%. Based on the phylogenetic and phenotypic characteristics, chemotaxonomic data and DNA-DNA hybridization, strain ZZ-8T is considered a novel species of the genus Flavobacterium, for which the name Flavobacterium zaozhuangense sp. nov. (type strain ZZ-8T = KCTC 62315 T = CCTCC AB 2017243T) is proposed.
Collapse
Affiliation(s)
- Qing Chen
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, Shandong, China
| | - Hong-Mei Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, Shandong, China
| | - Wen Zhuang
- College of City and Architecture Engineering, Zaozhuang University, Zaozhuang, 277160, Shandong, China
| | - Zhong-Guan Sun
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, Shandong, China
| | - Jing Chen
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, Shandong, China
| | - Yan Ge
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, Shandong, China
| | - Ji-Guo Qiu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Jian He
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| |
Collapse
|
15
|
Ren Q, Yu M, Li Y, Zhang Y, Shi X, Wu Y, Su Y, Wang Y, Wang X, Zhang XH. Flavobacterium ovatum sp. nov., a marine bacterium isolated from an Antarctic intertidal sandy beach. Int J Syst Evol Microbiol 2018; 68:795-800. [DOI: 10.1099/ijsem.0.002586] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Qiaomeng Ren
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Min Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yuying Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yan Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaochong Shi
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Yanhong Wu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Ying Su
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yanan Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaolei Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| |
Collapse
|
16
|
Ekwe AP, Kim SB. Flavobacterium commune sp. nov., isolated from freshwater and emended description of Flavobacterium seoulense. Int J Syst Evol Microbiol 2018; 68:93-98. [DOI: 10.1099/ijsem.0.002463] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Adaeze Precious Ekwe
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, Republic of Korea
| |
Collapse
|
17
|
Moya G, Yan ZF, Won KH, Yang JE, Kook MC, Yi TH. Flavobacterium limi sp. nov., isolated from forest mud. Int J Syst Evol Microbiol 2017; 67:4667-4673. [PMID: 28984563 DOI: 10.1099/ijsem.0.002354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile, yellow and rod-shaped bacterial strain was isolated from forest mud located at Kyung Hee University, South Korea. Strain THG-AG6.4T grew at 10-35 °C, pH 6.0-9.5 and in the presence of 0-1.5 % (w/v) NaCl. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that strain THG-AG6.4T was most closely related to Flavobacterium gyeonganense HME 7524T (97.66 %), Flavobacterium defluvii EMB 117T (96.93 %) and Flavobacterium arsenitoxidans S2-3HT (96.80 %). The DNA G+C content of strain THG-AG6.4T was 30.2 mol%. The DNA-DNA relatedness values between strain THG-AG6.4T and its closest phylogenetic neighbour, F. gyeonganense HME 7524T, were below 61.0 %. The predominant quinone of strain THG-AG6.4T was MK-6. The major polar lipids were phosphatidylethanolamine, an unidentified phospholipid, five unidentified glycolipids, phosphatidylserine, an unidentified lipid, an unidentified aminophospholipid, two unidentified aminolipids and two unidentified aminoglycolipids. The major fatty acids were C16 : 0, C18 : 0 10-methyl, summed feature 3 and C18 : 1ω9c. The major polyamine was homospermidine. On the basis of the phenotypic, genotypic and phylogenetic characterization of strain THG-AG6.4T, it is concluded that the isolate represents a novel species of the genus Flavobacterium, for which the name Flavobacterium limi sp. nov. is proposed, with THG-AG6.4T as the type strain (=KACC 18851T=CGMCC 1.16060T).
Collapse
Affiliation(s)
- Gabriela Moya
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Zheng-Fei Yan
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Kyung-Hwa Won
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Jung-Eun Yang
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Moo-Chang Kook
- Department of Food Nutrition, Baewha Women's University, Seoul 03039, Republic of Korea
| | - Tae-Hoo Yi
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| |
Collapse
|
18
|
Zhou MY, Zhang XY, Yang XD, Zhang YJ, He HL, Ning D. Flavobacterium ardleyense sp. nov., isolated from Antarctic soil. Int J Syst Evol Microbiol 2017; 67:3996-4001. [DOI: 10.1099/ijsem.0.002241] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ming-Yang Zhou
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, Jinan 250353, PR China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Xiao-Deng Yang
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, Jinan 250353, PR China
| | - Yan-Jiao Zhang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Hai-Lun He
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, PR China
| | - Daling Ning
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Oklahoma, USA
| |
Collapse
|
19
|
Nam GG, Joung Y, Park M, Kim S, Jeon HT, Cho JC. Flavobacterium soyangense sp. nov., a psychrotolerant bacterium, isolated from an oligotrophic freshwater lake. Int J Syst Evol Microbiol 2017; 67:2440-2445. [PMID: 28742006 DOI: 10.1099/ijsem.0.001987] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated IMCC26223T, was isolated from an oligotrophic freshwater lake, Lake Soyang, Korea. Cells of strain IMCC26223T were Gram-staining negative, strictly aerobic, non-motile and short-rod-shaped. Growth occurred at pH 6-8 (optimum, pH 7.0), at 4-25 °C (optimum, 15 °C) and with 0-0.5 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain IMCC26223T was identified as a member of the genus Flavobacterium and most closely related to Flavobacterium fluvii H7T (97.6 %), Flavobacterium segetis AT1048T (97.5 %) and Flavobacterium weaverense AT1042T (97.2 %). DNA-DNA relatedness between strain IMCC26223T and F. fluvii H7T was 41.5-51.7 % in the reciprocal hybridization. Strain IMCC26223T contained MK-6 as the major respiratory quinone. The major cellular fatty acids consisted of C16 : 0, iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), and the polar lipids were phosphatidylethanolamine, an unidentified aminolipid and two unidentified lipids. The DNA G+C content of strain IMCC26223T was 34.5 mol%. On the basis of 16S rRNA gene phylogeny and phenotypic characterization, strain IMCC26223T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium soyangense sp. nov., is proposed. The type strain is IMCC26223T (=KCTC 52245T=JCM 31384T).
Collapse
Affiliation(s)
- Gi Gyun Nam
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Yochan Joung
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Miri Park
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Suhyun Kim
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Hyoung Tae Jeon
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| |
Collapse
|
20
|
Yang JA, Yang SH, Kim J, Kwon KK, Oh HM. Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus. J Microbiol 2017; 55:583-591. [PMID: 28664513 DOI: 10.1007/s12275-017-7172-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/07/2017] [Accepted: 06/19/2017] [Indexed: 12/19/2022]
Abstract
Here we report the comparative genomic analysis of strain UJ101 with 15 strains from the family Flavobacteriaceae, using the CGExplorer program. Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab, Atergatis reticulatus, from the East Sea near Korea. The complete genome of strain UJ101 is a 3,074,209 bp, single, circular chromosome with 30.74% GC content. While the UJ101 genome contains a number of annotated genes for many metabolic pathways, such as the Embden-Meyerhof pathway, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, genes for the Entner-Douddoroff pathway are not found in the UJ101 genome. Overall, carbon fixation processes were absent but nitrate reduction and denitrification pathways were conserved. The UJ101 genome was compared to genomes from other marine animals (three invertebrate strains and 5 fish strains) and other marine animal- derived genera. Notable results by genome comparisons showed that UJ101 is capable of denitrification and nitrate reduction, and that biotin-thiamine pathway participation varies among marine bacteria; fish-dwelling bacteria, freeliving bacteria, invertebrate-dwelling bacteria, and strain UJ101. Pan-genome analysis of the 16 strains in this study included 7,220 non-redundant genes that covered 62% of the pan-genome. A core-genome of 994 genes was present and consisted of 8% of the genes from the pan-genome. Strain UJ101 is a symbiotic hetero-organotroph isolated from xanthid crab, and is a metabolic generalist with nitrate-reducing abilities but without the ability to synthesize biotin. There is a general tendency of UJ101 and some fish pathogens to prefer thiamine-dependent glycolysis to gluconeogenesis. Biotin and thiamine auxotrophy or prototrophy may be used as important markers in microbial community studies.
Collapse
Affiliation(s)
- Jhung-Ahn Yang
- Departments of Marine-Bio Convergence Science, Specialized Graduate School Science & Technology Convergence, Pukyong National University, Busan, 48547, Republic of Korea
| | - Sung-Hyun Yang
- Marine Biotechnology Research Division, Korea Institute of Ocean Science & Technology, Ansan, 15627, Republic of Korea
| | - Junghee Kim
- Departments of Marine-Bio Convergence Science, Specialized Graduate School Science & Technology Convergence, Pukyong National University, Busan, 48547, Republic of Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Division, Korea Institute of Ocean Science & Technology, Ansan, 15627, Republic of Korea
| | - Hyun-Myung Oh
- Departments of Marine-Bio Convergence Science, Specialized Graduate School Science & Technology Convergence, Pukyong National University, Busan, 48547, Republic of Korea.
| |
Collapse
|
21
|
Ekwe AP, Ahn JH, Kim SB. Flavobacterium keumense sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2017; 67:2166-2170. [DOI: 10.1099/ijsem.0.001920] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Adaeze Precious Ekwe
- Department of Microbiology and Molecular Biology, Chungnam National University, 99 Daehak-Ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Joong-hyeon Ahn
- Department of Microbiology and Molecular Biology, Chungnam National University, 99 Daehak-Ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, 99 Daehak-Ro, Yuseong, Daejeon 34134, Republic of Korea
| |
Collapse
|
22
|
Chaudhary DK, Kim J. Flavobacterium olei sp. nov., a novel psychrotolerant bacterium isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2017; 67:2211-2218. [DOI: 10.1099/ijsem.0.001925] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| |
Collapse
|
23
|
Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
Collapse
Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
24
|
Moya G, Yan ZF, Trinh H, Won KH, Yang JE, Kook MC, Yi TH. Flavobacterium hibisci sp. nov., isolated from the rhizosphere of Hibiscus syriacus L. Int J Syst Evol Microbiol 2017; 67:537-542. [DOI: 10.1099/ijsem.0.001610] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Gabriela Moya
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Zheng-Fei Yan
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Huan Trinh
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Kyung-Hwa Won
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Jung-Eun Yang
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Moo-Chang Kook
- Department of Marine Biotechnology, Anyang University, Incheon 23038, Republic of Korea
| | - Tae-Hoo Yi
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| |
Collapse
|
25
|
Complete Genome Sequence of Flavobacteriales Bacterium Strain UJ101 Isolated from a Xanthid Crab. GENOME ANNOUNCEMENTS 2017; 5:5/5/e01551-16. [PMID: 28153900 PMCID: PMC5289686 DOI: 10.1128/genomea.01551-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab species collected from the East Sea of Korea. Here, we report the complete genome sequence of strain UJ101 for the study of major metabolic pathways related to microbial species from marine invertebrate species.
Collapse
|
26
|
Li AH, Liu HC, Zhou YG. Flavobacterium orientale sp. nov., isolated from lake water. Int J Syst Evol Microbiol 2017; 67:108-112. [DOI: 10.1099/ijsem.0.001544] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ai-Hua Li
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| |
Collapse
|
27
|
Flavobacterium inkyongense sp. nov., isolated from an artificial freshwater pond. Int J Syst Evol Microbiol 2017; 67:82-86. [DOI: 10.1099/ijsem.0.001575] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
28
|
Verma DK, Rathore G. New host record of five Flavobacterium species associated with tropical fresh water farmed fishes from North India. Braz J Microbiol 2016; 46:969-76. [PMID: 26691454 PMCID: PMC4704649 DOI: 10.1590/s1517-838246420131081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 08/04/2014] [Indexed: 11/22/2022] Open
Abstract
Yellow pigmented, filamentous, Gram-negative bacteria belonging to genus Flavobacterium are commonly associated with infections in stressed fish. In this study, inter-species diversity of Flavobacterium was studied in apparently healthy freshwater farmed fishes. For this, ninety one yellow pigmented bacteria were isolated from skin and gill samples (n = 38) of three farmed fish species i.e. Labeo rohita, Catla catla and Cyprinus carpio. Among them, only twelve bacterial isolates (13.18%) were identified as Flavobacterium spp. on the basis of morphological, biochemical tests, partial 16S rDNA gene sequencing and phylogenetic analysis. On the basis of 16S rDNA gene sequencing, all the 12 isolates were 97.6-100% similar to six different formally described species of genus Flavobacterium. The 16S rDNA based phylogenetic analysis grouped these strains into six different clades. Of the 12 isolates, six strains (Fl9S1-6) grouped with F. suncheonense, two strains (Fl6I2, Fl6I3) with F. indicum and the rest four strains (Fl1A1, Fl2G1, Fl3H1 and Fl10T1) clustered with F. aquaticum, F. granuli, F. hercynium and F. terrae, respectively. None of these species except, F. hercynium were previously reported from fish. All the isolated Flavobacterium species possessed the ability of adhesion and biofilm formation to colonize the external surface of healthy fish. The present study is the first record of tropical freshwater farmed fishes as hosts to five environmentally associated species of the Flavobacterium.
Collapse
|
29
|
Du J, Yi TH. Flavobacterium tyrosinilyticum sp. nov., isolated from the rhizosphere of wild strawberry. Int J Syst Evol Microbiol 2016; 66:2629-2634. [DOI: 10.1099/ijsem.0.001104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Juan Du
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, South Korea
| | - Tae-Hoo Yi
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, South Korea
| |
Collapse
|
30
|
López-Pérez M, Kimes NE, Haro-Moreno JM, Rodriguez-Valera F. Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea. Front Microbiol 2016; 7:996. [PMID: 27446036 PMCID: PMC4916215 DOI: 10.3389/fmicb.2016.00996] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/09/2016] [Indexed: 11/13/2022] Open
Abstract
We have used two metagenomic approaches, direct sequencing of natural samples and sequencing after enrichment, to characterize communities of prokaryotes associated to particles. In the first approximation, different size filters (0.22 and 5 μm) were used to identify prokaryotic microbes of free-living and particle-attached bacterial communities in the Mediterranean water column. A subtractive metagenomic approach was used to characterize the dominant microbial groups in the large size fraction that were not present in the free-living one. They belonged mainly to Actinobacteria, Planctomycetes, Flavobacteria and Proteobacteria. In addition, marine microbial communities enriched by incubation with different kinds of particulate material have been studied by metagenomic assembly. Different particle kinds (diatomaceous earth, sand, chitin and cellulose) were colonized by very different communities of bacteria belonging to Roseobacter, Vibrio, Bacteriovorax, and Lacinutrix that were distant relatives of genomes already described from marine habitats. Besides, using assembly from deep metagenomic sequencing from the particle-specific enrichments we were able to determine a total of 20 groups of contigs (eight of them with >50% completeness) and reconstruct de novo five new genomes of novel species within marine clades (>79% completeness and <1.8% contamination). We also describe for the first time the genome of a marine Rhizobiales phage that seems to infect a broad range of Alphaproteobacteria and live in habitats as diverse as soil, marine sediment and water column. The metagenomic recruitment of the communities found by direct sequencing of the large size filter and by enrichment had nearly no overlap. These results indicate that these reconstructed genomes are part of the rare biosphere which exists at nominal levels under natural conditions.
Collapse
|
31
|
Sun JQ, Xu L, Liu M, Wang XY, Wu XL. Flavobacterium suaedae sp. nov., an endophyte isolated from the root of Suaeda corniculata. Int J Syst Evol Microbiol 2016; 66:1943-1949. [DOI: 10.1099/ijsem.0.000967] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ji-Quan Sun
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
- College of Engineering, Peking University, Beijing 100871, PR China
| | - Lian Xu
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| | - Min Liu
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| | - Xin-Ying Wang
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing 100871, PR China
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| |
Collapse
|
32
|
Feng Q, Han L, Nogi Y, Hong Q, Lv J. Flavobacterium lutivivi sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2016; 66:1394-1400. [PMID: 26769164 DOI: 10.1099/ijsem.0.000892] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, yellow, rod-shaped bacterium, designated strain HQQT, was isolated from a municipal wastewater treatment plant in Hebei Province, PR China. Comparative 16S rRNA gene sequence analyses showed that strain HQQT is a member of the genus Flavobacterium and is closely related to 'Flavobacterium shanxiense' CCTCC AB 2014079T (94.8 %) and Flavobacterium macrobrachii DSM 22219T (94.7 %). Phylogenetic analysis showed that strain HQQT clustered with Flavobacterium fontis JCM 18212T and Flavobacterium squillarum KCTC 23915T. The polar lipid profile of strain HQQT revealed the presence of phosphatidylethanolamine, six unknown aminolipids, one unknown glycolipid and one unknown lipid and the only isoprenoid quinone was MK-6. The dominant fatty acids of strain HQQT were iso-C15 : 0, C15 : 0 and C16 : 1ω7c. The DNA G+C content of strain HQQT is 32 mol%. On the basis of the phylogenetic and phenotypic data, strain HQQT represents a novel species of the genus Flavobacterium, for which the name Flavobacterium lutivivi sp. nov. is proposed. The type strain is HQQT ( = CGMCC 1.15347T = KCTC 42935T).
Collapse
Affiliation(s)
- Qingqing Feng
- College of Life Science and Technology, Beijing University of Chemical Technology,15 Beisanhuan East Road, Chaoyang District, Beijing 100029,PR China
| | - Lu Han
- College of Life Science and Technology, Beijing University of Chemical Technology,15 Beisanhuan East Road, Chaoyang District, Beijing 100029,PR China
- School of Ecological and Environmental Sciences, East China Normal University,Shanghai 200241,PR China
| | - Yuichi Nogi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC),2-15 Natsushima-cho, Yokosuka 237-0061,Japan
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University,Nanjing 210095, Jiangsu,PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology,15 Beisanhuan East Road, Chaoyang District, Beijing 100029,PR China
| |
Collapse
|
33
|
Joung Y, Kang H, Kim H, Kim TS, Han JH, Kim SB, Ahn TS, Joh K. Flavobacterium paronense sp. nov., isolated from freshwater of an artificial vegetated island. Int J Syst Evol Microbiol 2016; 66:365-370. [DOI: 10.1099/ijsem.0.000727] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yochan Joung
- Department of Biological Science, Inha University, Incheon 402-751, Republic of Korea
| | - Heeyoung Kang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, 449-791, Republic of Korea
| | - Haneul Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, 449-791, Republic of Korea
| | - Tae-Su Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Ji-Hye Han
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Tae-Seok Ahn
- Department of Environmental Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, 449-791, Republic of Korea
| |
Collapse
|
34
|
Zeng Z, Chen C, Du H, Wang G, Li M. High quality draft genomic sequence of Flavobacterium enshiense DK69(T) and comparison among Flavobacterium genomes. Stand Genomic Sci 2015; 10:92. [PMID: 26561515 PMCID: PMC4641336 DOI: 10.1186/s40793-015-0084-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
Flavobacterium enshiense DK69(T) is a Gram-negative, aerobic, rod-shaped, non-motile and non-flagellated bacterium that belongs to the family Flavobacteriaceae in the phylum Bacteroidetes. The high quality draft genome of strain DK69(T) was obtained and has a 3,375,260 bp genome size with a G + C content of 37.7 mol % and 2848 protein coding genes. In addition, we sequenced five more genomes of Flavobacterium type strains and performed a comparative genomic analysis among 12 Flavobacterium genomes. The results show some specific genes within the fish pathogenic Flavobacterium strains which provide information for further analysis the pathogenicity.
Collapse
Affiliation(s)
- Zhipeng Zeng
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Chong Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Hailun Du
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Mingshun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| |
Collapse
|
35
|
Park SH, Kim JY, Kim YJ, Heo MS. Flavobacterium jejuensis sp. nov., isolated from marine brown alga Ecklonia cava. J Microbiol 2015; 53:756-61. [PMID: 26502959 DOI: 10.1007/s12275-015-5280-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 11/26/2022]
Abstract
A bacterial strain, designated EC11(T) was isolated from brown alga Ecklonia cava collected from Jeju Island, Korea. EC11(T) was identified as a Gram-negative, rod-shaped and yellow-pigmented bacterial strain. The strain EC11(T) grew over a temperature range of 10 °C to 30 °C (optimally at 25 °C), and a pH range of 6.0-10.5 (optimally at pH 7.5). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EC11(T) belongs to the genus Flavobacterium. Strain EC11(T) shared close similarity with Flavobacterium jumunjinense HME7102(T) (96.4%), Flavobacterium dongtanense LW30(T) (95.8%), Flavobacterium haoranii LQY-7(T) (95.3%), and Flavobacterium urocaniciphilum (95.1%). The major fatty acids (> 5%) were iso-C17:0 3-OH (22.4%), iso-C15:0 3-OH (19.0%), C15:0 (12.4%), summed feature 3 (comprising C16:1 ω7c/ C16:1 ω6c; 9.78%), iso-C15:1 G (9.6%), and iso-C16:0 3-OH (9.0%). The DNA G+C content was 28.1 mol% and the strain contained MK-6 as the predominant menaquinone. The major polar lipids were phosphatidylethanolamine, two unknown aminolipids and three unknown polar lipids. Based on phenotypic, chemotaxonomic and phylogenetic analysis, strain EC11T represents a novel species of the Flavobacterium genus, for which the name Flavobacterium jejuensis sp. nov. is proposed. The type strain of F. jejuensis is EC11(T) (=KCTC 42149(T) = JCM 30735(T)).
Collapse
Affiliation(s)
- So-Hyun Park
- Department of Aquatic Life Medicine, College of Ocean Science, Jeju National University, Jeju, 690-756, Republic of Korea
| | - Ji-Young Kim
- Research Institute for Basic Science, Jeju National University, Jeju, 690-756, Republic of Korea
- Jeju Biological Resource Co., Ltd, CTC Business Incubator, Jeju Tourism College, Jeju, 690-756, Republic of Korea
| | - Young-Ju Kim
- Jeju Biological Resource Co., Ltd, CTC Business Incubator, Jeju Tourism College, Jeju, 690-756, Republic of Korea.
| | - Moon-Soo Heo
- Department of Aquatic Life Medicine, College of Ocean Science, Jeju National University, Jeju, 690-756, Republic of Korea.
| |
Collapse
|
36
|
Feng Q, Han L, Yuan X, Tan X, Gao Y, Lv J. Flavobacterium procerum sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2015; 65:2702-2708. [DOI: 10.1099/ijs.0.000326] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, strictly aerobic, yellow-pigmented, rod-shaped bacterium, designated strain T3T, was isolated from freshwater of Chishui River flowing through Maotai town, Guizhou, south-west China. Analysis of the16S rRNA gene sequence indicated that strain T3T was a member of the genus Flavobacterium and closely related to Flavobacterium resistens DSM 19382T (96.8 %). The novel strain was able to grow at 10–34 °C (optimum 28 °C), pH 6.0–11.0 (optimum pH 8.0–9.0) and with 0–2.0 % (w/v) NaCl (optimum 0 %). The major polar lipids were phosphatidylethanolamine, two unknown glycolipids, five unknown aminolipids and four unidentified lipids, and the major respiratory quinone was MK-6. The predominant fatty acids were C16 : 1ω7c and/or C16 : 1ω6c and iso-C15 : 0. The DNA G+C content of the strain was 36 mol %. Based on these data, strain T3T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium procerum sp. nov. is proposed. The type strain is T3T ( = CGMCC 1.12926T = JCM 30113T).
Collapse
Affiliation(s)
- Qingqing Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Lu Han
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
- College of Resources and Environmental Science, East China Normal University, Shanghai, 200241, PR China
| | - Xin Yuan
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Xu Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
- Division of Nutraceutical Products, Tasly Holding Group, Tianjin 300040, PR China
| | - Yuan Gao
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| |
Collapse
|
37
|
Hahnke RL, Stackebrandt E, Meier-Kolthoff JP, Tindall BJ, Huang S, Rohde M, Lapidus A, Han J, Trong S, Haynes M, Reddy TBK, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Markowitz V, Woyke T, Göker M, Kyrpides NC, Klenk HP. High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes. Stand Genomic Sci 2015; 10:46. [PMID: 26380634 PMCID: PMC4572689 DOI: 10.1186/s40793-015-0032-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/29/2015] [Indexed: 11/23/2022] Open
Abstract
Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly published name, and has been isolated from the spring of a hard water rivulet in Northern Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA gene sequence phylogeny revealed a clustering of members of the genus Myroides as a monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2T and its next relatives seem more closely related to the genus Myroides than to the type species of the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391 protein-coding and 65 RNA genes is part of the GenomicEncyclopedia ofBacteria andArchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and one large CAZy rich gene cluster that might enable strain WB 3.3-2T to decompose plant and algae derived polysaccharides. Based on these results we propose F. rivuli as an interesting candidate for further physiological studies and the role of Bacteroidetes in the decomposition of complex polymers in the environment.
Collapse
Affiliation(s)
- Richard L Hahnke
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
| | - Erko Stackebrandt
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
| | - Brian J Tindall
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
| | - Sixing Huang
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
| | - Manfred Rohde
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, Germany
| | - Alla Lapidus
- St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Stephan Trong
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Matthew Haynes
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA ; School of Biology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
38
|
Flavobacterium daemonensis sp. nov., isolated from Daemo Mountain soil. Int J Syst Evol Microbiol 2015; 65:983-989. [DOI: 10.1099/ijs.0.000051] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, catalase- and oxidase-positive, obligately aerobic, motile by gliding, bright yellow and rod-shaped bacterial strain was isolated from soil of Daemo Mountain (Daemosan) in Seoul, Republic of Korea. Its taxonomic position was investigated by using a polyphasic study. On the basis of 16S rRNA gene sequence comparisons, strain THG–DJ7T was found to be most closely related to
Flavobacterium denitrificans
ED5T (97.9 % sequence similarity),
Flavobacterium ginsenosidimutans
THG 01T (97.6 %),
Flavobacterium kyungheensis
THG-107T (97.5 %),
Flavobacterium anhuiense
D3T (97.1 %) and
Flavobacterium ginsengisoli
DCY54T (97.0 %). The DNA–DNA relatedness between strain THG–DJ7T and its phylogenetically closest neighbours was below 40.0 %. The G+C content of the genomic DNA was determined to be 32.6 mol%. The only isoprenoid quinone detected in strain THG–DJ7T was menaquinone-6 (MK-6). The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were found to be phosphatidylethanolamine, phosphatidyldimethylethanolamine, an unidentified aminophosphoglycolipid, phosphatidylserine and an unidentified lipid. The major fatty acids were identified as iso-C15 : 0, iso-C15 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). These data support the affiliation of strain THG–DJ7T to the genus
Flavobacterium
. We report the phenotypic, genotypic and phylogenetic characterization of strain THG–DJ7T. Based on the findings presented, a novel species of the genus
Flavobacterium
, Flavobacterium daemonensis sp. nov. is proposed, with THG–DJ7T ( = KACC 17651T = JCM 19455T) as the type strain.
Collapse
|
39
|
Loch TP, Faisal M. Emerging flavobacterial infections in fish: A review. J Adv Res 2014; 6:283-300. [PMID: 26257926 PMCID: PMC4522593 DOI: 10.1016/j.jare.2014.10.009] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 12/05/2022] Open
Abstract
Flavobacterial diseases in fish are caused by multiple bacterial species within the family Flavobacteriaceae and are responsible for devastating losses in wild and farmed fish stocks around the world. In addition to directly imposing negative economic and ecological effects, flavobacterial disease outbreaks are also notoriously difficult to prevent and control despite nearly 100 years of scientific research. The emergence of recent reports linking previously uncharacterized flavobacteria to systemic infections and mortality events in fish stocks of Europe, South America, Asia, Africa, and North America is also of major concern and has highlighted some of the difficulties surrounding the diagnosis and chemotherapeutic treatment of flavobacterial fish diseases. Herein, we provide a review of the literature that focuses on Flavobacterium and Chryseobacterium spp. and emphasizes those associated with fish.
Collapse
Affiliation(s)
- Thomas P Loch
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, 174 Food Safety and Toxicology Building, Michigan State University, East Lansing, MI 48824, USA
| | - Mohamed Faisal
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, 174 Food Safety and Toxicology Building, Michigan State University, East Lansing, MI 48824, USA ; Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Natural Resources Building, Room 4, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
40
|
Khianngam S, Akaracharanya A, Lee JS, Lee KC, Kim KW, Tanasupawat S. Flavobacterium arsenitoxidans sp. nov., an arsenite-oxidizing bacterium from Thai soil. Antonie van Leeuwenhoek 2014; 106:1239-46. [PMID: 25267334 DOI: 10.1007/s10482-014-0294-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 09/22/2014] [Indexed: 11/24/2022]
Abstract
An arsenite-oxidizing bacterium, strain S2-3H(T), was isolated from arsenic-contaminated soil sample collected from Dantchaeng district, Suphanburi province, Thailand and was characterized based on polyphasic taxonomic study. The strain was observed to be a Gram-stain negative, aerobic, yellow pigmented, non-spore forming and rod-shaped bacterium. Major menaquinone was MK-6. Iso-C15:0, iso-C15:0 3OH, C16:1 ω7c/C16:1 ω6c, C16:0, iso-C17:0 3OH, and C16:0 3OH were the predominant cellular fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, unidentified phospholipids and unidentified aminophospholipids. The DNA G+C content was 37.0 mol%. Phylogenetic analysis using 16S rRNA sequence showed that strain S2-3H(T) is affiliated to the genus Flavobacterium, and is closely related to F. defluvii KCTC 12612(T) (97.0 %) and F. johnsoniae NBRC 14942(T) (97.0 %). The strain S2-3H(T) could be clearly distinguished from the related Flavobacterium species by its physiological and biochemical characteristics as well as its phylogenetic position and DNA-DNA relatedness. Therefore, the strain represents a novel species of the genus Flavobacterium, for which the name Flavobacterium arsenitoxidans sp. nov. (type strain S2-3H(T) = KCTC 22507(T) = NBRC 109607(T) = PCU 331(T) = TISTR 2238(T)) is proposed.
Collapse
Affiliation(s)
- Saowapar Khianngam
- Faculty of Animal Sciences and Agricultural Technology, Silpakorn University, Phetchaburi IT Campus, Phetchaburi, 76120, Thailand
| | | | | | | | | | | |
Collapse
|
41
|
Ao L, Zeng XC, Nie Y, Mu Y, Zhou L, Luo X. Flavobacterium arsenatis sp. nov., a novel arsenic-resistant bacterium from high-arsenic sediment. Int J Syst Evol Microbiol 2014; 64:3369-3374. [PMID: 25013224 DOI: 10.1099/ijs.0.063248-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
A novel bacterial strain Z(T) was isolated from the high-arsenic sediment in Jianghan Plain, China. The strain was Gram-staining-negative, rod-shaped and formed yellow colonies. This bacterium is capable of tolerating arsenate and arsenite, with MICs of 40 mM and 20 mM, respectively. The strain also possesses catalase and does not produce oxidase. The nucleotide sequence of the 16S rRNA gene of the isolate showed the highest similarity (96.9%) to that of the type strain of Flavobacterium soli. On the basis of the 16S rRNA gene sequence analysis and the phenotypic properties of strain Z(T), it was assigned to the genus Flavobacterium. The major respiratory menaquinone was MK-6 and the predominant fatty acids were iso-C15:0, summed feature 3 (containing C16:1ω6c and/or C16:1ω7c) and iso-C15:1G. The major polar lipids were phosphatidylethanolamine, three uncharacterized aminophospholipids and four unidentified phospholipids. The DNA G+C content was 32.1 mol%. Based on the phenotypic and genotypic data presented in this article, it can be concluded that this isolate represents a novel species of the genus Flavobacterium, for which the name Flavobacterium arsenatis sp. nov. is proposed. The type strain is Z(T) ( = CCTCC AB 2013048(T) = KCTC 32397(T)).
Collapse
Affiliation(s)
- Lian Ao
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Xian-Chun Zeng
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Yao Nie
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Yao Mu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Lingli Zhou
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Xuesong Luo
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| |
Collapse
|
42
|
Flavobacterium ahnfeltiae sp. nov., a new marine polysaccharide-degrading bacterium isolated from a Pacific red alga. Arch Microbiol 2014; 196:745-52. [DOI: 10.1007/s00203-014-1010-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 06/26/2014] [Accepted: 06/28/2014] [Indexed: 10/25/2022]
|
43
|
Kolton M, Sela N, Elad Y, Cytryn E. Comparative genomic analysis indicates that niche adaptation of terrestrial Flavobacteria is strongly linked to plant glycan metabolism. PLoS One 2013; 8:e76704. [PMID: 24086761 PMCID: PMC3784431 DOI: 10.1371/journal.pone.0076704] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 08/26/2013] [Indexed: 11/17/2022] Open
Abstract
Flavobacteria are important members of aquatic and terrestrial bacterial communities, displaying extreme variations in lifestyle, geographical distribution and genome size. They are ubiquitous in soil, but are often strongly enriched in the rhizosphere and phyllosphere of plants. In this study, we compared the genome of a root-associated Flavobacterium that we recently isolated, physiologically characterized and sequenced, to 14 additional Flavobacterium genomes, in order to pinpoint characteristics associated with its high abundance in the rhizosphere. Interestingly, flavobacterial genomes vary in size by approximately two-fold, with terrestrial isolates having predominantly larger genomes than those from aquatic environments. Comparative functional gene analysis revealed that terrestrial and aquatic Flavobacteria generally segregated into two distinct clades. Members of the aquatic clade had a higher ratio of peptide and protein utilization genes, whereas members of the terrestrial clade were characterized by a significantly higher abundance and diversity of genes involved in metabolism of carbohydrates such as xylose, arabinose and pectin. Interestingly, genes encoding glycoside hydrolase (GH) families GH78 and GH106, responsible for rhamnogalacturonan utilization (exclusively associated with terrestrial plant hemicelluloses), were only present in terrestrial clade genomes, suggesting adaptation of the terrestrial strains to plant-related carbohydrate metabolism. The Peptidase/GH ratio of aquatic clade Flavobacteria was significantly higher than that of terrestrial strains (1.7±0.7 and 9.7±4.7, respectively), supporting the concept that this relation can be used to infer Flavobacterium lifestyles. Collectively, our research suggests that terrestrial Flavobacteria are highly adapted to plant carbohydrate metabolism, which appears to be a key to their profusion in plant environments.
Collapse
Affiliation(s)
- Max Kolton
- Institute of Soil, Water and Environmental Sciences, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Research, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Research, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, the Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
| |
Collapse
|
44
|
Zhu L, Liu Q, Liu H, Zhang J, Dong X, Zhou Y, Xin Y. Flavobacterium noncentrifugens sp. nov., a psychrotolerant bacterium isolated from glacier meltwater. Int J Syst Evol Microbiol 2013; 63:2032-2037. [DOI: 10.1099/ijs.0.045534-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A non-motile, Gram-stain-negative bacterium, designated R-HLS-17T, was isolated from the meltwater of Hailuogou Glacier located in Sichuan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus
Flavobacterium
, with the closest relatives being
Flavobacterium antarcticum
JCM 12383T (95.5 % 16S rRNA gene sequence similarity),
F. omnivorum
JCM 11313T (95.0 %) and
F. fryxellicola
LMG 22022T (95.2 %). Growth occurred at 0–29 °C (optimum, 10–20 °C) and pH 6.0–8.5 (optimum, 7.0–8.0). The DNA G+C content was 46.5 mol%. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0), iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The predominant menaquinone was MK-6. Based on the genotypic and phenotypic characteristics, we propose that strain R-HLS-17T represents a novel species of the genus
Flavobacterium
, Flavobacterium noncentrifugens sp. nov. The type strain is R-HLS-17T ( = CGMCC 1.10076T = NBRC 108844T).
Collapse
Affiliation(s)
- Lang Zhu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Qing Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hongcan Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jianli Zhang
- School of Life Science and Technology, Beijing Institute of Technology, Beijing 100081, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yuguang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yuhua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| |
Collapse
|
45
|
Dong K, Xu B, Zhu F, Wang G. Flavobacterium hauense sp. nov., isolated from soil and emended descriptions of Flavobacterium subsaxonicum, Flavobacterium beibuense and Flavobacterium rivuli. Int J Syst Evol Microbiol 2013; 63:3237-3242. [PMID: 23456809 DOI: 10.1099/ijs.0.048652-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly aerobic, Gram-staining-negative, rod-shaped, non-motile, yellow-pigmented bacterial strain, designated BX12(T), was isolated from soil collected from the peak area of Wudang Mountain in the city of Shiyan, Hubei province, China. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain BX12(T) was most closely related to Flavobacterium subsaxonicum WB 4.1-42(T) (95.9% 16S rRNA gene sequence similarity), followed by Flavobacterium beibuense F44-8(T) (95.6%) and Flavobacterium rivuli WB 3.3-2(T) (94.1%). The major fatty acids (≥5%) of strain BX12(T) were summed feature 3 (comprising C(16:1)ω7c and/or C(16:1)ω6c), iso-C(15:0), C(16:0), iso-C(17:0) 3-OH, and C(16:0) 3-OH. The major polar lipid was phosphatidylethanolamine, and the major respiratory quinone was menaquinone-6. The genomic DNA G+C content was 43.9 mol%. On the basis of a high number of phenotypic differentiating properties and phylogenetic uniqueness, strain BX12(T) represents a novel species of the genus Flavobacterium for which the name Flavobacterium hauense sp. nov. is proposed. The type strain is BX12(T) ( =CCTCC AB 2012197(T) =KCTC 32147(T)). Emended descriptions of Flavobacterium subsaxonicum, Flavobacterium beibuense and Flavobacterium rivuli are also proposed.
Collapse
Affiliation(s)
- Kun Dong
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Biao Xu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Fengqiu Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| |
Collapse
|
46
|
Hu G, Zhang J, Yang G, Li YY, Guan YT, Wang J, Li SP, Hong Q. Flavobacterium yanchengense sp. nov., isolated from soil. Int J Syst Evol Microbiol 2013; 63:2848-2852. [PMID: 23315414 DOI: 10.1099/ijs.0.048801-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-spore-forming, rod-shaped bacterial strain, hg(T), resembling members of the genus Flavobacterium, was isolated from soil, and subjected to a taxonomic study using a polyphasic approach. Strain hg(T) grew optimally at pH 7.0 and 30 °C in the presence of 1 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 34 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain hg(T) belonged to the genus Flavobacterium. Levels of 16S rRNA gene sequence similarity between strain hg(T) and the type strains of species of the genus Flavobacterium were below 94.7 %. Strain hg(T) differed from phylogenetically related species of the genus Flavobacterium in several phenotypic characteristics. On the basis of phenotypic and phylogenetic distinctiveness, strain hg(T) (= CCTCC AB 2012099(T) = KACC 16855(T)) was classified in the genus Flavobacterium as the type strain of a novel species, for which the name Flavobacterium yanchengense sp. nov. is proposed.
Collapse
Affiliation(s)
- Gang Hu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jun Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Guiqin Yang
- Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, Guangdong 510650, China
| | - Yang-Yang Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yi-Ting Guan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jun Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Shun-Peng Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| |
Collapse
|
47
|
Lata P, Lal D, Lal R. Flavobacterium ummariense sp. nov., isolated from hexachlorocyclohexane-contaminated soil, and emended description of
Flavobacterium ceti
Vela et al. 2007. Int J Syst Evol Microbiol 2012; 62:2674-2679. [DOI: 10.1099/ijs.0.030916-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, strictly aerobic, yellow bacterial strain, designated DS-12T, was isolated from hexachlorocyclohexane-contaminated soil in Lucknow, Uttar Pradesh, India. Strain DS-12T showed the highest 16S rRNA gene sequence similarity with
Flavobacterium ceti
454-2T (94.2 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-12T belonged to the genus
Flavobacterium
. Strain DS-12T produced flexirubin-type pigments. Gliding motility was not observed. The major fatty acids of strain DS-12T were iso-C15 : 0 (48.0 %), summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl; 19.3 %), iso-C17 : 0 3-OH (8.5 %) and summed feature 3 (comprising one or more of C16 : 1ω7c, C16 : 1ω6c and iso-C15 : 0 2-OH; 7.2 %). The only respiratory quinone was menaquinone-6 and the major polyamine was homospermidine. Strain DS-12T contained phosphatidyldimethylethanolamine, phosphatidylserine, phosphatidylethanolamine, one unknown phospholipid and one unknown aminolipid. The DNA G+C content was 37.4 mol%. Phylogenetic inference and phenotypic properties indicated that strain DS-12T represents a novel species of the genus
Flavobacterium
, for which the name Flavobacterium ummariense sp. nov. is proposed. The type strain is DS-12T ( = CCM 7847T = MTCC 10766T). An emended description of
Flavobacterium ceti
is also given.
Collapse
Affiliation(s)
- Pushp Lata
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110 007, India
| | - Devi Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110 007, India
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110 007, India
| |
Collapse
|
48
|
Kim JJ, Kanaya E, Weon HY, Koga Y, Takano K, Dunfield PF, Kwon SW, Kanaya S. Flavobacterium compostarboris sp. nov., isolated from leaf-and-branch compost, and emended descriptions of
Flavobacterium hercynium
,
Flavobacterium resistens
and
Flavobacterium johnsoniae. Int J Syst Evol Microbiol 2012; 62:2018-2024. [DOI: 10.1099/ijs.0.032920-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly aerobic, Gram-negative, yellow-pigmented, non-spore-forming rod, designated 15C3T, was isolated from aerobic leaf-and-branch compost at EXPO Park in Osaka, Japan. Growth was observed at 9–33 °C (optimum 25 °C) and pH 5.6–7.9 (optimum pH 6.1–7.0). No growth occurred with >2 % (w/v) NaCl. Strain 15C3T reduced nitrate to nitrogen and showed catalase activity but not oxidase activity. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH). The isolate contained phosphatidylethanolamine as the major polar lipid and menaquinone-6 as the major respiratory quinone. The G+C content of the genomic DNA of strain 15C3T was 33.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 15C3T belonged to the genus
Flavobacterium
and was most closely related to
Flavobacterium hercynium
WB 4.2-33T (96.9 % sequence similarity). On the basis of phenotypic and phylogenetic distinctiveness, strain 15C3T is considered to represent a novel species in the genus
Flavobacterium
, for which the name Flavobacterium compostarboris sp. nov. is proposed. The type strain is 15C3T ( = KACC 14224T = JCM 16527T). Emended descriptions of
F. hercynium
,
Flavobacterium resistens
and
Flavobacterium johnsoniae
are also given.
Collapse
Affiliation(s)
- Joong-Jae Kim
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Eiko Kanaya
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hang-Yeon Weon
- Korean Agricultural Culture Collection (KACC), National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-853, Republic of Korea
| | - Yuichi Koga
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazufumi Takano
- CREST, JST, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Peter F. Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-853, Republic of Korea
| | - Shigenori Kanaya
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| |
Collapse
|
49
|
Kaur I, Kaur C, Khan F, Mayilraj S. Flavobacterium rakeshii sp. nov., isolated from marine sediment, and emended description of Flavobacterium beibuense Fu et al. 2011. Int J Syst Evol Microbiol 2012; 62:2897-2902. [PMID: 22247214 DOI: 10.1099/ijs.0.035691-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile bacterial strain that formed straight rods and straw yellow colonies, designated FCS-5(T), was isolated from a marine sediment from the Arabian Sea. The isolate exhibited most of the phenotypic properties expected for a member of the genus Flavobacterium. The major fatty acids were iso-C(15:0), iso-C(17:0) 3-OH, C(17:1)ω9c and summed feature 3 (comprising iso-C(15:0) 2-OH and/or C(16:1)ω7c). The only isoprenoid quinone was MK-6. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The G+C content of the genomic DNA was 32.4 mol%. According to 16S rRNA gene sequence analysis, strain FCS-5(T) belonged to the genus Flavobacterium and exhibited 99.3% 16S rRNA gene sequence similarity with Flavobacterium beibuense F44-8(T) and 90.9-94.6% sequence similarity with other members of the genus Flavobacterium. The results of physiological and biochemical tests allowed the discrimination of the isolate from its phylogenetic relatives. Strain FCS-5(T) is a representative of a novel species of the genus Flavobacterium, for which the name Flavobacterium rakeshii sp. nov. is proposed. The type strain is FCS-5(T) ( = MTCC 10967(T) = JCM 17928(T)). An emended description of F. beibuense is also proposed.
Collapse
Affiliation(s)
- Ishwinder Kaur
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, 160 036, India
| | - Chandandeep Kaur
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, 160 036, India
| | - Fazlurrahman Khan
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, 160 036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, 160 036, India
| |
Collapse
|
50
|
Kim SR, Kim YJ, Nguyen NL, Min JW, Jeon JN, Yang DU, Yang DC. Flavobacterium ginsengiterrae sp. nov., isolated from a ginseng field. J GEN APPL MICROBIOL 2011; 57:341-6. [PMID: 22353739 DOI: 10.2323/jgam.57.341] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
MESH Headings
- Bacterial Typing Techniques
- Base Composition
- Cluster Analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Flavobacterium/classification
- Flavobacterium/genetics
- Flavobacterium/isolation & purification
- Flavobacterium/physiology
- Locomotion
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Panax/microbiology
- Phylogeny
- Pigments, Biological/metabolism
- RNA, Ribosomal, 16S/genetics
- Republic of Korea
- Sequence Analysis, DNA
- Soil Microbiology
- Vitamin K 2/analysis
Collapse
Affiliation(s)
- Sang-Rae Kim
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung Hee University, 1 Seocheon-dong, Gyeonggi-do, South Korea
| | | | | | | | | | | | | |
Collapse
|