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Pinpimai K, Punnarak P, Thitiphuree T, Songploy S, Panichpol A, Chankong A, Chavanich S, Viyakarn V. 16S rRNA amplicon sequencing of seawater microbiota from Rayong Province, Thailand, affected by oil spills. Microbiol Resour Announc 2024; 13:e0096623. [PMID: 38426730 PMCID: PMC11008116 DOI: 10.1128/mra.00966-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
We reported on microbial communities isolated from 18 seawater samples affected by oil spills in Rayong province, Thailand, using the V3-V4 region of 16S rRNA gene sequencing.
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Affiliation(s)
- Komkiew Pinpimai
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Porntep Punnarak
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Tongchai Thitiphuree
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Se Songploy
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Arnupap Panichpol
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | | | - Suchana Chavanich
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Voranop Viyakarn
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Xu X, Shen Y, Zhang Y, Li Q, Wang W, Chen L, Chen G, Ng WL, Islam MN, Punnarak P, Zheng H, Zhu X. A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea. Front Plant Sci 2023; 13:1075353. [PMID: 36684775 PMCID: PMC9845719 DOI: 10.3389/fpls.2022.1075353] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
In 2003, Kandelia obovata was identified as a new mangrove species differentiated from Kandelia candel. However, little is known about their chloroplast (cp) genome differences and their possible ecological significance. In this study, 25 whole cp genomes, with seven samples of K. candel from Malaysia, Thailand, and Bangladesh and 18 samples of K. obovata from China, were sequenced for comparison. The cp genomes of both species encoded 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes, but the cp genome size of K. obovata was ~2 kb larger than that of K. candle due to the presence of more and longer repeat sequences. Of these, tandem repeats and simple sequence repeats exhibited great differences. Principal component analysis based on indels, and phylogenetic tree analyses constructed with homologous protein genes from the single-copy genes, as well as 38 homologous pair genes among 13 mangrove species, gave strong support to the separation of the two species within the Kandelia genus. Homologous genes ndhD and atpA showed intraspecific consistency and interspecific differences. Molecular dynamics simulations of their corresponding proteins, NAD(P)H dehydrogenase chain 4 (NDH-D) and ATP synthase subunit alpha (ATP-A), predicted them to be significantly different in the functions of photosynthetic electron transport and ATP generation in the two species. These results suggest that the energy requirement was a pivotal factor in their adaptation to differential environments geographically separated by the South China Sea. Our results also provide clues for future research on their physiological and molecular adaptation mechanisms to light and temperature.
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Affiliation(s)
- Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yuchen Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qianying Li
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Wenqing Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Luzhen Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Guangcheng Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Selangor Darul Ehsan, Malaysia
| | - Md Nazrul Islam
- Forestry and Wood Technology Discipline, Khulna University, Khulna, Bangladesh
| | - Porntep Punnarak
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Hailei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xueyi Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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Huang H, Punnarak P, Zhang Q, Piumsomboon A, Wang L, Li W, Chen S, Chen G, Ou D. Aureimonas mangrovi sp. nov., a marine alphaproteobacterium isolated from mangrove sediment in Thailand. Int J Syst Evol Microbiol 2021; 71. [PMID: 34224346 DOI: 10.1099/ijsem.0.004820] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, designated as 1-4-3T and 1-4-4, were isolated from a mangrove sediment cultured with coastal seawater. The cells were Gram-stain-negative, motile, short, rod-shaped bacteria with flagella. Growth occurred at 4-37 °C, pH 7.0-9.0, and 0-7% NaCl. The predominant fatty acids of the novel strains were C18 : 1 ω7c, C19 : 0 cyclo ω8c, C18 : 0, and C16 : 0. A phylogenetic analysis based on 16S rRNA gene sequences and whole genome phylogeny analysis based on distance matrix revealed an affiliation between the two strains and the genus Aureimonas, with closest sequence similarity to A. populi 4M3-2T (96.41 and 96.64% similarity, respectively) and A. glaciistagni (96.01 and 96.23% similarity, respectively). The DNA G+C content of strain 1-4-3T was 66.80 mol%. Strain 1-4-3T displayed low DNA-DNA relatedness to A. populi 4M3-2T, with an average nucleotide identity value of 77.47 % and digital DNA-DNA hybridization value of 22.83 %. Genotypic, chemotaxonomic, and phenotypic data indicate that strains 1-4-3T and 1-4-4 represent a novel species of the genus Aureimonas, for which we propose the name Aureimonas mangrovi sp. nov. The type strain is 1-4-3T (=LMG 31693T=CGMCC 1.18507T).
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Affiliation(s)
- Hao Huang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
| | - Porntep Punnarak
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok 10330, Thailand
| | - Qinghua Zhang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
| | | | - Lei Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
| | - Weiwen Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
| | - Shunyang Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
| | - Guangcheng Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
| | - Danyun Ou
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai 536015, PR China
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Fu Z, Piumsomboon A, Punnarak P, Uttayarnmanee P, Leaw CP, Lim PT, Wang A, Gu H. Diversity and distribution of harmful microalgae in the Gulf of Thailand assessed by DNA metabarcoding. Harmful Algae 2021; 106:102063. [PMID: 34154784 DOI: 10.1016/j.hal.2021.102063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Information on the diversity and distribution of harmful microalgae in the Gulf of Thailand is very limited and mainly based on microscopic observations. Here, we collected 44 water samples from the Gulf of Thailand and its adjacent water (Perhentian Island, Malaysia) for comparison in 2018. DNA metabarcoding was performed targeting the partial large subunit ribosomal RNA gene (LSU rDNA D1-D3) and the internal transcribed spacers (ITS1 and ITS2). A total of 50 dinoflagellate genera (made up of 72 species) were identified based on the LSU rDNA dataset, while the results of ITS1 and ITS2 datasets revealed 33 and 32 dinoflagellate genera comprising 69 and 64 species, respectively. Five potentially toxic Pseudo-nitzschia (Bacillariophyceae) species were detected, with four as newly recorded species in the water (Pseudo-nitzschia americana/brasilliana, Pseudo-nitzschia simulans/delicatissima, P. galaxiae and P. multistriata). The highest relative abundances of P. galaxiae and P. multistriata were found in Trat Bay and Chumphon (accounting for 0.20% and 0.06% of total ASVs abundance, respectively). Three paralytic shellfish toxin producing dinoflagellate species were detected: Alexandrium tamiyavanichii, Alexandrium fragae, and Gymnodinium catenatum. The highest abundance of A. tamiyavanichii was found in the surface sample of Chumphon (CHO7 station), accounting for 1.95% of total ASVs abundance. Two azaspiracid producing dinoflagellate species, Azadinium poporum ribotype B, Azadinium spinosum ribotype A, and a pinnatoxin producing dinoflagellate species Vulcanodinium rugosum, with two ribotypes B and C, were revealed from the datasets although with very low abundances. Six fish killing dinoflagellate species, including Margalefidinium polykrikoides group IV, Margalefidinium fulvescens, Karenia mikimotoi, Karenia selliformis ribotype B, Karlodinium australe, and Karlodinium digitatum were detected and all representing new records in this area. The findings of numerous harmful microalgal species in the Gulf of Thailand highlight the potential risk of human intoxication and fish killing events.
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Affiliation(s)
- Zhengxu Fu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | | | - Porntep Punnarak
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok 10330, Thailand
| | - Praderm Uttayarnmanee
- Marine and Coastal Resources Research and Development Center, Central Gulf of Thailand, Department of Marine and Coastal Resources, Chumphon 86000, Thailand
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Po Teen Lim
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Aijun Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Haifeng Gu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China.
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Punnarak P, Santos MD, Hwang SD, Kondo H, Hirono I, Kikuchi Y, Aoki T. RNA aptamers inhibit the growth of the fish pathogen viral hemorrhagic septicemia virus (VHSV). Mar Biotechnol (NY) 2012; 14:752-761. [PMID: 22527269 DOI: 10.1007/s10126-012-9448-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/18/2012] [Indexed: 05/31/2023]
Abstract
Viral hemorrhagic septicemia virus (VHSV) is a serious disease impacting wild and cultured fish worldwide. Hence, an effective therapeutic method against VHSV infection needs to be developed. Aptamer technology is a new and promising method for diagnostics and therapeutics. It revolves around the use of an aptamer molecule, an artificial ligand (nucleic acid or protein), which has the capacity to recognize target molecules with high affinity and specificity. Here, we aimed at selecting RNA aptamers that can specifically bind to and inhibit the growth of a strain of fish VHSV both in vitro and in vivo. Three VHSV-specific RNA aptamers (F1, F2, and C6) were selected from a pool of artificially and randomly produced oligonucleotides using systematic evolution of ligands by exponential enrichment. The three RNA aptamers showed obvious binding to VHSV in an electrophoretic mobility shift assay but not to other tested viruses. The RNA aptamers were tested for their ability to inhibit VHSV in vitro using hirame natural embryo (HINAE) cells. Cytopathic effect and plaque assays showed that all aptamers inhibited the growth of VHSV in HINAE cells. In vivo tests using RNA aptamers produced by Rhodovulum sulfidophilum showed that extracellular RNA aptamers inhibited VHSV infection in Japanese flounder. These results suggest that the RNA aptamers are a useful tool for protection against VHSV infection in Japanese flounder.
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Affiliation(s)
- Porntep Punnarak
- Laboratory of Genome Science, Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
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Hwang SD, Midorikawa N, Punnarak P, Kikuchi Y, Kondo H, Hirono I, Aoki T. Inhibition of Hirame rhabdovirus growth by RNA aptamers. J Fish Dis 2012; 35:927-934. [PMID: 22943666 DOI: 10.1111/jfd.12000] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Revised: 07/19/2012] [Accepted: 07/24/2012] [Indexed: 06/01/2023]
Abstract
RNA aptamers are artificial nucleic acids that specifically bind to a wide variety of targets. They are an effective tool for pharmaceutical research and development of antiviral agents. Here, we describe four Hirame rhabdovirus (HIRRV)-RNA aptamers (H1, H2, H3 and H4) that we obtained from an in vitro process called the systematic evolution of ligands by exponential enrichment (SELEX). The HIRRV-RNA aptamers specifically bind to HIRRV. Hirame natural embryo (HINAE) cells treated with virus and the RNA aptamer showed a decrease in appearance of cytopathic effect when compared with control (treated only with virus). Rhodovulum sulfidophilum was transformed with genes for the RNA aptamers, and the aptamers were detected in the culture medium, indicating that they were secreted from the cells. Thus, the recombinant R. sulfidophilum might be a powerful tool for the prevention of HIRRV in aquaculture.
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Affiliation(s)
- S D Hwang
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Minato-ku, Tokyo, Japan
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