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Ríos-Castro R, Romero A, Aranguren R, Pallavicini A, Banchi E, Novoa B, Figueras A. High-Throughput Sequencing of Environmental DNA as a Tool for Monitoring Eukaryotic Communities and Potential Pathogens in a Coastal Upwelling Ecosystem. Front Vet Sci 2021; 8:765606. [PMID: 34805343 PMCID: PMC8595318 DOI: 10.3389/fvets.2021.765606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/08/2021] [Indexed: 12/04/2022] Open
Abstract
The marine environment includes diverse microeukaryotic organisms that play important functional roles in the ecosystem. With molecular approaches, eukaryotic taxonomy has been improved, complementing classical analysis. In this study, DNA metabarcoding was performed to describe putative pathogenic eukaryotic microorganisms in sediment and marine water fractions collected in Galicia (NW Spain) from 2016 to 2018. The composition of eukaryotic communities was distinct between sediment and water fractions. Protists were the most diverse group, with the clade TSAR (Stramenopiles, Alveolata, Rhizaria, and Telonemida) as the primary representative organisms in the environment. Harmful algae and invasive species were frequently detected. Potential pathogens, invasive pathogenic organisms as well as the causative agents of harmful phytoplanktonic blooms were identified in this marine ecosystem. Most of the identified pathogens have a crucial impact on the aquacultural sector or affect to relevant species in the marine ecosystem, such as diatoms. Moreover, pathogens with medical and veterinary importance worldwide were also found, as well as pathogens that affect diatoms. The evaluation of the health of a marine ecosystem that directly affects the aquacultural sector with a zoonotic concern was performed with the metabarcoding assay.
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Affiliation(s)
- Raquel Ríos-Castro
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Alejandro Romero
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Raquel Aranguren
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Trieste, Italy.,Division of Oceanography, National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Elisa Banchi
- Department of Life Sciences, University of Trieste, Trieste, Italy.,Division of Oceanography, National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Beatriz Novoa
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Antonio Figueras
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
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Sharma A, Sharma D, Verma SK. Zinc binding proteome of a phytopathogen Xanthomonas translucens pv. undulosa. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190369. [PMID: 31598288 PMCID: PMC6774946 DOI: 10.1098/rsos.190369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/21/2019] [Indexed: 05/15/2023]
Abstract
Xanthomonas translucens pv. undulosa (Xtu) is a proteobacteria which causes bacterial leaf streak (BLS) or bacterial chaff disease in wheat and barley. The constant competition for zinc (Zn) metal nutrients contributes significantly in plant-pathogen interactions. In this study, we have employed a systematic in silico approach to study the Zn-binding proteins of Xtu. From the whole proteome of Xtu, we have identified approximately 7.9% of proteins having Zn-binding sequence and structural motifs. Further, 115 proteins were found homologous to plant-pathogen interaction database. Among these 115 proteins, 11 were predicted as putative secretory proteins. The functional diversity in Zn-binding proteins was revealed by functional domain, gene ontology and subcellular localization analysis. The roles of Zn-binding proteins were found to be varied in the range from metabolism, proteolysis, protein biosynthesis, transport, cell signalling, protein folding, transcription regulation, DNA repair, response to oxidative stress, RNA processing, antimicrobial resistance, DNA replication and DNA integration. This study provides preliminary information on putative Zn-binding proteins of Xtu which may further help in designing new metal-based antimicrobial agents for controlling BLS and bacterial chaff infections on staple crops.
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Hirose E, Nakayama K, Yanagida T, Nawata A, Kitamura SI. Measurement of Tunic Hardness in an Edible Ascidian, Halocynthia roretzi, with Remarks on Soft Tunic Syndrome. Zoolog Sci 2018; 35:548-552. [DOI: 10.2108/zs180072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Euichi Hirose
- Department of Chemistry, Biology, and Marine Science, Faculty of Science, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Kei Nakayama
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Tetsuya Yanagida
- Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Akatsuki Nawata
- Miyagi Prefecture Fisheries Technology Institute, Ishinomaki, Miyagi 986-2135, Japan
| | - Shin-Ichi Kitamura
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime 790-8577, Japan
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Kumagai A, Tanabe T, Nawata A, Suto A. Disinfection of fertilized eggs of the edible ascidian Halocynthia roretzi for prevention of soft tunic syndrome. DISEASES OF AQUATIC ORGANISMS 2016; 118:153-158. [PMID: 26912045 DOI: 10.3354/dao02966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Azumiobodo hoyamushi, the causative agent of soft tunic syndrome, was likely introduced to farming sites of the edible ascidian Halocynthia roretzi via ascidian spat. The source of infection is thought to be cysts of A. hoyamushi that reside in the substrates on which the ascidian spat are attached, but not the spat themselves. Thus, there is a need to develop methods to prevent contamination of the substrates with A. hoyamushi during seed production of the ascidian. We evaluated the protozoacidal effects of sodium hypochlorite and povidone-iodine against the flagellate and temporary cyst forms of A. hoyamushi. Additionally, we evaluated the effects of these disinfectants on the development of fertilized ascidian eggs. The flagellate form of A. hoyamushi was completely inactivated by povidone-iodine (5 ppm, 1 min) and sodium hypochlorite (1 ppm, 1 min). The temporary cysts of A. hoyamushi were completely inactivated by both disinfectants (5 ppm, 1 min). Disinfection with 50 ppm povidone-iodine for 15 min or 5 ppm sodium hypochlorite for 15 min had no effect on ascidian embryogenesis. Thus, horizontal transmission of A. hoyamushi via the substrates can be efficiently prevented by disinfecting ascidian eggs or tools used for spawning with povidone-iodine baths ranging from 5 ppm for 1 min to 50 ppm for 15 min without any side effects.
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Affiliation(s)
- Akira Kumagai
- Miyagi Prefecture Fisheries Technology Institute, Kesennuma Fisheries Experimental Station, Kesennuma, Miyagi 988-0181, Japan
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Kimura S, Nakayama K, Wada M, Kim UJ, Azumi K, Ojima T, Nozawa A, Kitamura SI, Hirose E. Cellulose is not degraded in the tunic of the edible ascidian Halocynthia roretzi contracting soft tunic syndrome. DISEASES OF AQUATIC ORGANISMS 2015; 116:143-148. [PMID: 26480917 DOI: 10.3354/dao02913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Soft tunic syndrome is a fatal disease in the edible ascidian Halocynthia roretzi, causing serious damage to ascidian aquaculture in Korea and Japan. In diseased individuals, the tunic, an integumentary extracellular matrix of ascidians, softens and eventually tears. This is an infectious disease caused by the kinetoplastid flagellate Azumiobodo hoyamushi. However, the mechanism of tunic softening remains unknown. Because cellulose fibrils are the main component of the tunic, we compared the contents and structures of cellulose in healthy and diseased tunics by means of biochemical quantification and X-ray diffractometry. Unexpectedly, the cellulose contents and structures of cellulose microfibrils were almost the same regardless of the presence or absence of the disease. Therefore, it is unlikely that thinning of the microfibrils occurred in the softened tunic, because digestion should have resulted in decreases in crystallinity index and crystallite size. Moreover, cellulase was not detected in pure cultures of A. hoyamushi in biochemical and expressed sequence tag analyses. These results indicate that cellulose degradation does not occur in the softened tunic.
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Affiliation(s)
- Satoshi Kimura
- Department of Biomaterial Science, Graduate School of Agricultural and Life Science, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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Nawata A, Hirose E, Kitamura SI, Kumagai A. Encystment and excystment of kinetoplastid Azumiobodo hoyamushi, causal agent of soft tunic syndrome in ascidian aquaculture. DISEASES OF AQUATIC ORGANISMS 2015; 115:253-262. [PMID: 26290510 DOI: 10.3354/dao02897] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Soft tunic syndrome in the edible ascidian Halocynthia roretzi is caused by the kinetoplastid flagellate Azumiobodo hoyamushi, which was found to assume a fusiform cell form with 2 flagella in axenic, pure culture. When the flagellate form was incubated in sterilized artificial seawater (pH 8.4), some of the cells became cyst-like and adhered to the bottom of the culture plate. The cyst-like forms were spherical or cuboidal, and each had 2 flagella encapsulated in its cytoplasm. Encystment was also induced in culture medium alkalified to the pH of seawater (8.4) but not in unmodified (pH 7.2) or acidified media (pH 6.4). More than 95% of the cyst-like cells converted to the flagellate form within 1 d following transfer to seawater containing ascidian tunic extracts from host ascidians. The cyst-like cells were able to survive in seawater with no added nutrients for up to 2 wk at 20°C and for a few months at 5 to 15°C. The survival period in seawater depended on temperature: some cyst-like cells survived 3 mo at 10°C, and ca. 95% of these converted to flagellate forms in seawater containing tunic extracts. Thus, A. hoyamushi is able to persist under adverse conditions in a cyst-like form able to adhere to organic and inorganic substrata for protracted periods of time.
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Affiliation(s)
- Akatsuki Nawata
- Miyagi Prefecture Fisheries Technology Institute, Ishinomaki, Miyagi 986-2135, Japan
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Shin YK, Nam KW, Park KH, Yoon JM, Park KI. Quantitative assessment of Azumiobodo hoyamushi distribution in the tunic of soft tunic syndrome-affected ascidian Halocynthia roretzi using real-time polymerase chain reaction. Parasit Vectors 2014; 7:539. [PMID: 25425505 PMCID: PMC4253000 DOI: 10.1186/s13071-014-0539-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/13/2014] [Indexed: 11/10/2022] Open
Abstract
Background The kinetoplastid parasite, Azumiobodo hoyamushi, is the causative agent of soft tunic syndrome (STS) in ascidians and leads to their mass mortality in Korean waters. This study was conducted to quantify A. hoyamushi density during the development of STS in the tunics of ascidians (Halocynthia roretzi) using real-time polymerase chain reaction (qPCR). Findings The infection intensity of A. hoyamushi, as measured by qPCR, varied depending on the part of the tunic analyzed, as well as the stage of STS development. The highest infection intensity was recorded in the tunics of the siphons. The infection intensity of A. hoyamushi in the siphons was only 2.9 cell/tunic (area, 0.25 cm2) or 106.0 cell/gram tunic (GT) in the early phase of STS, but this value increased dramatically to 16,066 cells/tunic (0.25 cm2) or 617,004 cell/GT at the time of death. The number of A. hoyamushi parasites increased gradually and their distribution spread from the siphons to the other parts of the tunics. Conclusions qPCR enabled the quantitation of A. hoyamushi and the results revealed that parasite density increased as STS progressed. In addition, our results suggested that the siphons might function as the portal of entry for A. hoyamushi during infection.
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Affiliation(s)
- Yun-Kyung Shin
- National Fisheries Research and Development Institute, Busan, 619-705, Republic of Korea.
| | - Ki-Woong Nam
- Department of Aquatic Life Medicine, College of Ocean Science and Technology, Kunsan National University, 558 Daehakno, Gunsan, 573-701, Republic of Korea.
| | - Kwan Ha Park
- Department of Aquatic Life Medicine, College of Ocean Science and Technology, Kunsan National University, 558 Daehakno, Gunsan, 573-701, Republic of Korea.
| | - Jong-Man Yoon
- Department of Aquatic Life Medicine, College of Ocean Science and Technology, Kunsan National University, 558 Daehakno, Gunsan, 573-701, Republic of Korea.
| | - Kyung-Il Park
- Department of Aquatic Life Medicine, College of Ocean Science and Technology, Kunsan National University, 558 Daehakno, Gunsan, 573-701, Republic of Korea.
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Hirose E, Kumagai A, Nawata A, Kitamura SI. Azumiobodo hoyamushi, the kinetoplastid causing soft tunic syndrome in ascidians, may invade through the siphon wall. DISEASES OF AQUATIC ORGANISMS 2014; 109:251-256. [PMID: 24991851 DOI: 10.3354/dao02744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The infectious kinetoplastid Azumiobodo hoyamushi causes 'soft tunic syndrome', a serious problem in aquaculture of the edible ascidian Halocynthia roretzi. Infection tests using diseased tunics demonstrated that juvenile (0.8 yr old) individuals never developed soft tunic syndrome, but all individuals in the other age groups (1.8, 2.8, and 3.8 yr old) showed the disease symptoms. In the infection tests, tunic softening was first observed at the tunic around siphons. Based on ultrastructural observation of the inner wall of the branchial siphon, the tunic lining the inner wall in juveniles (0.5 yr old) was completely covered with cuticle, which had a dense structure to prevent bacterial and protist invasion. In contrast, the tunic was often partly damaged and not covered with cuticle in healthy adults (≥2.5 yr old). The damaged tunic in the siphon wall could be an entrance for A. hoyamushi into the tunic of adult hosts.
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Affiliation(s)
- Euichi Hirose
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
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Park SB, Jang HB, Fagutao FF, Kim YK, Nho SW, Cha IS, Yu JE, Jung TS. Combination treatment against scuticociliatosis by reducing the inhibitor effect of mucus in olive flounder, Paralichthys olivaceus. FISH & SHELLFISH IMMUNOLOGY 2014; 38:282-286. [PMID: 24704417 DOI: 10.1016/j.fsi.2014.03.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 03/13/2014] [Accepted: 03/15/2014] [Indexed: 06/03/2023]
Abstract
The olive flounder, Paralichthys olivaceus, is an economically important food fish in Japan and Korea. Scuticociliatosis is a major parasitic disease, and fatal infection with scuticociliates, or mixed infections with scuticociliates and other pathogenic agents (e.g., Vibrio spp.) cause severe mortalities in farmed olive flounders. To date, however, effective chemotherapeutic treatment of scuticociliatosis has only been reported at the in vitro level. In this study, we employed combination treatment, using benzalkonium chloride (to remove excess mucus from the body surface) and bronopol (to kill the parasites), to overcome the protective effect of mucus by some medicine to the scuticociliates. In the presence of the mucus mixture, the higher dose of bronopol (156 ppm) yielded morphologies and motilities similar to those of ciliates treated with the lower dose of bronopol (80 ppm) in the absence of mucus. We also investigated the in vivo effects of this treatment in field trials involving a total of 15,025 naturally infected flounders. We observed that short-term bath treatments with benzalkonium chloride (50 ppm) followed by bronopol (500 ppm) were effective, assessed by the relative percentage mortality (RPS) value. Thus, this study provides a notable therapeutic strategy by removing the mucus to treat scuticociliatosis in olive flounders at the aquaculture field level.
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Affiliation(s)
- Seong Bin Park
- Lab. of Aquatic Animal Diseases, Research Institute of Life Science, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Gyeongnam, South Korea
| | - Ho Bin Jang
- Lab. of Aquatic Animal Diseases, Research Institute of Life Science, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Gyeongnam, South Korea
| | - Fernand F Fagutao
- Lab. of Aquatic Animal Diseases, Research Institute of Life Science, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Gyeongnam, South Korea
| | - Young Kyu Kim
- Lab. of Aquatic Animal Diseases, Research Institute of Life Science, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Gyeongnam, South Korea
| | - Seong Won Nho
- Lab. of Aquatic Animal Diseases, Research Institute of Life Science, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Gyeongnam, South Korea
| | - In Seok Cha
- Lab. of Aquatic Animal Diseases, Research Institute of Life Science, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Gyeongnam, South Korea
| | - Jong Earn Yu
- Lab. of Aquatic Animal Diseases, Research Institute of Life Science, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Gyeongnam, South Korea
| | - Tae Sung Jung
- Lab. of Aquatic Animal Diseases, Research Institute of Life Science, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701, Gyeongnam, South Korea.
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Kim HJ, Park JS, Park KH, Shin YK, Park KI. The kinetoplastid parasite Azumiobodo hoyamushi, the causative agent of soft tunic syndrome of the sea squirt Halocynthia roretzi, resides in the East Sea of Korea. J Invertebr Pathol 2014; 116:36-42. [DOI: 10.1016/j.jip.2013.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/14/2013] [Accepted: 12/17/2013] [Indexed: 10/25/2022]
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Phylogenomic network and comparative genomics reveal a diverged member of the ΦKZ-related group, marine vibrio phage ΦJM-2012. J Virol 2013; 87:12866-78. [PMID: 24067958 DOI: 10.1128/jvi.02656-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages are the largest reservoir of genetic diversity. Here we describe the novel phage ΦJM-2012. This natural isolate from marine Vibrio cyclitrophicus possesses very few gene contents relevant to other well-studied marine Vibrio phages. To better understand its evolutionary history, we built a mathematical model of pairwise relationships among 1,221 phage genomes, in which the genomes (nodes) are linked by edges representing the normalized number of shared orthologous protein families. This weighted network revealed that ΦJM-2012 was connected to only five members of the Pseudomonas ΦKZ-like phage family in an isolated network, strongly indicating that it belongs to this phage group. However, comparative genomic analyses highlighted an almost complete loss of colinearity with the ΦKZ-related genomes and little conservation of gene order, probably reflecting the action of distinct evolutionary forces on the genome of ΦJM-2012. In this phage, typical conserved core genes, including six RNA polymerase genes, were frequently displaced and the hyperplastic regions were rich in both unique genes and predicted unidirectional promoters with highly correlated orientations. Further, analysis of the ΦJM-2012 genome showed that segments of the conserved N-terminal parts of ΦKZ tail fiber paralogs exhibited evidence of combinatorial assortment, having switched transcriptional orientation, and there was recruitment and/or structural changes among phage endolysins and tail spike protein. Thus, this naturally occurring phage appears to have branched from a common ancestor of the ΦKZ-related groups, showing a distinct genomic architecture and unique genes that most likely reflect adaptation to its chosen host and environment.
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