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Pavić D, Geček S, Miljanović A, Grbin D, Bielen A. Characterization of Bacterial Communities on Trout Skin and Eggs in Relation to Saprolegnia parasitica Infection Status. Microorganisms 2024; 12:1733. [PMID: 39203577 PMCID: PMC11357440 DOI: 10.3390/microorganisms12081733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 09/03/2024] Open
Abstract
We have investigated the changes in the microbial communities on the surface of trout eggs and the skin of adult trout in relation to the presence of Saprolegnia parasitica. This pathogen causes saprolegniosis, a disease responsible for significant losses in salmonid farms and hatcheries. It is known from other disease systems that the host-associated microbiome plays a crucial role in the defence against pathogens, but if the pathogen predominates, this can lead to dysbiosis. However, analyses of the effects of S. parasitica on the diversity, composition, and function of microbial communities on fish skin and eggs are scarce. Thus, we have collected skin swabs from injured and healthy trout (N = 12), which differed in S. parasitica load, from three different fish farms in Croatia (Kostanjevac, Radovan, and Solin), while trout egg samples (N = 12) were infected with S. parasitica in the laboratory. Illumina sequencing of the V4 region of the 16S rRNA marker gene showed that infection with S. parasitica reduced the microbial diversity on the surface of the eggs, as evidenced by decreased Pielou's evenness and Shannon's indices. We further determined whether the bacterial genera with a relative abundance of >5.0% in the egg/skin samples were present at significantly different abundances in relation to the presence of S. parasitica. The results have shown that some genera, such as Pseudomonas and Flavobacterium, decreased significantly in the presence of the pathogen on the egg surface. On the other hand, some bacterial taxa, such as Acinetobacter and Janthinobacterium, as well as Aeromonas, were more abundant on the diseased eggs and the injured trout skin, respectively. Finally, beta diversity analyses (weighted UniFrac, unweighted UniFrac, Bray-Curtis) have shown that the sampling location (i.e., fish farm), along with S. parasitica infection status, also has a significant influence on the microbial communities' composition on the trout skin and eggs, demonstrating the strong influence of the environment on the shaping of the host surface microbiome. Overall, we have shown that the presence of S. parasitica was associated with changes in the diversity and structure of the trout skin/egg microbiome. The results obtained could support the development of new strategies for the management of saprolegniosis in aquaculture.
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Affiliation(s)
- Dora Pavić
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia; (D.P.); (A.M.); (D.G.)
| | - Sunčana Geček
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia;
| | - Anđela Miljanović
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia; (D.P.); (A.M.); (D.G.)
| | - Dorotea Grbin
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia; (D.P.); (A.M.); (D.G.)
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Ana Bielen
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia; (D.P.); (A.M.); (D.G.)
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Hammond SW, Lodolo L, Hu SK, Pasulka AL. Methodological 'lenses' influence the characterization of phytoplankton dynamics in a coastal upwelling ecosystem. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:897-906. [PMID: 36071313 DOI: 10.1111/1758-2229.13116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
New technologies enable the opportunity to improve our monitoring and understanding of marine phytoplankton communities. However, careful consideration for how different methodological approaches, or 'lenses', influence our interpretation of phytoplankton ecology is important, particularly when drawing conclusions about change over time or space. Using both high-throughput 18S rRNA gene sequencing and microscopy, we explored how phytoplankton community structure varied over the course of a year within a nearshore semi-enclosed coastal embayment along the Central Coast of California. The seasonal shift in the relative community dominance (i.e., diatom vs. dinoflagellate dominance) was captured in the microscopy results but not effectively captured in the molecular-based findings. However, the molecular approach explained more of the variability in composition across seasons relative to the microscopy approach. Temporal dynamics of specific bloom-forming taxa also differed between the molecular and microscopy results. Overall, the observed differences between the molecular- and microscopy-derived characterization of phytoplankton dynamics suggest that the approaches are best suited to answer different research questions. Moreover, the approaches complement each other for a more comprehensive perspective of a coastal phytoplankton ecosystem. Therefore, identifying the biases of each approach within natural communities is necessary to effectively and accurately characterize phytoplankton communities.
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Affiliation(s)
- S William Hammond
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, USA
| | - Laura Lodolo
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, USA
| | - Sarah K Hu
- Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Alexis L Pasulka
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, USA
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Pavić D, Grbin D, Hudina S, Prosenc Zmrzljak U, Miljanović A, Košir R, Varga F, Ćurko J, Marčić Z, Bielen A. Tracing the oomycete pathogen Saprolegnia parasitica in aquaculture and the environment. Sci Rep 2022; 12:16646. [PMID: 36198674 PMCID: PMC9534867 DOI: 10.1038/s41598-022-16553-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/12/2022] [Indexed: 11/25/2022] Open
Abstract
Saprolegnia parasitica causes saprolegniosis, a disease responsible for significant economic losses in aquaculture and declines of fish populations in the wild, but the knowledge of its distribution and prevalence in the environment is limited. We developed a fast, sensitive and specific S. parasitica droplet digital PCR (ddPCR) assay and demonstrated its applicability for the detection and quantification of the pathogen in environmental samples: swab DNA collected from the host (trout skin, surface of eggs) and environmental DNA extracted from water. The developed assay was used to assess how abiotic (i.e. physico-chemical parameters of the water) and biotic (health status of the host) factors influence the S. parasitica load in the environment. The pathogen load in water samples was positively correlated with some site-specific abiotic parameters such as electrical conductivity (EC) and calcium, while fluorides were negatively correlated, suggesting that physico-chemical parameters are important for determining S. parasitica load in natural waters. Furthermore, skin swabs of injured trout had significantly higher pathogen load than swabs collected from healthy fish, confirming that S. parasitica is a widespread opportunistic pathogen. Our results provide new insights into various environmental factors that influence the distribution and abundance of S. parasitica.
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Affiliation(s)
- Dora Pavić
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia
| | - Dorotea Grbin
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia.,Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Sandra Hudina
- Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | | | - Anđela Miljanović
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia
| | - Rok Košir
- Labena Ltd, BIA Separations CRO - Molecular Biology Laboratory, 1000, Ljubljana, Slovenia
| | - Filip Varga
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, 10000, Zagreb, Croatia.,Centre of Excellence for Biodiversity and Molecular Plant Breeding, CoE CroP-BioDiv), 10000, Zagreb, Croatia
| | - Josip Ćurko
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia
| | - Zoran Marčić
- Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia.
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Ali FF, Al-Taee SK, Al-Jumaa ZM. Isolation, molecular identification, and pathological lesions of Saprolegnia spp. isolated from common carp, Cyprinus carpio in floating cages in Mosul, Iraq. Vet World 2020; 13:2759-2764. [PMID: 33487995 PMCID: PMC7811552 DOI: 10.14202/vetworld.2020.2759-2764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/05/2020] [Indexed: 12/02/2022] Open
Abstract
Background and Aim: Saprolegniasis is a fungal disease that infects freshwater fish. The condition is characterized by a cotton-like appearance in the gills and body. This study aimed to isolate Saprolegnia from common carp, Cyprinus carpio, raised in a floating cage in Wana district, Mosul, Iraq. Materials and Methods: Samples were collected from 15 infected fish and examined microbiologically, molecularly, and histopathologically. Saprolegnia DNA was extracted which was amplified using universal primers give a 540 bp DNA fragment, and gill and muscle tissue were also examined for histopathological changes. Results: Isolated colonies of Saprolegnia were characterized by a circular, white cottony appearance with long hair. Lactophenol staining demonstrated hyphae as branched non-septate, transparent masses. The genomic DNA of isolates was consistent with Saprolegnia spp. The infected tissue samples showed variable pathology in gills. Severe hemorrhage and edema were observed in primary gill filaments with hyperplasia in epithelial cells and infusion in secondary gill filaments. Hyphae of Saprolegnia were seen between necrotic and edematous myofiber with inflammatory cells infiltration. Conclusion: Saprolegnia can cause economic impacts through lethal infection of fish. Clinical signs of Saprolegnia infection were confirmed molecularly and microscopically, and these findings were supported by histopathological lesions in gill and muscle tissues.
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Affiliation(s)
- Fawwaz Fadhil Ali
- Department of Animal Production, Institute of Mosul, Northern Technical University, Mosul, Iraq
| | - Shahbaa Khalil Al-Taee
- Department of Pathology and poultry diseases, College of Veterinary Medicine, Mosul, Iraq
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Ravasi D, De Respinis S, Wahli T. Multilocus sequence typing reveals clonality in Saprolegnia parasitica outbreaks. JOURNAL OF FISH DISEASES 2018; 41:1653-1665. [PMID: 30051543 DOI: 10.1111/jfd.12869] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
The molecular epidemiology of fish pathogen Saprolegnia parasitica is still largely unknown. We developed a multilocus sequence typing scheme based on seven housekeeping genes to characterize 77 S. parasitica strains isolated from different fish host species at different times and from different geographic areas in Switzerland between 2015 and 2017. Ten different diploid sequence types (DSTs) were identified. The majority (52%) of outbreaks in Switzerland seemed to be caused by one genotype, namely DST3, which was recovered from farm-raised and wild-caught fish in all the geographic areas and river basins included in the study. DST3 was also recovered from the rivers Bienne (eastern France) and Doubs, where the episodes of massive mortality due to saprolegniosis started in 2009. Another genotype (DST7) showed, to a lesser extent, a distribution across different river basins, while eight DSTs were unique to a defined geographic area or river basin. The occurrence of sporadic DSTs indicates a certain degree of diversity within S. parasitica in the environment. The wide distribution of DST3 suggests that a clonal population may have spread in eastern France and Switzerland across geographic barriers, with strong implications for the management of both captive and wild fish populations.
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Affiliation(s)
- Damiana Ravasi
- Laboratory of applied microbiology, University of Applied Sciences and Arts of Southern Switzerland, Bellinzona, Switzerland
| | - Sophie De Respinis
- Laboratory of applied microbiology, University of Applied Sciences and Arts of Southern Switzerland, Bellinzona, Switzerland
| | - Thomas Wahli
- Centre for Fish and Wildlife Health, Institute of Animal Pathology, University of Bern, Bern, Switzerland
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