Flavobacteria, a Never Ending Threat for Fish: a Review

Wahli, Thomas; Madsen, Lone

doi:10.1007/s40588-018-0086-x

Cited by 33 publications

(31 citation statements)

References 124 publications

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“…and could be a target site for future fluorescent in situ hybridization probe or quantitative PCR (qPCR) assays. There is a growing recognition of the large number of opportunistic fish pathogens in the genus Flavobacterium , and these microorganisms have been implicated in both aquacultural and wild fish die-offs (38–40), which suggests that management of this genus is critical in recirculating aquaculture. However, control of Flavobacterium spp.…”

Section: Resultsmentioning

confidence: 99%

Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems

Bartelme

Smith

Sepulveda‐Villet

et al. 2019

mSphere

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Flowthrough and pond aquaculture system microbiome management practices aim to mitigate fish disease and stress. However, the operational success of recirculating aquaculture systems (RAS) depends directly on system microbial community activities. In RAS, each component environment is engineered for a specific microbial niche for waste management, as the water continuously flowing through the system must be processed before returning to the rearing tank. In this study, we compared waste management component microbiomes (rearing tank water, pH correction tank, solid-waste clarifier, biofilter, and degassing tower) within a commercial-scale freshwater RAS by high-throughput 16S rRNA gene sequencing. To assess consistency among freshwater RAS microbiomes, we also compared the microbial community compositions of six aquaculture and aquaponic farms. Community assemblages reflected site and source water relationships, and the presence of a hydroponic subsystem was a major community determinant. In contrast to the facility-specific community composition, some sequence variants, mainly classified into Flavobacterium, Cetobacterium, the family Sphingomonadaceae, and nitrifying guilds of ammonia-oxidizing archaea and Nitrospira, were common across all facilities. The findings of this study suggest that, independently of system design, core taxa exist across RAS rearing similar fish species but that system design informs the individual aquatic microbiome assemblages. Future RAS design would benefit from understanding the roles of these core taxa and then capitalizing on their activities to further reduce system waste/added operational controls. IMPORTANCE Recirculating aquaculture systems (RAS) are agroecosystems for intensive on-land cultivation of products of fisheries. Practitioners that incorporate edible plant production into RAS refer to these facilities as aquaponic systems (AP). RAS have the potential to offset declining production levels of wild global fisheries while reducing waste and product distance to market, but system optimization is needed to reduce costs. Both RAS and AP rely on microbial consortia for maintaining water quality and promoting fish/plant health, but little is known about the microorganisms actually present. This lack of knowledge prevents optimization of designs and operational controls to target the growth of beneficial microbial species or consortia. The significance of our research is in identifying the common microorganisms that inhabit production RAS and AP and the operational factors that influence which microorganisms colonize and become abundant. Identifying these organisms is a first step toward advanced control of microbial activities that improve reproducibility and reduce costs.

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Section: Resultsmentioning

confidence: 99%

Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems

Bartelme

Smith

Sepulveda‐Villet

et al. 2019

mSphere

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“…Meanwhile, it was one of the core microbiota in the three examined fish groups with different feeding habits, suggesting its essential role for GI microbial functions. We also identified that the phylum Flavobacteriia, widely considered as an opportunistic pathogens for serious diseases in both farmed and wild fishes [38], appeared much more frequently in BP than in other fishes. Flavobacteriia have the remarkable ability to transform higher-molecular-weight compounds into lower molecules, and uptake hydrogen gas that is produced during nitrogen gas fixation [39].…”

Section: Discussionmentioning

confidence: 99%

A Comparative Metagenomics Study on Gastrointestinal Microbiota in Amphibious Mudskippers and Other Vertebrate Animals

Liang

Wang

et al. 2019

Animals

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Gut microbiomes in various fish species were widely investigated with the rapid development of next-generation sequencing technologies. However, little is known about gastrointestinal (GI) microbial communities in mudskippers, a representative group of marine amphibious fishes, and their comparisons with other vertebrate animals from different habitats. Here, we performed a comprehensive analysis on microbial composition in five representative vertebrate groups (including amphibious mudskippers, marine and freshwater aquatic fishes, amphibians, and terrestrial animals) via operational taxonomic unit (OTU) survey and obtained a microbial gene catalog of five common fish species by metagenome sequencing. We observed that Cyanobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Fusobacteria were the most substantial bacteria in mudskippers. Differential variances in composition patterns of GI microbiota among the vertebrate groups were determined, although Proteobacteria and Firmicutes were the shared phyla with high abundance. In addition, Cetobacterium and Photobacterium were the most abundant genera in core OTUs of these examined omnivores, carnivores, and herbivores. Our metagenomic analysis also showed significant differences between the representative blue-spotted mudskipper and grass carp (both are herbivorous fishes) in microbes at the phylum and class levels and functional gene terms. Moreover, several bacteriocin-related genes were identified in the five common fishes, suggesting their potential contributions to pathogen resistance. In summary, our present work not only sheds new light on the correlation of GI microbiota composition with living habitats and feeding habits of the hosts, but also provides valuable bacterial genetic resources for healthy growth of aquaculture fishes.

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“…It is the etiological agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome (RTFS), both of which principally impact salmonid species (family Salmonidae [2]). These diseases cause significant mortality in farmed/hatchery-reared salmonids and can result in substantial economic losses (2,3). Since its initial description in 1948 in Washington (4), this bacterium has been reported from at least five continents (including Asia, Europe, North America, Australia, and South America), giving it a nearly worldwide distribution, particularly where salmonids are indigenous or introduced (5).…”

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confidence: 99%

Large-Scale Analysis of Flavobacterium psychrophilum Multilocus Sequence Typing Genotypes Recovered from North American Salmonids Indicates that both Newly Identified and Recurrent Clonal Complexes Are Associated with Disease

Knupp

Wiens

Faisal

et al. 2019

Appl Environ Microbiol

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Flavobacterium psychrophilum, the etiological agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome (RTFS), causes significant economic losses in salmonid aquaculture, particularly in rainbow trout (Oncorhynchus mykiss). Prior studies have used multilocus sequence typing (MLST) to examine genetic heterogeneity withinF. psychrophilum. At present, however, its population structure in North America is incompletely understood, as only 107 isolates have been genotyped. Herein, MLST was used to investigate the genetic diversity of an additional 314 North AmericanF. psychrophilumisolates that were recovered from ten fish host species from 20 U.S. states and 1 Canadian province over nearly four decades. These isolates were placed into 66 sequence types (STs), 47 of which were novel, increasing the number of clonal complexes (CCs) in North America from 7 to 12. Newly identified CCs were diverse in terms of host association, distribution, and association with disease. The largestF. psychrophilumCC identified was CC-ST10, within which 10 novel genotypes were discovered, most of which came fromO. mykissexperiencing BCWD. This discovery, among others, provides evidence for the hypothesis that ST10 (i.e., the founding ST of CC-ST10) originated in North America. Furthermore, ST275 (in CC-ST10) was recovered from wild/feral adult steelhead and marks the first recovery of CC-ST10 from wild/feral fish in North America. Analyses also revealed that at the allele level, the diversification ofF. psychrophilumin North America is driven three times more frequently by recombination than random nucleic acid mutation, possibly indicating how new phenotypes emerge within this species.IMPORTANCEFlavobacterium psychrophilumis the causative agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome (RTFS), both of which cause substantial losses in farmed fish populations worldwide. To better prevent and control BCWD and RTFS outbreaks, we sought to characterize the genetic diversity of several hundredF. psychrophilumisolates that were recovered from diseased fish across North America. Results highlighted multipleF. psychrophilumgenetic strains that appear to play an important role in disease events in North American aquaculture facilities and suggest that the practice of trading fish eggs has led to the continental and transcontinental spread of this bacterium. The knowledge generated herein will be invaluable toward guiding the development of future disease prevention techniques.

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Flavobacteria, a Never Ending Threat for Fish: a Review

Cited by 33 publications

References 124 publications

Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems

Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems

A Comparative Metagenomics Study on Gastrointestinal Microbiota in Amphibious Mudskippers and Other Vertebrate Animals

Large-Scale Analysis of Flavobacterium psychrophilum Multilocus Sequence Typing Genotypes Recovered from North American Salmonids Indicates that both Newly Identified and Recurrent Clonal Complexes Are Associated with Disease

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