Impact of abiotic factors and husbandry on saprolegniosis in salmonid farms

Oomycetes of the genus Saprolegnia are widespread in freshwater environment and are among the main path- ogens causing economic losses in salmonid aquaculture. Infections by mycotic agents in fish farming are generally considered to result from chronic stress and poor fish condition associated with water quality problems, adverse environmental conditions, frequent/rough/incorrect handling, concurrent infections, physiological changes associated with reproduction and immunocompromised animals. To identify risk factors for Saprolegnia infections in trout and Atlantic salmon farming, longitudinal studies were carried out in different Italian, Spanish, and Scottish fish farms. Prevalence of saprolegniosis and fish mortality were monitored over time and statistically analysed with respect to husbandry and environmental factors. Overall, statistical results by production cycle (trout vs salmon farming) and by country indicate that the prevalence of Saprolegnia may be influenced by peculiarities of the culture system and farming environment. Nevertheless, a specific set of parameters, including lower water temperature, and handling procedures increased Saprolegnia prevalence in all the considered farms. Particularly, in trout farms Saprolegnia infections represented an important contribution to mortality, and prevalence was influenced by water temperature and pH, and by fish density within the tanks. Similarly, temperature and water quality were the main factors influencing the prev- alence of Saprolegnia in Atlantic salmon farms. Moreover, molecular analyses confirmed the role of S. parasitica as the main pathogenic oomycete in trout and salmon farming in the considered countries. The identification of risk factors for introduction and increase of Saprolegnia infection in fish farms will allow the correct design of bio- security and pathogen control strategie

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi

Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica.

Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica

Competition and parasitism in the native White Clawed Crayfish Austropotamobius pallipes and the invasive Signal Crayfish Pacifastacus leniusculus in the UK

Many crayfish species have been introduced to novel habitats worldwide, often threatening extinction of native species. Here we investigate competitive interactions and parasite infections in the native Austropotamobius pallipes and the invasive Pacifastacus leniusculus from single and mixed species populations in theUK. We found A. pallipes individuals to be significantly smaller in mixed compared to single species populations; conversely P. leniusculus individuals were larger in mixed than in single species populations. Our data provide no support for reproductive interference as a mechanism of competitive displacement and instead suggest competitive exclusion of A. pallipes from refuges by P. leniusculus leading to differential predation. We screened 52 P. leniusculus and 12 A. pallipes for microsporidian infection using PCR. We present the first molecular confirmation of Thelohania contejeani in the native A. pallipes; in addition, we provide the first evidence for T. contejeani in the invasive P. leniusculus. Three novel parasite sequenceswere also isolated fromP. leniusculus with an overall prevalence of microsporidian infection of 38% within this species; we discuss the identity of and the similarity between these three novel sequences. We also screened a subset of fifteen P. leniusculus and three A. pallipes for Aphanomyces astaci, the causative agent of crayfish plague and for the protistan crayfish parasite Psorospermium haeckeli. We found no evidence for infection by either agent in any of the crayfish screened. The high prevalence of microsporidian parasites and occurrence of shared T. contejeani infection lead us to propose that future studies should consider the impact of these parasites on native and invasive host fitness and their potential effects upon the dynamics of native-invader systems

Finding needles in haystacks:Linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.The Intramural Research Programs of the National Center for Biotechnology Information, National Library of Medicine and the National Human Genome Research Institute, both at the National Institutes of Health.http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353am201

Finding needles in haystacks : linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.The Intramural Research Programs of the National Center for Biotechnology Information, National Library of Medicine and the National Human Genome Research Institute, both at the National Institutes of Health.http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353am201

STUDIO DEI FATTORI DI RISCHIO PER SAPROLEGNIOSI IN TROTICOLTURA

Gli oomiceti del genere Saprolegnia hanno un\u2019ampia diffusione in ambiente dulciacquicolo e causano importanti perdite economiche nell\u2019allevamento di specie ittiche d\u2019acqua dolce, in particolare salmonidi. Obiettivo della presente ricerca \ue8 stato quello di indagare i fattori di rischio in grado di favorire l\u2019insorgenza della saprolegniosi in troticoltura mediante uno studio epidemiologico longitudinale. Lo studio \ue8 stato condotto in 10 troticolture (5 in Italia e 5 in Spagna); gli allevamenti sono stati selezionati sulla base della presenza documentata di fattori gestionali considerati rilevanti in riferimento alla saprolegniosi (spremitura dei riproduttori, vaccinazione, selezione, frequenti cambi di vasca, ecc.). Le specie considerate nello studio sono state la trota iridea Onchorhynchus mykiss, la trota marmorata Salmo marmoratus e la trota fario Salmo trutta. In ciascun allevamento sono state condotte da Febbraio 2017 a Gennaio 2018 visite periodiche durante le quali le vasche oggetto di studio sono state controllate periodicamente per valutare la presenza di lesioni riferibili a saprolegniosi e sono state raccolte informazioni relative a fattori gestionali di diverso tipo, presenza di infezioni concomitanti e mortalit\ue0. Durante ciascuna visita sono stati inoltre registrati i paramentri ambientali (pH, temperatura e ossigeno disciolto). Il monitoraggio in continuo della temperatura dell'acqua \ue8 stato effettuato posizionando un data logger all\u2019interno di ciascuna vasca selezionata. Le specie di Saprolegnia circolanti sono state caratterizzate mediante identificazione molecolare dei ceppi isolati da trote campionate in ciascun allevamento nel corso della prima visita. I dati raccolti sono stati analizzati statisticamente con l\u2019obiettivo di correlare prevalenza di saprolegniosi e mortalit\ue0 a diverse pratiche gestionali e fattori ambientali. Tutti gli isolati da trote con segni clinici appartenevano alla specie Saprolegnia parasitica. I risultati delle analisi statistiche indicano che la saprolegniosi rappresenta un\u2019importante causa di mortalit\ue0 nelle troticolture italiane e spagnole oggetto di studio. Con riferimento ai parametri ambientali, \ue8 stato evidenziato un contributo importante della temperatura e del pH dell\u2019acqua. In particolare, si \ue8 confermato come la prevalenza di Saprolegnia sia mediamente pi\uf9 alta durante i mesi freddi (temperatura dell\u2019acqua inferiore a 10\ub0C) evidenziando l\u2019influenza positiva di valori di pH alcalini. Riguardo agli aspetti gestionali, diverse tipologie di \u201chandling\u201d sono risultate fattori di rischio importanti. In uno degli allevamenti monitorati, \ue8 stato rilevato un incremento dei valori di prevalenza per saprolegniosi in seguito a vaccinazione intraperitoneale anche a temperature dell\u2019acqua relativamente elevate (14\ub0C). Inoltre, \ue8 stato osservato come frequenti cambi di vasca siano associati a valori di prevalenza pi\uf9 elevati anche quando, in seguito allo spostamento, la densit\ue0 all\u2019interno delle vasche viene ridotta. L\u2019identificazione dei fattori di rischio per saprolegniosi \ue8 uno step fondamentale per una corretta progettazione ed implementazione di misure di biosicurezza e strategie di gestione finalizzate al controllo di questa parassitosi negli allevamenti di salmonidi