Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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The fish egg microbiome : diversity and activity against the oomycete pathogen Saprolegnia
Liu, Y. - \ 2016
Wageningen University. Promotor(en): Francine Govers; Jos Raaijmakers, co-promotor(en): Irene de Bruijn. - Wageningen : Wageningen University - ISBN 9789462577671 - 169
salmon - fish eggs - marine microorganisms - microbial diversity - bioinformatics - genomics - saprolegnia - oomycota - fish diseases - suppression - fungal antagonists - zalm - visseneieren - mariene micro-organismen - microbiële diversiteit - bio-informatica - genomica - saprolegnia - oömycota - visziekten - onderdrukking - schimmelantagonisten

Y. Liu

Prof. dr. F. Govers (promotor); Prof. dr. J.M. Raaijmakers (promotor); Dr. I. de Bruijn (co-promotor); Wageningen University, 13 June 2016, 170 pp.

The fish egg microbiome: diversity and activity against the oomycete pathogen Saprolegnia

Emerging oomycete pathogens increasingly threaten biodiversity and food security. This thesis describes the study of the microbiome of Atlantic salmon (Salmo salar L.) eggs and analyses of the effects of infections by the oomycete pathogen Saprolegnia on the microbial architecture. A low incidence of Saprolegniosis was correlated with a relatively high abundance and richness of specific commensal Actinobacteria. Among the bacterial community, the isolates Frondihabitans sp. 762G35 (Microbacteriaceae) and Pseudomonas sp. H6 significantly inhibited hyphal attachment of Saprolegnia diclina to live salmon eggs. Chemical profiling showed that these two isolates produce furancarboxylic acid-derived metabolites and a lipopeptide viscosin-like biosurfactant, respectively, which inhibited hyphal growth of S. diclina in vitro. Among the fungal community, the fungal isolates obtained from salmon eggs were closely related to Microdochium lycopodinum/Microdochium phragmitis and Trichoderma viride. Both a quantitative and qualitative difference in the Trichoderma population between Saprolegnia-infected and healthy salmon eggs was observed, which suggested that mycoparasitic Trichoderma species could play a role in Saprolegnia suppression in aquaculture. This research provides a scientific framework for studying the diversity and dynamics of microbial communities to mitigate emerging diseases. The Frondihabitans, Pseudomonas and Trichoderma isolates, and/or their bioactive metabolites, are proposed as effective candidates to control Saprolegniosis.

Diversity of aquatic Pseudomonas species and their activity against the fish pathogenic oomycete Saprolegnia
Liu, Y. ; Rzeszutek, E. ; Voort, M. van der; Wu, C.H. ; Thoen, E. ; Skaar, I. ; Bulone, V. ; Dorrestein, P.C. ; Raaijmakers, J.M. ; Bruijn, I. de - \ 2015
PLoS ONE 10 (2015)8. - ISSN 1932-6203 - 17 p.
cyclic lipopeptide surfactants - anguilla-australis richardson - media strain a199 - fluorescens - biosynthesis - parasitica - bacteria - chytridiomycosis - aquaculture - infections
Emerging fungal and oomycete pathogens are increasingly threatening animals and plants globally. Amongst oomycetes, Saprolegnia species adversely affect wild and cultivated populations of amphibians and fish, leading to substantial reductions in biodiversity and food productivity. With the ban of several chemical control measures, new sustainable methods are needed to mitigate Saprolegnia infections in aquaculture. Here, PhyloChip-based community analyses showed that the Pseudomonadales, particularly Pseudomonas species, represent one of the largest bacterial orders associated with salmon eggs from a commercial hatchery. Among the Pseudomonas species isolated from salmon eggs, significantly more biosurfactant producers were retrieved from healthy salmon eggs than from Saprolegnia-infected eggs. Subsequent in vivo activity bioassays showed that Pseudomonas isolate H6 significantly reduced salmon egg mortality caused by Saprolegnia diclina. Live colony mass spectrometry showed that strain H6 produces a viscosin-like lipopeptide surfactant. This biosurfactant inhibited growth of Saprolegnia in vitro, but no significant protection of salmon eggs against Saprolegniosis was observed. These results indicate that live inocula of aquatic Pseudomonas strains, instead of their bioactive compound, can provide new (micro)biological and sustainable means to mitigate oomycete diseases in aquaculture.
Bacterie beschermt zalmeitje tegen schimmel (interview met I. de Bruijn en Y. Liu)
Bruijn, Irene de; Liu, Yiying - \ 2014
Deciphering microbial landscapes of fish eggs to mitigate emerging diseases
Liu, Y. ; Bruijn, I. de; Jack, A.L.H. ; Drynan, K. ; Berg, A.H. van den; Thoen, E. ; Sandoval-Sierra, V. ; Skaar, I. ; West, P. van; Diéguez-Uribeondo, J. ; Voort, M. van der; Mendez, R. ; Mazzola, M. ; Raaijmakers, J.M. - \ 2014
ISME Journal 8 (2014). - ISSN 1751-7362 - p. 2002 - 2014.
saprolegnia-parasitica - rhizosphere microbiome - aphanomyces-invadans - virulence factors - maternal transfer - wild populations - sp nov. - fungi - bacteria - molds
Animals and plants are increasingly suffering from diseases caused by fungi and oomycetes. These emerging pathogens are now recognized as a global threat to biodiversity and food security. Among oomycetes, Saprolegnia species cause significant declines in fish and amphibian populations. Fish eggs have an immature adaptive immune system and depend on nonspecific innate defences to ward off pathogens. Here, meta-taxonomic analyses revealed that Atlantic salmon eggs are home to diverse fungal, oomycete and bacterial communities. Although virulent Saprolegnia isolates were found in all salmon egg samples, a low incidence of Saprolegniosis was strongly correlated with a high richness and abundance of specific commensal Actinobacteria, with the genus Frondihabitans (Microbacteriaceae) effectively inhibiting attachment of Saprolegniato salmon eggs. These results highlight that fundamental insights into microbial landscapes of fish eggs may provide new sustainable means to mitigate emerging diseases.
Bacterie beschermt zalmeitje tegen schimmel (interview met I. de Bruijn en Y. Liu)
Ramaker, R. ; Bruijn, I. de; Liu, Y. - \ 2014
Resource: weekblad voor Wageningen UR 8 (2014)16. - ISSN 1874-3625 - p. 9 - 9.
aquacultuur - zalmteelt - gastheer parasiet relaties - saprolegnia - oömyceten - visseneieren - actinobacteria - wetenschappelijk onderzoek - aquaculture - salmon culture - host parasite relationships - oomycetes - fish eggs - scientific research
Een bacterie die leeft op zalmeitjes, beschermt zijn gastheer tegen een schadelijke schimmelsoort. Dit ontdekten ecologen van Wageningen Universiteit en het NIOO. De vinding moet ervoor zorgen dat minder eitjes sterven tijdens de zalmkweek.
Interactions between bacteria and Saprolegnia parasitica, causal agent of Saprolegniosis in fish and amphibians
Liu, Y. - \ 2011
In: Book of Abstracts of the EPS PhD Autumn School 'Host-Microbe Interactomics', Wageningen, The Netherlands, 1-3 November 2011. - Wageningen, the Netherlands : - p. 35 - 35.
PO-24 Interactions between bacteria and Saprolegnia parasitica, causal agent of Saprolegniosis in fish and amphibians Yiying Liu EU-SAPRO (Marie Curie International Training Network), The Netherlands Saprolegniosis is a devastating oomycete disease of fish and amphibians and causes substantial economic and environmental damage in aquaculture and natural ecosystems. The predominant causal agents of Saprolegniosis are Saprolegnia parasitica and Saprolegnia declina. In our project, bacterial communities associated with fish eggs were characterized and tested for their ability to inhibit growth of these two oomycete pathogens. BOX-PCR analysis and 16S-rDNA sequencing revealed that the bacterial communities associated with salmon eggs are genetically diverse. Most of the bacterial isolates that inhibit hyphal growth of Saprolegnia were identified as Pseudomonas species. Subsequent in vitro assays showed that many of these antagonistic Pseudomonas strains produce biosurfactants and other extracellular bioactive compounds that cease or restrict Saprolegnia hyphal growth. Fungal strains that were associated with salmon eggs were identified by ITS-sequencing as Trichoderma and Microdochium species. The potential of the identified bacterial and fungal isolates to protect eggs from Saprolegnia infections is ongoing. Also the mechanisms, genes and bioactive compounds involved in inhibition of the growth and pathogenicity of Saprolegnia will be elucidated.
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