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.

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    We will mail you new results for this query: keywords==microbiële diversiteit
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Impact of microbial variability on food safety and quality
Aryani, D.C. - \ 2016
Wageningen University. Promotor(en): Marcel Zwietering, co-promotor(en): Heidy den Besten. - Wageningen : Wageningen University - ISBN 9789462577381 - 190 p.
listeria monocytogenes - lactobacillus plantarum - growth analysis - kinetics - growth models - inactivation - heat stress - strain differences - food safety - milk - ham - microbial diversity - food quality - groeianalyse - kinetica - groeimodellen - inactivatie - warmtestress - stamverschillen - voedselveiligheid - melk - microbiële diversiteit - voedselkwaliteit
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 p.
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 - 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.

Exploring microbial diversity of marine sponges by culture-dependent and molecular approaches
Naim, M.A. - \ 2015
Wageningen University. Promotor(en): Hauke Smidt, co-promotor(en): Detmer Sipkema. - Wageningen : Wageningen University - ISBN 9789462572867 - 220
sponsen - microbiële diversiteit - symbiose - gastheerspecificiteit - zeeschimmels - biodiversiteit - sponges - microbial diversity - symbiosis - host specificity - marine fungi - biodiversity
Summary

Discovery of sponge-grade metazoans dated 650 million years ago proved that sponges have been around since the Precambrian era. Their resilience to ever-changing environmental conditions and their global distribution is one of the features attributed to the symbionts in sponges, which include Archaea, Bacteria and Eukarya. It is yet unknown how sponges attract and select their bacterial associates but mechanisms to maintain or newly acquire their symbionts have been demonstrated, such as vertical and horizontal transmission.

Discovery of species-specific bacterial communities in the marine sponges H. panicea, H. oculata and H. xena which are dominated by an alpha, beta- and gammaproteobacterium, respectively, confirmed host-specificity of bacterial associates in marine sponges from the North Sea, although their function remains unknown. Detection of Chlamydiae in high relative abundance raised the question as to what is their function in the sponge holobiont as they were only distantly related to other known Chlamydiae.

Little is known about the fungal community in marine sponges. This prompted the study of sponge-associated fungi based on molecular analysis. This was previously a difficult enterprise due the large amount of ‘contaminating’ sponge DNA, which is susceptible to amplification with fungi-specific PCR primers as well. The advent of next generation sequencing technology now for the first time allowed to overcome this hurdle by the sheer numbers of sequences that can be generated. This lead to discovery of novel yeast lineages from the phyla Ascomycota and Basidiomycota in North Sea and Mediterranean marine sponges, indicating a much higher diversity of fungi yet to be explored. For instance, yeasts from the order Malasseziales, which are common pathogens of marine animals, were found as the dominant yeasts in many of the sponges tested that were without apparent disease.

A complementary cultivation-dependent approach provided access to fungal isolates. Fungi belonging to the genus Penicillium were found to be the dominant fungi recovered by isolation from the Mediterranean sponges Aplysina aerophoba, Petrosia ficiformis and Corticium candelabrum. In addition, fungi belonging to the order Alternaria and yeasts affiliated to the genus Rhodotorula were isolated multiple times. No overlap was found with the fungal species observed through the molecular study, which indicates that the great plate anomaly also exists for fungi. Many of the fungal Pencilillium and Alternaria strains isolated were shown to have the genetic capacity for producing polyketide synthases (PKS) or PKS-non ribosomal peptide synthase (PKS-NRPS) hybrids. These enzyme complexes are generally responsible for the production of secondary metabolites with a high biological activity.

Isolation of bacteria from H. panicea in a cultivation experiment with a large diversification of media and growth conditions and subsequent comparison of the retrieved microorganisms to bacteria found in the sponge tissue by a molecular approach revealed the presence of bacterial genera that dominate the cultivation library, but comprise of represent minor components of the sponge microbiome. This includes genera such as Bacillus, Paracoccus and Shewanella. Another genus that was commonly isolated from many marine sponges, but only is found at low relative abundance in the sponge microbiome is Pseudovibrio. Phenotypic characterization based on antibiotic resistance and genotypic differentiation based on bacterial BOX elements and presence of halogenase-encoding genes could discriminate closely related strains that could not be distinguished based on their 16 rRNA gene sequence.

In conclusion, this thesis helps to bridge the gap between cultivation-dependent and cultivation-independent studies of sponge-associated bacteria and fungi by clearly defining the frontiers of the gap. The knowledge derived from this thesis could serve as a scientific foundation and inspiration for future microbial diversity studies and provides perspective for analysing and exploiting sponge symbionts.

Community dynamics of complex starter cultures for Gouda-type cheeses and its functional consequences
Erkus, O. - \ 2014
Wageningen University. Promotor(en): Michiel Kleerebezem, co-promotor(en): Eddy Smid. - Wageningen UR : Wageningen - ISBN 9789462570108 - 215
goudse kaas - lactococcus lactis - microbiële diversiteit - gouda cheese - microbial diversity

Lactic acid bacteria (LAB) are used as starter and adjunct cultures for the production of artisanal and industrial fermented milk products such as yoghurt and cheese. Artisanal fermentations is propagated with the transfer of an inoculum from old batch of fermented food to the new batch (back-slopping) to initiate the fermentation with the activity of the indigenous microbiota present in the inoculum. In industrial production, these inocula with indigenous microbiota are replaced with the starter cultures that contain lower numbers of LAB species for better controlled fermentation process and consistent final product quality. Cheese manufacturing is still performed in both artisanal ways and with the use of starter cultures. Gouda cheese starter cultures constitute several strains from the subspecies of Lactococcus lactisand Leuconostocs mesenteroidesin different combinations. The mixed and undefined type of starter culture may harbour variable number of strains that contribute unique functionalities to the cheese manufacturing process. Therefore, understanding, controlling and predicting the cheese manufacturing processes require the determination of strain level diversity in the starter culture, their collective and specific metabolic complement, and their activity throughout the cheese manufacturing process, including the interactions between the strains. The first two studies that are covered in this thesis describes the development of a high resolution AFLP fingerprinting tool allowing the discrimination of closely related strains in the starter culture and the subsequent analysis of the microbial community of Gouda cheese starter with this implemented technique and with metagenomics. Furthermore, the thesis includes the development of another tool to selectively amplify DNA only from live fraction of the microbial community in cheese using propidium monoazide (PMA), which is required to study community dynamics with culture independent approaches. The last study in the thesis describes the effects of the variation in propagation regime on the community composition of a mixed starter culture and connects the composition change to the functionalities that impact on flavour development during cheese manufacturing. Overall, the approaches presented in this thesis are intended to eventually enable accurate prediction and control of the cheese manufacturing process using (un)defined starter cultures, but may also allow rational design and development of new starter cultures.

Analysis of diversity and function of the human small intestinal microbiota
Booijink, C.C.G.M. - \ 2009
Wageningen University. Promotor(en): Willem de Vos; Michiel Kleerebezem; Erwin Zoetendal. - [S.l. : S.n. - ISBN 9789085853626 - 138
darmmicro-organismen - dunne darm - genexpressie - ileostomie - koolhydraatmetabolisme - metabolisme - microbiële diversiteit - functionele biodiversiteit - functionele genomica - genexpressieanalyse - intestinal microorganisms - small intestine - gene expression - ileostomy - carbohydrate metabolism - metabolism - microbial diversity - functional biodiversity - functional genomics - genomics
The gastrointestinal (GI) tract is the main site where the conversion and absorption of food components takes place in humans. As the small intestine is the first site of interaction between the microbiota and ingested food, knowledge about the microbial composition as well as functionality is essential for a complete understanding of the symbiotic interactions and to the potential modulation of metabolically important groups. Subjects carrying an ileostomy were chosen as model system and ileostomy effluent samples were collected over time. The diversity as well as activity of the inhabiting microbiota was analysed in ileostomy effluent samples of five healthy individuals, collected in the morning and afternoon over a period of 28 days. This revealed that the diversity of the ileostomy effluent microbiota was different from that in the faeces, mainly concerning the lower complexity and stability over time. In terms of composition the relative abundance of species belonging to the genera Streptococcus and Veillonella was higher, whereas a lower relative abundance of species related to the Ruminococcus obeum, R. gnavus and Bacteroides plebeius-like organisms was observed in ileostomy effluent samples. Marked differences in microbiota composition between the five subjects with an ileostomy were found, indicative for a highly personal ileal microbiota profile. Differences in microbiota composition profiles were observed over time, even visible within one day, although the overall fluctuations were around a relatively large stable core group, consisting of species belonging to three streptococci-related groups (S. bovis, S. intermedius and S. smitis), Clostridium cluster I, Enterococcus, Veillonella and Oxalobacter formigenes. Overall, the data presented in this thesis indicated that the genus Streptococcus is not only numerically abundant, but also predominates randomly generated metabolic activity profiles of the microbial ecosystem of the ileostomy effluent microbiota. Predominant functions exerted were related to metabolism, especially carbohydrate metabolism and transport. The fast transit of the ileal contents appears to generate an environment in which the capacity to rapidly metabolise the available carbohydrates is an important selective advantage.
Experimental ecology and evolution of microbial diversity : the role of spatial structure
Habets, M.G.J.L. - \ 2008
Wageningen University. Promotor(en): Rolf Hoekstra, co-promotor(en): Arjan de Visser. - S.l. : s.n. - ISBN 9789085048619 - 102
micro-organismen - diversiteit - biodiversiteit - evolutie - ecologie - adaptatie - heterogeniteit - mutanten - microbiële diversiteit - microorganisms - diversity - biodiversity - evolution - ecology - adaptation - heterogeneity - mutants - microbial diversity
In the light of the competitive exclusion principle, which states that complete competitors cannot coexist, many explanations have been sought to explain the high diversity found in nature. The most common explanation is the niche differentiation hypothesis: coexistence is obtained through differentiation of species in ecological niches. Spatial structure is thought to be a factor capable of providing opportunities for niche differentiation. We have focused on four aspects of spatial structure enabling genetic diversity to emerge and /or to be maintained.
First of all, population fragmentation, resulting from growth in spatially structured habitats, can increase diversity, because the resulting smaller subpopulations, due to their smaller population size, are more likely to adaptively diverge. By allowing small and large populations of E. coli to evolve for 500 generations in two different nutrient environments, we test this hypothesis. The results demonstrate higher variance in fitness among small populations, and consequently more heterogeneous adaptive trajectories for small populations, some of which surprisingly lead to higher fitness peaks than reached by even the best adapted large population.
In a short-term invasion experiment between a superior E. coli competitor and its inferior ancestor, we demonstrate that populations residing in structured environments experience slower invasion dynamics of beneficial mutations than well-mixed populations due to limited dispersal, and therefore local competition. Moreover, our results demonstrate a deceleration of invasion with increasing size of the invading subpopulation. This is caused by a decrease of inter specific competition relative to intra specific competition. Since inferior competitors are present in the community for a longer period of time, they can recombine with other persisting lineages or obtain new mutations, some of which might be beneficial. It is therefore possible that polymorphisms arise which would not have had the opportunity to emerge in a well-mixed environment. Even though both population fragmentation and slower competitive dynamics can increase the emergence of diversity, they do not provide a means for their maintenance.
Environmental heterogeneity on the other hand can cause maintenance of diversity. Environmental heterogeneity can be introduced by spatial structure, e.g. by providing gradients in biotic and abiotic factors, thereby increasing the number of niches. By allowing E. coli populations to evolve for 900 generations in either a well-mixed environment or two structured environments (with or without dispersal), we demonstrate stable coexistence of diversity in structured populations without dispersal. This can be attributed to negative frequency-dependent fitness interactions among niche specialists that either inhabit existing niches provided by the heterogeneous environment or new niches constructed by organisms inhabiting the environment.
In addition to examining aspects of spatial structure that provide means for populations to diversify, we examine a specific consequence of slower dynamics and environmental heterogeneity: the probability of mutators to hitchhike to fixation. Understanding the emergence of mutators is not only scientifically important, but also relevant for human health, since high frequencies of mutators have been found in bacterial populations and drug resistant mutants arise more often in mutator populations. E. coli mutator populations were introduced at different starting frequencies in a well-mixed environment and two structured environments differing in their dispersal rate. Contrary to expectations, we find an advantage in the rate of invasion for mutators in well-mixed environments. Faster competitive dynamics may allow a rapid increase of population size and hence a greater supply of mutations for subsequent adaptation. Due to a delay in mutator extinction in structured environments at low frequencies, mutators may gain from fluctuating conditions.






The significance of microbial diversity in agricultural soil for disease suppressiveness
Garbeva, P. - \ 2005
Wageningen University; Leiden University. Promotor(en): J.A. van Veen; J.D. van Elsas, co-promotor(en): E.J.J. Lugtenberg; Lijbert Brussaard. - NWO - 169
micro-organismen - bodemflora - microbiële ecologie - diversiteit - plantenziekten - bedrijfssystemen - bodembeheer - plantenziektebestrijding - microbiële diversiteit - microorganisms - soil flora - microbial ecology - diversity - plant diseases - farming systems - soil management - plant disease control - microbial diversity
Microbial diversity in archived agricultural soils; the past as a guide to the future
Dolfing, J. ; Vos, A. ; Bloem, J. ; Kuikman, P.J. - \ 2004
Wageningen : Alterra (Alterra-rapport 916) - 55
bodembiologie - bodembacteriën - organische verbeteraars - mest - bodembeheer - organisch bodemmateriaal - geschiedenis - landbouwgronden - microbiële diversiteit - soil biology - soil bacteria - organic amendments - manures - soil management - soil organic matter - history - agricultural soils - microbial diversity
Bacterial diversity and bacterially mediated processes are considered key to soil ecosystem functioning through decomposition and mineralization. However, there is a lack of understanding as to how activity and diversity of prokaryotic communities respond to changes in the environment. At present this issue is mostly addressed by real-time monitoring of long term field experiments, which is costly and slow. Using modern molecular methods we re-analyzed soil samples of up to 50 years old that have been stored in the Alterra soil archive TAGA. We showed that it is indeed possible to detect bacterial fingerprints in those samples and that fingerprints from different samples can be distinctly different, for example between fields that have or have not received organic amendments. These results are a promising first step towards unlocking the microbial information present in archived soil samples. This will help to assess the (likelihood of) changes in soil microbial diversity in response to environmental change (climate change) and human interference (fertilization) and to establish a reference condition and situation. This may further enable coupling to more functional assessments of soil functioning in standardized decomposition essays with the stored samples with known differences in diversity.
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