37 results on '"Boon, Nico"'
Search Results
2. Greenhouse gas emissions from rice microcosms amended with a plant microbial fuel cell
- Author
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Arends, Jan B. A., Speeckaert, Jonas, Blondeel, Evelyne, De Vrieze, Jo, Boeckx, Pascal, Verstraete, Willy, Rabaey, Korneel, and Boon, Nico
- Published
- 2014
- Full Text
- View/download PDF
3. Microbiology and immunology of fish larvae
- Author
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Vadstein, Olav, Bergh, Oivind, Gatesoupe, Francois, Galindo-Villegas, Jorge, Mulero, Victoriano, Picchietti, Simona, Scapigliati, Giuseppe, Makridis, Pavlos, Olsen, Yngvar, Dierckens, Kristof, Defoirdt, Tom, Boon, Nico, De Schryver, Peter, Bossier, Peter, Norwegian Institute of Marine Research, Nutrition, Aquaculture et Génomique (NUAGE), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Department of Cell Biology and Histology, Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA)-University of Amsterdam [Amsterdam] (UvA)-Center for Immunology Amsterdam, Department of Science for Innovative Biology, Agroindustry and Forestry, Tuscia University, Institute of Aquaculture, Laboratory of Aquaculture and Artemia Reference Center, University of Gent, Laboratory of Microbial Ecology and Technology, Universiteit Gent = Ghent University [Belgium] (UGENT), Luis Conceicao, Amos Tandler, Department of Biotechnology, Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU), Nutrition, Métabolisme, Aquaculture (NUMEA), Institut National de la Recherche Agronomique (INRA), Hellenic Center for Marine Research (HCMR), This work was supported in part by the cost action FAO801 LARVANET: Critical success factors for fish larval production in European Aquaculture: a multidisciplinary network, and by the European FP7 project ‘Promicrobe – Microbes as positive actors for more sustainable aquaculture’ (Project Reference: 227197), and by Research Foundation of Flanders (FWO) project ‘Probiont induced functional responses in aquatic organisms’., ProdInra, Archive Ouverte, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA), University of Amsterdam [Amsterdam] (UvA)-Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA)-Center for Immunology Amsterdam, and Ghent University [Belgium] (UGENT)
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microorganism ,animal structures ,[SDV.BA] Life Sciences [q-bio]/Animal biology ,[SDV.IMM] Life Sciences [q-bio]/Immunology ,host-microbe interaction ,genetic structures ,microbial ecology ,poisson ,microbiote ,piscidin ,parasitic diseases ,immunologie ,microbiologie ,[SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology ,fish ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,fungi ,quorum sensing ,larve ,microbe ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,aquaculture ,[SDV.IMM]Life Sciences [q-bio]/Immunology ,mast cell ,human activities - Abstract
International audience; For most marine aquaculture species, one of the main bottlenecks is the stable production of high quality juveniles. The high and unpredictable mortality in the first weeks after hatching of marine fish larvae remains a challenging problem that needs to be solved. The severity of the problem differs between species, but cannot be considered adequately solved for any species. Both scientific evidence and experience in hatcheries for a variety of fish, shrimp and shellfish species are accumulating as support for the hypothesis that detrimental fish–microbe interactions are the cause of these problems. Host–microbe interactions in reared fish are still poorly understood, except for a few pathogens, and empirical data of the quality required to test this hypothesis, are lacking. This article provides an overview on the current knowledge of the microbial environment of fish larvae, including methodological aspects to characterize the microbial community (both using culture-dependent and culture-independent methods). Further, the current knowledge of the immunology of fish larvae is reviewed, including recent advances in the understanding of toll-like receptors, inflammatory cytokines, mast cells and piscidins, and the ontogeny of the adaptive immune system. Finally, we provide an overview of the state of the art with respect to steering of microbial communities associated with fish larvae – both steering of community composition and of its activity (e.g. by quorum sensing interference)
- Published
- 2018
4. Rearing water microbiomes in white leg shrimp (Litopenaeus vannamei) larviculture assemble stochastically and are influenced by the microbiomes of live feed products.
- Author
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Heyse, Jasmine, Props, Ruben, Kongnuan, Pantipa, De Schryver, Peter, Rombaut, Geert, Defoirdt, Tom, and Boon, Nico
- Subjects
WHITELEG shrimp ,MICROBIAL ecology ,WATER ,ANIMAL feeds ,WHITE spot syndrome virus ,ARTEMIA - Abstract
Summary: The development of effective management strategies to reduce the occurrence of diseases in aquaculture is hampered by the limited knowledge on the microbial ecology of these systems. In this study, the dynamics and dominant community assembly processes in the rearing water of Litopenaeus vannamei larviculture tanks were determined. Additionally, the contribution of peripheral microbiomes, such as those of live and dry feeds, to the rearing water microbiome were quantified. The community assembly in the hatchery rearing water over time was dominated by stochasticity, which explains the observed heterogeneity between replicate cultivations. The community undergoes two shifts that match with the dynamics of the algal abundances in the rearing water. Source tracking analysis revealed that 37% of all bacteria in the hatchery rearing water were introduced either by the live or dry feeds, or during water exchanges. The contribution of the microbiome from the algae was the largest, followed by that of the Artemia, the exchange water and the dry feeds. Our findings provide fundamental knowledge on the assembly processes and dynamics of rearing water microbiomes and illustrate the crucial role of these peripheral microbiomes in maintaining health‐promoting rearing water microbiomes. [ABSTRACT FROM AUTHOR]
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- 2021
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- View/download PDF
5. Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals.
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De Vrieze, Jo, De Mulder, Thijs, Matassa, Silvio, Zhou, Jizhong, Angenent, Largus T., Boon, Nico, and Verstraete, Willy
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SUSTAINABLE development ,MICROBIOLOGY ,MICROBIAL communities ,STOCHASTIC processes ,DETERMINISTIC processes ,METAPOPULATION (Ecology) ,MICROBIAL ecology - Abstract
Summary: Pure (single) cultures of microorganisms and mixed microbial communities (microbiomes) have been important for centuries in providing renewable energy, clean water and food products to human society and will continue to play a crucial role to pursue the Sustainable Development Goals. To use microorganisms effectively, microbial engineered processes require adequate control. Microbial communities are shaped by manageable deterministic processes, but also by stochastic processes, which can promote unforeseeable variations and adaptations. Here, we highlight the impact of stochasticity in single culture and microbiome engineering. First, we discuss the concepts and mechanisms of stochasticity in relation to microbial ecology of single cultures and microbiomes. Second, we discuss the consequences of stochasticity in relation to process performance and human health, which are reflected in key disadvantages and important opportunities. Third, we propose a suitable decision tool to deal with stochasticity in which monitoring of stochasticity and setting the boundaries of stochasticity by regulators are central aspects. Stochasticity may give rise to some risks, such as the presence of pathogens in microbiomes. We argue here that by taking the necessary precautions and through clever monitoring and interpretation, these risks can be mitigated. [ABSTRACT FROM AUTHOR]
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- 2020
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6. Discriminating Bacterial Phenotypes at the Population and Single‐Cell Level: A Comparison of Flow Cytometry and Raman Spectroscopy Fingerprinting.
- Author
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García‐Timermans, Cristina, Rubbens, Peter, Heyse, Jasmine, Kerckhof, Frederiek‐Maarten, Props, Ruben, Skirtach, Andre G., Waegeman, Willem, and Boon, Nico
- Abstract
Investigating phenotypic heterogeneity can help to better understand and manage microbial communities. However, characterizing phenotypic heterogeneity remains a challenge, as there is no standardized analysis framework. Several optical tools are available, such as flow cytometry and Raman spectroscopy, which describe optical properties of the individual cell. In this work, we compare Raman spectroscopy and flow cytometry to study phenotypic heterogeneity in bacterial populations. The growth stages of three replicate Escherichia coli populations were characterized using both technologies. Our findings show that flow cytometry detects and quantifies shifts in phenotypic heterogeneity at the population level due to its high‐throughput nature. Raman spectroscopy, on the other hand, offers a much higher resolution at the single‐cell level (i.e., more biochemical information is recorded). Therefore, it can identify distinct phenotypic populations when coupled with analyses tailored toward single‐cell data. In addition, it provides information about biomolecules that are present, which can be linked to cell functionality. We propose a computational workflow to distinguish between bacterial phenotypic populations using Raman spectroscopy and validated this approach with an external data set. We recommend using flow cytometry to quantify phenotypic heterogeneity at the population level, and Raman spectroscopy to perform a more in‐depth analysis of heterogeneity at the single‐cell level. © 2019 International Society for Advancement of Cytometry [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
7. Individual-Based Modelling of Invasion in Bioaugmented Sand Filter Communities.
- Author
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Daly, Aisling J., Baetens, Jan M., Vandermaesen, Johanna, Boon, Nico, Springael, Dirk, and De Baets, Bernard
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SEWAGE filtration ,MICROBIAL communities ,MICROBIAL ecology ,CELL populations ,CELL proliferation - Abstract
Using experimental data obtained from in vitro bioaugmentation studies of a sand filter community of 13 bacterial species, we develop an individual-based model representing the in silico counterpart of this synthetic microbial community. We assess the inter-species interactions, first by identifying strain identity effects in the data then by synthesizing these effects into a competition structure for our model. Pairwise competition outcomes are determined based on interaction effects in terms of functionality. We also consider non-deterministic competition, where winning probabilities are assigned based on the relative intrinsic competitiveness of each strain. Our model is able to reproduce the key qualitative dynamics observed in in vitro experiments with similar synthetic sand filter communities. Simulation outcomes can be explained based on the underlying competition structures and the resulting spatial dynamics. Our results highlight the importance of community diversity and in particular evenness in stabilizing the community dynamics, allowing us to study the establishment and development of these communities, and thereby illustrate the potential of the individual-based modelling approach for addressing microbial ecological theories related to synthetic communities. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
8. Greenhouse gas (GHG) emissions from rice paddy soils amended with a plant microbial fuel cell
- Author
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Arends, Jan, Blondeel, Evelyne, Boeckx, Pascal, Verstraete, Willy, Rabaey, Korneel, and Boon, Nico
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Microbial ecology ,Nitrous oxide ,Earth and Environmental Sciences ,Rhizosphere ,Oryza sativa ,Hydrogenotrophic methanogens ,Methane ,Bioelectrochemical system ,Electrode material - Abstract
Microbial metabolism in a mixed culture anode of microbial fuel cell fed with mixed sources of organic carbon largely resembles the metabolism found in anaerobic environments (digesters, sediments) where CH4 is the end product instead of electrical current. It is hypothesized that current generation is a viable competitor to steer or control CH4 emissions from (cultivated) wetlands. It has already been shown that a plant-MFC is capable of efficiently converting organic carbon derived from rhizodeposition into an electrical current. To understand the interaction between methanogenic metabolism and current generation in waterlogged sediments, several microcosm studies have been carried out.
- Published
- 2012
9. Reconciliation between operational taxonomic units and species boundaries.
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Mysara, Mohamed, Vandamme, Peter, Props, Ruben, Kerckhof, Frederiek-Maarten, Leys, Natalie, Boon, Nico, Raes, Jeroen, and Monsieurs, Pieter
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MICROBIAL diversity ,RIBOSOMAL RNA genetics ,SYMPATRIC speciation ,MOLECULAR genetics ,MICROBIAL ecology - Abstract
The development of high-throughput sequencing technologies has revolutionised the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into operational taxonomic units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for bacterial species. Our results show that the robustness of such a generalised cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene. It will lead to biases in diversity metrics and makes it hard to compare results obtained with amplicons derived with different primer sets. The method introduced within this work takes into account the differential evolutional rates of taxonomic lineages in order to define a dynamic and taxonomic-dependent OTU clustering cut-off score. For a taxonomic family consisting of species showing high evolutionary conservation in the amplified variable regions, the cut-off will be more stringent than 97%. By taking into consideration the amplified variable regions and the taxonomic family when defining this cut-off, such a threshold will lead to more robust results and closer correspondence between OTUs and species. This approach has been implemented in a publicly available software package called DynamiC. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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10. Impact of bio-palladium nanoparticles (bio-Pd NPs) on the activity and structure of a marine microbial community.
- Author
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Nuzzo, Andrea, Hosseinkhani, Baharak, Boon, Nico, Zanaroli, Giulio, and Fava, Fabio
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NANOPARTICLES ,BIOREMEDIATION ,MICROBIAL ecology ,PALLADIUM ,ECOLOGY ,SAFETY - Abstract
Biogenic palladium nanoparticles (bio-Pd NPs) represent a promising catalyst for organohalide remediation in water and sediments. However, the available information regarding their possible impact in case of release into the environment, particularly on the environmental microbiota, is limited. In this study the toxicity of bio-Pd NPs on the model marine bacterium V. fischeri was assessed. The impacts of different concentrations of bio-Pd NPs on the respiratory metabolisms (i.e. organohalide respiration, sulfate reduction and methanogenesis) and the structure of a PCB-dechlorinating microbial community enriched form a marine sediment were also investigated in microcosms mimicking the actual sampling site conditions. Bio-Pd NPs had no toxic effect on V. fischeri . In addition, they had no significant effects on PCB-dehalogenating activity, while showing a partial, dose-dependent inhibitory effect on sulfate reduction as well as on methanogenesis. No toxic effects by bio-Pd NPs could be also observed on the total bacterial community structure, as its biodiversity was increased compared to the not exposed community. In addition, resilience of the microbial community to bio-Pd NPs exposure was observed, being the final community organization (Gini coefficient) of samples exposed to bio-Pd NPs similar to that of the not exposed one. Considering all the factors evaluated, bio-Pd NPs could be deemed as non-toxic to the marine microbiota in the conditions tested. This is the first study in which the impact of bio-Pd NPs is extensively evaluated over a microbial community in relevant environmental conditions, providing important information for the assessment of their environmental safety. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
11. Measuring the biodiversity of microbial communities by flow cytometry.
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Props, Ruben, Monsieurs, Pieter, Mysara, Mohamed, Clement, Lieven, Boon, Nico, and Hodgson, David
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MICROBIAL diversity ,BIODIVERSITY ,FLOW cytometry ,ECOSYSTEM dynamics ,RIBOSOMAL RNA genetics ,MICROBIAL ecology - Abstract
Measuring the microbial diversity in natural and engineered environments is important for ecosystem characterization, ecosystem monitoring and hypothesis testing. Although the conventional assessment through single marker gene surveys has resulted in major advances, the complete procedure remains slow (i.e. weeks to months), labour-intensive and susceptible to multiple sources of laboratory and data processing bias. Growing interest, in highly resolved, temporal surveys of microbial diversity, necessitates rapid, inexpensive and robust analytical platforms that require limited computational effort., Here, we demonstrate that sensitive single-cell measurements of phenotypic attributes, obtained via flow cytometry, can provide fast (i.e. within minutes) first-line assessments of microbial diversity dynamics, without demanding extensive sample preparation and downstream data processing. We developed a data processing pipeline that fits bivariate kernel density functions to phenotypic parameter combinations of an entire microbial community and concatenates them to a single one-dimensional phenotypic fingerprint. By calculating established diversity metrics from such phenotypic fingerprints, we construct an alternative interpretation of the microbial diversity that incorporates distinct phenotypic traits underlying cell-to-cell heterogeneity (i.e. morphology and nucleic acid content)., Based on a detailed longitudinal study of a highly dynamic microbial ecosystem, our approach delivered temporal alpha diversity profiles that strongly correlated with the reference diversity, as estimated by 16S rRNA amplicon sequencing. This strongly suggests that the distribution of a limited amount of phenotypic features within a microbial community already provides sufficient resolving power for the measurement of diversity dynamics at the species level., We present a fast, robust analysis method for monitoring the microbial biodiversity of natural and engineered ecosystems that correlates well with the conventional marker gene surveys. Our work has both applied and fundamental implications that stretch from ecosystem monitoring and studies on microbial community dynamics, to supervised sampling strategies. Furthermore, our approach offers perspectives for the development of online and in situ monitoring systems for microbial ecosystems. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
12. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System.
- Author
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Adrian Ho, Angel, Roey, Veraart, Annelies J., Daebeler, Anne, Zhongjun Jia, Sang Yoon Kim, Kerckhof, Frederiek-Maarten, Boon, Nico, and Bodelier, Paul L. E.
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BIOGEOCHEMICAL cycles ,MICROBIAL ecology ,OXIDATION ,METHANE - Abstract
Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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13. Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofilters.
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Bagchi, Samik, Vlaeminck, Siegfried E., Sauder, Laura A., Mosquera, Mariela, Neufeld, Josh D., and Boon, Nico
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AMMONIA-oxidizing archaebacteria ,AQUARIUM animals ,BIOFILTERS ,NITRIFYING bacteria ,QUANTITATIVE research ,POLYMERASE chain reaction - Abstract
Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4–5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥81–86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium biofilters, and that AOA community composition within a given aquarium is stable over time and across biofilter support material types. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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- View/download PDF
14. The more, the merrier: heterotroph richness stimulates methanotrophic activity.
- Author
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Ho, Adrian, de Roy, Karen, Thas, Olivier, De Neve, Jan, Hoefman, Sven, Vandamme, Peter, Heylen, Kim, and Boon, Nico
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HETEROTROPHIC bacteria ,METHANOTROPHS ,MICROBIAL ecology ,OXIDATION ,METHANE ,MICROBIAL diversity - Abstract
Although microorganisms coexist in the same environment, it is still unclear how their interaction regulates ecosystem functioning. Using a methanotroph as a model microorganism, we determined how methane oxidation responds to heterotroph diversity. Artificial communities comprising of a methanotroph and increasing heterotroph richness, while holding equal starting cell numbers were assembled. We considered methane oxidation rate as a functional response variable. Our results showed a significant increase of methane oxidation with increasing heterotroph richness, suggesting a complex interaction in the cocultures leading to a stimulation of methanotrophic activity. Therefore, not only is the methanotroph diversity directly correlated to methanotrophic activity for some methanotroph groups as shown before, but also the richness of heterotroph interacting partners is relevant to enhance methane oxidation too. In this unprecedented study, we provide direct evidence showing how heterotroph richness exerts a response in methanotroph-heterotroph interaction, resulting in increased methanotrophic activity. Our study has broad implications in how methanotroph and heterotroph interact to regulate methane oxidation, and is particularly relevant in methane-driven ecosystems. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
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15. Optimized Cryopreservation of Mixed Microbial Communities for Conserved Functionality and Diversity.
- Author
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Kerckhof, Frederiek-Maarten, Courtens, Emilie N. P., Geirnaert, Annelies, Hoefman, Sven, Ho, Adrian, Vilchez-Vargas, Ramiro, Pieper, Dietmar H., Jauregui, Ruy, Vlaeminck, Siegfried E., Van de Wiele, Tom, Vandamme, Peter, Heylen, Kim, and Boon, Nico
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CRYOPRESERVATION of organs, tissues, etc. ,MICROBIAL diversity ,BIOMES ,CRYOPROTECTIVE agents ,METHANOTROPHS ,GREENHOUSE gases ,POLLUTANTS - Abstract
The use of mixed microbial communities (microbiomes) for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA). Microbiomes were selected based upon relevance towards applications: (1) a methanotrophic co-culture (MOB), with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2) an oxygen limited autotrophic nitrification/denitrification (OLAND) biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3) fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at −80°C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB) and anaerobic AOB (AnAOB, anammox) in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO) and DMSO plus trehalose and tryptic soy broth (DMSO+TT)] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing) was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. This will allow individual laboratories and culture collections to boost the use of microbiomes in biotechnological applications. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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16. Characterization of Staphylococcus and Corynebacterium Clusters in the Human Axillary Region.
- Author
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Callewaert, Chris, Kerckhof, Frederiek-Maarten, Granitsiotis, Michael S., Van Gele, Mireille, Van de Wiele, Tom, and Boon, Nico
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CORYNEBACTERIUM ,AXILLARY artery ,STAPHYLOCOCCUS ,MICROBIOLOGY ,DERMATOLOGY ,SKIN infections ,SYMMETRY (Biology) - Abstract
The skin microbial community is regarded as essential for human health and well-being, but likewise plays an important role in the formation of body odor in, for instance, the axillae. Few molecular-based research was done on the axillary microbiome. This study typified the axillary microbiome of a group of 53 healthy subjects. A profound view was obtained of the interpersonal, intrapersonal and temporal diversity of the human axillary microbiota. Denaturing gradient gel electrophoresis (DGGE) and next generation sequencing on 16S rRNA gene region were combined and used as extent to each other. Two important clusters were characterized, where Staphylococcus and Corynebacterium species were the abundant species. Females predominantly clustered within the Staphylococcus cluster (87%, n = 17), whereas males clustered more in the Corynebacterium cluster (39%, n = 36). The axillary microbiota was unique to each individual. Left-right asymmetry occurred in about half of the human population. For the first time, an elaborate study was performed on the dynamics of the axillary microbiome. A relatively stable axillary microbiome was noticed, although a few subjects evolved towards another stable community. The deodorant usage had a proportional linear influence on the species diversity of the axillary microbiome. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
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17. Microbiology and immunology of fish larvae.
- Author
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Vadstein, Olav, Bergh, Øivind, Gatesoupe, François-Joel, Galindo-Villegas, Jorge, Mulero, Victoriano, Picchietti, Simona, Scapigliati, Giuseppe, Makridis, Pavlos, Olsen, Yngvar, Dierckens, Kristof, Defoirdt, Tom, Boon, Nico, De Schryver, Peter, and Bossier, Peter
- Subjects
FISH immunology ,MICROBIOLOGY ,FISH larvae microbiology ,FISH larvae physiology ,CYTOKINES ,QUORUM sensing - Abstract
For most marine aquaculture species, one of the main bottlenecks is the stable production of high quality juveniles. The high and unpredictable mortality in the first weeks after hatching of marine fish larvae remains a challenging problem that needs to be solved. The severity of the problem differs between species, but cannot be considered adequately solved for any species. Both scientific evidence and experience in hatcheries for a variety of fish, shrimp and shellfish species are accumulating as support for the hypothesis that detrimental fish-microbe interactions are the cause of these problems. Host-microbe interactions in reared fish are still poorly understood, except for a few pathogens, and empirical data of the quality required to test this hypothesis, are lacking. This article provides an overview on the current knowledge of the microbial environment of fish larvae, including methodological aspects to characterize the microbial community (both using culture-dependent and culture-independent methods). Further, the current knowledge of the immunology of fish larvae is reviewed, including recent advances in the understanding of toll-like receptors, inflammatory cytokines, mast cells and piscidins, and the ontogeny of the adaptive immune system. Finally, we provide an overview of the state of the art with respect to steering of microbial communities associated with fish larvae - both steering of community composition and of its activity (e.g. by quorum sensing interference). [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
18. Nutrient gradients in a granular activated carbon biofilter drives bacterial community organization and dynamics
- Author
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Boon, Nico, Pycke, Benny F.G., Marzorati, Massimo, and Hammes, Frederik
- Subjects
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ACTIVATED carbon , *WATER filters , *AQUATIC microbiology , *DRINKING water , *WATER quality , *BIOTIC communities , *SPECIES diversity , *BIOLOGICAL nutrient removal - Abstract
Abstract: The quality of drinking water is ensured by hygienic barriers and filtration steps, such as ozonation and granular activated carbon (GAC) filtration. Apart from adsorption, GAC filtration involves microbial processes that remove biodegradable organic carbon from the ozonated ground or surface water and ensures biological stability of the treated water. In this study, microbial community dynamics in were monitored during the start-up and maturation of an undisturbed pilot-scale GAC filter at 4 depths (10, 45, 80 and 115 cm) over a period of 6 months. New ecological tools, based on 16S rRNA gene-DGGE, were correlated to filter performance and microbial activity and showed that the microbial gradients developing in the filter was of importance. At 10 cm from the top, receiving the freshly ozonated water with the highest concentration of nutrients, the microbial community dynamics were minimal and the species richness remained low. However, the GAC samples at 80–115 cm showed a 2–3 times higher species richness than the 10–45 cm samples. The highest biomass densities were observed at 45–80 cm, which corresponded with maximum removal of dissolved and assimilable organic carbon. Furthermore, the start-up period was clearly distinguishable using the Lorenz analysis, as after 80 days, the microbial community shifted to an apparent steady-state condition with increased evenness. This study showed that GAC biofilter performance is not necessarily correlated to biomass concentration, but rather that an elevated functionality can be the result of increased microbial community richness, evenness and dynamics. [Copyright &y& Elsevier]
- Published
- 2011
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- View/download PDF
19. Bacterial community structure corresponds to performance during cathodic nitrate reduction.
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Wrighton, Kelly C., Virdis, Bernardino, Clauwaert, Peter, Read, Suzanne T., Daly, Rebecca A., Boon, Nico, Piceno, Yvette, Andersen, Gary L., Coates, John D., and Rabaey, Korneel
- Subjects
MICROBIAL ecology ,MICROBIAL fuel cells ,MICROBIAL biotechnology ,CATHODES ,BIOFILMS - Abstract
Microbial fuel cells (MFCs) have applications other than electricity production, including the capacity to power desirable reactions in the cathode chamber. However, current knowledge of the microbial ecology and physiology of biocathodes is minimal, and as a result more research dedicated to understanding the microbial communities active in cathode biofilms is required. Here we characterize the microbiology of denitrifying bacterial communities stimulated by reducing equivalents generated from the anodic oxidation of acetate. We analyzed biofilms isolated from two types of cathodic denitrification systems: (1) a loop format where the effluent from the carbon oxidation step in the anode is subjected to a nitrifying reactor which is fed to the cathode chamber and (2) an alternative non-loop format where anodic and cathodic feed streams are separated. The results of our study indicate the superior performance of the loop reactor in terms of enhanced current production and nitrate removal rates. We hypothesized that phylogenetic or structural features of the microbial communities could explain the increased performance of the loop reactor. We used PhyloChip with 16S rRNA (cDNA) and fluorescent in situ hybridization to characterize the active bacterial communities. Our study results reveal a greater richness, as well as an increased phylogenetic diversity, active in denitrifying biofilms than was previously identified in cathodic systems. Specifically, we identified Proteobacteria, Firmicutes and Chloroflexi members that were dominant in denitrifying cathodes. In addition, our study results indicate that it is the structural component, in terms of bacterial richness and evenness, rather than the phylogenetic affiliation of dominant bacteria, that best corresponds to cathode performance. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
20. How to get more out of molecular fingerprints: practical tools for microbial ecology.
- Author
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Marzorati, Massimo, Wittebolle, Lieven, Boon, Nico, Daffonchio, Daniele, and Verstraete, Willy
- Subjects
MICROBIAL ecology ,GENETIC polymorphisms ,DENATURING gradient gel electrophoresis ,POLYMORPHISM (Zoology) ,HUMAN fingerprints ,MESSENGER RNA ,ENVIRONMENTAL sciences ,POPULATION biology ,ECOLOGY - Abstract
Community-level molecular techniques are widely used in comparative microbial ecology to assess the diversity of microbial communities and their response to changing environments. These include among others denaturing and temperature gradient gel electrophoresis (DGGE/TGGE), single-strand conformation polymorphism (SSCP), length heterogeneity-PCR (LH-PCR), terminal-restriction fragment length polymorphism (tRFLP) and 16S rRNA gene clone libraries. The amount of data derived from these techniques available in literature is continuously increasing and the lack of a universal way to interpret the raw fingerprint itself makes it difficult to compare between different results. Taking the DGGE technique as an example, we propose a setting-independent theoretical interpretation of the DGGE pattern, based on a straightforward processing on three levels of analysis: (i) the range-weighted richness ( Rr) reflecting the carrying capacity of the system, (ii) the dynamics ( Dy) reflecting the specific rate of species coming to significance, and (iii) functional organization ( Fo), defined through a relation between the structure of a microbial community and its functionality. These Rr, Dy and Fo values, each representing a score to describe a microbial community, can be plotted in a 3D graph. The latter represents a visual ecological interpretation of the initial raw fingerprinting pattern. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
21. The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers.
- Author
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Heylen, Kim, Gevers, Dirk, Vanparys, Bram, Wittebolle, Lieven, Geets, Joke, Boon, Nico, and De Vos, Paul
- Subjects
NITRIFICATION ,HEREDITY ,GENETIC transformation ,DENITRIFYING bacteria ,HABITATS ,MICROBIAL ecology - Abstract
Gene sequence analysis of nirS and nirK, both encoding nitrite reductases, was performed on cultivated denitrifiers to assess their incidence in different bacterial taxa and their taxonomical value. Almost half of the 227 investigated denitrifying strains did not render an nir amplicon with any of five previously described primers. NirK and nirS were found to be prevalent in Alphaproteobacteria and Betaproteobacteria, respectively, nirK was detected in the Firmicutes and Bacteroidetes and nirS and nirK with equal frequency in the Gammaproteobacteria. These observations deviated from the hitherto reported incidence of nir genes in bacterial taxa. NirS gene phylogeny was congruent with the 16S rRNA gene phylogeny on family or genus level, although some strains did group within clusters of other bacterial classes. Phylogenetic nirK gene sequence analysis was incongruent with the 16S rRNA gene phylogeny. NirK sequences were also found to be significantly more similar to nirK sequences from the same habitat than to nirK sequences retrieved from highly related taxa. This study supports the hypothesis that horizontal gene transfer events of denitrification genes have occurred and underlines that denitrification genes should not be linked with organism diversity of denitrifiers in cultivation-independent studies. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
22. Evolutionary algorithms and flow cytometry to examine the parameters influencing transconjugant formation.
- Author
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Boon, Nico, Depuydt, Stephen, and Verstraete, Willy
- Subjects
- *
ALGORITHMS , *PSEUDOMONAS , *FLOW cytometry , *ESCHERICHIA coli , *PLASMIDS , *MICROBIAL ecology - Abstract
An evolutionary algorithm was used to determine the optimal combination of parameters for transconjugant formation. As a model system, a gfp tagged TOL plasmid pWW0 was chosen to examine transfer from Pseudomonas putida to Escherichia coli. A comparison of flow cytometry results with plating and microscopy showed that the majority of transconjugants were not culturable. The transconjugant ratio therefore was determined by flow cytometry. The evolutionary algorithm showed that the optimal conditions were obtained at 28°C and at the highest nutrient concentrations. This work demonstrates that evolutionary algorithms can be used to find optimal parameter interactions in environmental microbiology. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
23. Legionella pneumophila in the Environment: The Occurrence of a Fastidious Bacterium in Oligotrophic Conditions.
- Author
-
Devos, Liesbet, Boon, Nico, and Verstraete, Willy
- Subjects
LEGIONELLA pneumophila ,MICROBIAL ecology ,AQUATIC habitats ,ECOLOGY ,MICROORGANISMS - Abstract
Legionella pneumophila, a micro-organism encountered in aquatic environments, can cause serious intracellular infections among humans. Since the bacterium is ubiquitous in aquatic habitats, it appears to be impossible to prevent L. pneumophila from entering man-made water systems. However, many questions concerning the survival and/or growth in the environment, the partners and opponents of L. pneumophila remain unanswered. This review focuses on the factors governing the ecology of L. pneumophila, since there is considerable divergence and even contradiction in literature on its environmental requirements. A key question to be resolved is the discrepancy between the fastidious nature of L. pneumophila in axenic cultures (e.g. 400 mg l
−1 L-cysteine and 250 mg l-1 ferric iron) and the nutritionally poor environments in which it is commonly detected. It is assumed that dense microbial communities, as occurring in sediments and biofilms – but not likely in surface and drinking water, – can provide the necessary growth requirements for L. pneumophila. However, most of the studies concerning L. pneumophila have led to the general opinion that the organism can only multiply in the aquatic environment as a parasite in certain protozoa. The discovery of the non-classical siderophore legiobactin also indicates that the iron requirement for survival and autonomous growth is not as high as has been assumed. It thus appears that in order to control Legionella in the environment, focus should be on the eradication of microbial hotspots in which L. pneumophila resides. [ABSTRACT FROM AUTHOR]- Published
- 2005
- Full Text
- View/download PDF
24. Biofuel Cells Select for Microbial Consortia That Self-Mediate Electron Transfer.
- Author
-
Rabaey, Korneel, Boon, Nico, Siciliano, Steven D., Verhaege, Marc, and Verstraete, Willy
- Subjects
- *
FUEL cells , *BIOTECHNOLOGY , *MICROBIAL ecology , *ELECTRODES , *CHARGE exchange , *DENATURING gradient gel electrophoresis , *PSEUDOMONAS aeruginosa , *ELECTROCHEMICALS industry - Abstract
Microbial fuel cells hold great promise as a sustainable biotechnological solution to future energy needs. Current efforts to improve the efficiency of such fuel cells are limited by the lack of knowledge about the microbial ecology of these systems. The purposes of this study were (i) to elucidate whether a bacterial community, either suspended or attached to an electrode, can evolve in a microbial fuel cell to bring about higher power output, and (ii) to identify species responsible for the electricity generation. Enrichment by repeated transfer of a bacterial consortium harvested from the anode compartment of a biofuel cell in which glucose was used increased the output from an initial level of 0.6 W m-2 of electrode surface to a maximal level of 4.31 W m-2 (664 mV, 30.9 mA) when plain graphite electrodes were used. This result was obtained with an average loading rate of I g of glucose liter-1 day-1 and corresponded to 81% efficiency for electron transfer from glucose to electricity. Cyclic voltammetry indicated that the enhanced microbial consortium had either membrane-bound or excreted redox components that were not initially detected in the community. Dominant species of the enhanced culture were identified by denaturing gradient gel electrophoresis and culturing. The community consisted mainly of facultative anaerobic bacteria, such as Alcaligenes faecalis and Enterococcus gallinarum, which are capable of hydrogen production. Pseudomonas aeruginosa and other Pseudomonas species were also isolated. For several isolates, electrochemical activity was mainly due to excreted redox mediators, and one of these mediators, pyocyanin produced by P. aeruginosa, could be characterized. Overall, the enrichment procedure, irrespective of whether only attached or suspended bacteria were examined, selected for organisms capable of mediating the electron transfer either by direct bacterial transfer or by excretion of redox components. [ABSTRACT FROM AUTHOR]
- Published
- 2004
- Full Text
- View/download PDF
25. Bioaugmentation of soils by increasing microbial richness: missing links.
- Author
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Dejonghe, Winnie, Boon, Nico, Seghers, Dave, Top, Eva M., and Verstraete, Willy
- Subjects
- *
MICROBIAL ecology - Abstract
Presents an erratum on the article 'Bioaugmentation of soils by increasing microbial richness: missing links' published on the periodical Environmental Microbiology.
- Published
- 2001
- Full Text
- View/download PDF
26. The inoculum effect on the ammonia-oxidizing bacterial communities in parallel sequential batch reactors
- Author
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Wittebolle, Lieven, Verstraete, Willy, and Boon, Nico
- Subjects
- *
SEWAGE disposal plants , *BATCH processing , *BIOLOGICAL nutrient removal , *NITRIFICATION , *DENITRIFICATION , *GEL electrophoresis , *POLYMERASE chain reaction , *NITRIFYING bacteria , *WATER quality management , *MICROBIAL ecology - Abstract
Abstract: Three identical sequential batch reactors (SBRs) were each inoculated with sludge from a full-scale wastewater treatment plant (WWTP) treating a waste stream of different origin, i.e. a hospital, a meat processing company, and a municipal WWTP. The SBRs were run in parallel for 84 consecutive days to investigate whether the reactors would become more phylogenetically similar or stay separated concerning their functionality and microbial communities. Overall, the nitrification functionality was high throughout the experiment, and the size and structure of the sludge flocs were very similar. The total bacterial and ammonia-oxidizing bacterial (AOB) communities were analyzed by PCR-DGGE. Cluster analysis demonstrated very distinct bacterial communities in the three SBRs, not showing any trend becoming more similar. The carrying capacity, dynamics and functional organization of the communities were assessed by DGGE analysis and based on these patterns the range-weighted richness, moving window analysis, and constructing Pareto–Lorenz evenness distribution curves were calculated. Between the SBRs, highly comparable internal structure and dynamics of the AOB communities were observed, although they had only one AOB DGGE band in common. These observations indicate that community characteristics such as the extent of biodiversity and dynamics are more important indicators of good microbial functionality than the presence of certain specific species. [Copyright &y& Elsevier]
- Published
- 2009
- Full Text
- View/download PDF
27. Detection of microbial disturbances in a drinking water microbial community through continuous acquisition and advanced analysis of flow cytometry data.
- Author
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Props, Ruben, Rubbens, Peter, Besmer, Michael, Buysschaert, Benjamin, Sigrist, Jurg, Weilenmann, Hansueli, Waegeman, Willem, Boon, Nico, and Hammes, Frederik
- Subjects
- *
DRINKING water microbiology , *ECOLOGICAL disturbances , *MICROBIAL communities , *FLOW cytometry , *HUMAN fingerprints - Abstract
Abstract Detecting disturbances in microbial communities is an important aspect of managing natural and engineered microbial communities. Here, we implemented a custom-built continuous staining device in combination with real-time flow cytometry (RT-FCM) data acquisition, which, combined with advanced FCM fingerprinting methods, presents a powerful new approach to track and quantify disturbances in aquatic microbial communities. Through this new approach we were able to resolve various natural community and single-species microbial contaminations in a flow-through drinking water reactor. Next to conventional FCM metrics, we applied metrics from a recently developed fingerprinting technique in order to gain additional insight into the microbial dynamics during these contamination events. Importantly, we found that multiple community FCM metrics based on different statistical approaches were required to fully characterize all contaminations. Furthermore we found that for accurate cell concentration measurements and accurate inference from the FCM metrics (coefficient of variation ≤ 5%), at least 1000 cells should be measured, which makes the achievable temporal resolution a function of the prevalent bacterial concentration in the system-of-interest. The integrated RT-FCM acquisition and analysis approach presented herein provides a considerable improvement in the temporal resolution by which microbial disturbances can be observed and simultaneously provides a multi-faceted toolset to characterize such disturbances. Graphical abstract Image 1 Highlights • Real-time flow cytometry is combined with advanced flow cytometric fingerprinting data analysis. • Conventional and advanced fingerprinting metrics grant complementary insights in microbial dynamics. • Guidelines for data acquisition and analysis are proposed. • RT-FCM and fingerprinting metrics extend toolset for studying microbial community disturbances. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
28. High-rate activated sludge communities have a distinctly different structure compared to low-rate sludge communities, and are less sensitive towards environmental and operational variables.
- Author
-
Meerburg, Francis A., Vlaeminck, Siegfried E., Roume, Hugo, Seuntjens, Dries, Pieper, Dietmar H., Jauregui, Ruy, Vilchez-Vargas, Ramiro, and Boon, Nico
- Subjects
- *
ACTIVATED sludge process , *WASTE recycling , *WASTEWATER treatment , *AQUATIC microbiology , *MICROBIAL ecology , *SEWAGE disposal plants - Abstract
High-rate activated sludge processes allow for the recovery of organics and energy from wastewaters. These systems are operated at a short sludge retention time and high sludge-specific loading rates, which results in a higher sludge yield and better digestibility than conventional, low-rate activated sludge. Little is known about the microbial ecology of high-rate systems. In this work, we address the need for a fundamental understanding of how high-rate microbial communities differ from low-rate communities. We investigated the high-rate and low-rate communities in a sewage treatment plant in relation to environmental and operational variables over a period of ten months. We demonstrated that (1) high-rate and low-rate communities are distinctly different in terms of richness, evenness and composition, (2) high-rate community dynamics are more variable and less shaped by deterministic factors compared to low-rate communities, (3) sub-communities of continuously core and transitional members are more shaped by deterministic factors than the continuously rare members, both in high-rate and low-rate communities, and (4) high-rate community members showed a co-occurrence pattern similar to that of low-rate community members, but were less likely to be correlated to environmental and operational variables. These findings provide a basis for further optimization of high-rate systems, in order to facilitate resource recovery from wastewater. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
29. Routine bacterial analysis with automated flow cytometry.
- Author
-
Van Nevel, Sam, Koetzsch, Stefan, Weilenmann, Hans-Ulrich, Boon, Nico, and Hammes, Frederik
- Subjects
- *
BACTERIAL cells , *FLOW cytometry , *FLUORESCENCE , *MICROBIOLOGY , *MICROBIAL ecology , *BACTERIA cytology - Abstract
Abstract: The impact of multi-well plate automation on bacterial flow cytometric analyses was investigated. Cell concentrations in up to 96 samples can be measured accurately, as long as a reproducible staining protocol and a total measurement time of below 80min is used. Fluorescence distribution in the samples may, however, display some variability. [Copyright &y& Elsevier]
- Published
- 2013
- Full Text
- View/download PDF
30. Microbial production and environmental applications of Pd nanoparticles for treatment of halogenated compounds
- Author
-
Hennebel, Tom, De Corte, Simon, Verstraete, Willy, and Boon, Nico
- Subjects
- *
HALOGEN compounds , *PALLADIUM , *NANOPARTICLES , *BACTERIA , *PRECIOUS metal reclamation , *POLLUTANTS , *MICROBIAL ecology , *BIOTECHNOLOGY - Abstract
New biological inspired methods were recently developed to recover precious metals from waste streams and to concomitantly produce palladium nanoparticles on bacteria, that is, bio-Pd. This technology offers a variety of opportunities, as the process can considered to be green, tunable, affordable and scalable. The nanoparticle formation and the specific role of the bacteria in the reclamation process are highlighted. The effective performance of bio-Pd as catalyst in dehalogenation reactions, as well as in hydrogenation, reduction and Cg reactions has been extensively described in literature. Especially dehalogenation of environmental contaminants represents a promising market for application of bio-Pd. Therefore, several treatment technologies based on bio-Pd in the different environmental compartments are considered and domains, in which bio-Pd can be used at full scale are described. Finally, the perspectives for implementation of the bio-Pd technology in the future are set forward. [Copyright &y& Elsevier]
- Published
- 2012
- Full Text
- View/download PDF
31. A method for the specific detection of resident bacteria in brine shrimp larvae
- Author
-
Niu, Yufeng, Defoirdt, Tom, Rekecki, Anamaria, De Schryver, Peter, Van den Broeck, Wim, Dong, Shuanglin, Sorgeloos, Patrick, Boon, Nico, and Bossier, Peter
- Subjects
- *
DETECTION of microorganisms , *ARTEMIA , *FISH larvae , *FUNGUS-bacterium relationships , *BACTERIA , *GEL electrophoresis , *MICROBIAL ecology - Abstract
Abstract: In this study, we describe an easy but efficient method to specifically target the intestinal resident microbiota in brine shrimp larvae during DGGE analysis, hereby excluding the interference of both transient (luminal) bacteria and body surface bacteria. This effective technique has several advantages over alternative methods, with respect of ease of use and rapidity. [Copyright &y& Elsevier]
- Published
- 2012
- Full Text
- View/download PDF
32. Flow cytometry for fast microbial community fingerprinting
- Author
-
De Roy, Karen, Clement, Lieven, Thas, Olivier, Wang, Yingying, and Boon, Nico
- Subjects
- *
FLOW cytometry , *HUMAN fingerprints , *MICROBIAL removal (Water purification) , *SEWAGE disposal plants , *COMPOSITION of water , *WATER sampling , *MICROBIAL ecology - Abstract
Abstract: Characterizing the microbial community of water is important in different domains, ranging from food and beverage production to wastewater treatment. Conventional methods, such as heterotrophic plate count, selective plating and molecular techniques, are time consuming and labor intensive. A flow cytometry based approach was developed for a fast and objective comparison of microbial communities based on the distribution of cellular features from single cells within these communities. The method consists of two main parts, firstly the generation of fingerprint data by flow cytometry and secondly a novel statistical pipeline for the analysis of flow cytometric data. The combined method was shown to be useful for the discrimination and classification of different brands of drinking water. It was also successfully applied to detect changes in microbial community composition of drinking water caused by changing environmental factors. Generally, the method can be used as a fast fingerprinting method of microbial communities in aquatic samples and as a tool to detect shifts within these communities. [Copyright &y& Elsevier]
- Published
- 2012
- Full Text
- View/download PDF
33. Inoculation and start-up of a biotricking filter removing dimethyl sulfide
- Author
-
Sercu, Bram, Núñez, Dariela, Aroca, Germán, Boon, Nico, Verstraete, Willy, and Van Langenhove, Herman
- Subjects
- *
DIMETHYL sulfide , *BIOFILTRATION , *ELECTROPHORESIS , *ETHANES - Abstract
Abstract: Two Hyphomicrobium VS inoculation protocols were compared for start-up of a biotrickling filter removing dimethyl sulfide (DMS). One biotrickling filter (HBF 1) was filled with rings that were submerged in a nutrient medium containing Hyphomicrobium VS fed with DMS, another biotrickling filter (HBF 2) was similarly filled with rings that were submerged in nutrient medium, but continuously supplied with actively growing Hyphomicrobium VS and fed with methanol. Initially, about 40 times more Hyphomicrobium VS cells were attached to the rings in HBF 2. During the experiment, two to three times more Hyphomicrobium VS cells were still found to be present on the rings in HBF 2 compared to HBF 1. The maximal DMS elimination capacity at 90% removal efficiency of HBF 1 was 7.2gm−3 h−1 after 30 days of operation. The elimination capacity decreased, however, when the inlet loading rate exceeded 15gm−3 h−1 (200ppmv inlet concentration). The performance of HBF 2 was much better, with an elimination capacity of 8.3gm−3 h−1 (90% removal efficiency) after 2 days of operation, increasing to a maximum of 57gm−3 h−1 at 92% removal efficiency. Microbial community analysis with denaturing gradient gel electrophoresis showed very different microbial communities in both biotrickling filters (Pearson correlation coefficient of 0%). Moreover, the decreased DMS elimination capacity of HBF 1 at higher influent loading rate corresponded with a drastic change of the microbial community on the rings. The latter observations suggest that the functional efficiency of the microbial community in a biotrickling filter can be related to its composition. [Copyright &y& Elsevier]
- Published
- 2005
- Full Text
- View/download PDF
34. Microbial population and community dynamics in natural and managed freshwater systems : from methodology development to mechanistic insights
- Author
-
Props, Ruben, Boon, Nico, Denef, Vincent, and Monsieurs, Pieter
- Subjects
Earth and Environmental Sciences ,flow cytometry ,Biology and Life Sciences ,aquatic ,microbial ecology ,biodiversity - Abstract
Natural and managed freshwater ecosystems are hotspots of biodiversity, biogeochemical cycling, and provide numerous societal services (e.g., drinking water production, wastewater treatment). The microbial communities that inhabit these systems form complex assemblages of interacting microbial taxa, for which the community structure and function are not yet fully understood. This research presents new insights into the microbial community ecology of both natural and managed freshwater systems by developing and validating new technologies to study them and by investigating the genomic adaptations to their freshwater habitat. A first line of hypotheses focused on the development and application of novel flow cytometry tools to monitor the structure of aquatic microbial communities in a fast and non-invasive manner. These tools were then applied to both natural (Lake Michigan) and managed (cooling and drinking water) freshwater ecosystems. In parallel, a second line of hypotheses delved into the genomic properties that some of the abundant populations in these communities have evolved to their freshwater environment.
- Published
- 2018
35. Microbially managed organic growing media for greenhouse horticulture
- Author
-
Grunert, Oliver, Boon, Nico, Reheul, Dirk, and Van Labeke, Marie-Christine
- Subjects
Agriculture and Food Sciences ,organic fertilizer ,horticulture ,Growing media ,Biology and Life Sciences ,soilless culture systems ,tomato ,microbial ecology ,hairy roots syndrome - Abstract
The production of vegetables in growing media is an efficient way to produce vegetables in soilless culture systems. The management of the microbial community associated with growing media may serve as potential sustainable pathway to increase eco-efficiency. Consequently, it is important to find out how biotic and abiotic factors affect the composition and diversity of microbial communities associated with growing media. The aim of this PhD thesis was to study the ecology of the microbial community in soilless culture systems. First, the microbial community of a mineral and an organic growing medium was examined and it was found that both growing media have a distinct, microbial community structure. Second, key functionalities of growing media and their individual constituents were quantified. Particularly, the nitrogen dynamics were studied in relation to the microbial community associated with plant and growing medium. Third, the valorization of recycled nutrients as a high-value microalgae fertilizer and struvite was investigated. In addition, an adapted fertigation strategy in combination with organic fertilizers was developed to narrow the yield gap with a pure mineral growing medium when cultivating tomatoes. Afterwards, the microbial community structure of four contrasting soil and soilless tomato cultivating systems were studied. Finally, the effect of fertilizers and plant type on the microbial community structure of the rhizosphere and the bulk zone were investigated. Overall, organic growing media show a potential for developing novel cultivating systems fitting into a more sustainable horticulture.
- Published
- 2017
36. The methanotrophic interactome: microbial partnerships for sustainable methane cycling
- Author
-
Kerckhof, Frederiek-Maarten, Boon, Nico, and Heylen, Kim
- Subjects
Cryopreservation ,Methanotrophs ,Biology and Life Sciences ,Methane ,Microbiology ,Microbial Ecology - Abstract
Methane (CH4) is an important greenhouse gas, and the majority (ca. 60%) of its emission originates from anthropogenic sources. Methane oxidizing bacteria (MOB) are characterized by their unique ability to use CH4 as a sole carbon and energy source. Recently, accumulating evidence demonstrated that methane oxidation is stimulated when MOB are interacting with non-methanotrophic microbes. These interactions can be very specific, although it is not yet entirely elucidated what the determining factors to a successful partnership are. Hence, it seems that a methanotrophic interactome is required for effective biological aerobic methane oxidation, rather than individual obligate methanotrophic bacteria. In this dissertation, we focused on bacterial interactions between MOB and non-MOB and try to assess what are the determinants for non-MOB partner selection in the methanotrophic interactome. We focus specifically on representatives of alpha- and gammaproteobacterial MOB, which are known to exhibit differential functional traits which can in turn be conceptualized as distinct life strategies. The impact of these differences in MOB life strategies on interactions with non-MOB has not been studied. An increased insight in the co-existence and the extent of co-dependence of MOB and non-MOB partners is required to fully understand the essential ecosystem service of biological methane oxidation. In PART 1 (TOP-DOWN APPROACH), we dissected a methanotrophic enrichment culture (optimal methanotrophic interactome) by means of time-resolved stable isotope probing combined with 454-pyrosequencing of the 16S rRNA genes to assess which interactome partners are most intricately involved in the assimilation of 13CH4-derived carbon. In PART 2 (BOTTOM-UP APPROACH), we artificially assembled an optimal methanotrophic interactome by piecing together multiple non-MOB strains with MOB (co-cultivation). Firstly, we supervised the selection of MOB for non-MOB partners by establishing compatibility and matching selected MOB with non-MOB partners. Microbial adaptation and abundance of all partners was investigated using q-PCR. Secondly, we allowed an unsupervised selection for non-MOB partners by the MOB and these interactions were monitored by DGGE. In PART 3 (CRYOPRESERVETION), we develop a cryopreservation protocol based on DMSO (and DMSO+TT) as a cryopretactant, which can used to adequately preserve optimal interactomes (preservation of key functional characteristics as well as composition) to allow possible biotechnological applications. In PART 1, we found that 13CH4-derived carbon is differentially distributed among interactome partners through time. We suggested that the most intricately associated non-MOB partners would be the first to assimilate 13CH4-C and could hence be considered “primary consumers” of whereas organisms labeled later in the time-course SIP experiment are more loosely associated with the MOB and may be “secondary consumers” of organic carbon derived from both the MOB and the primary consumers. In PART 2a, we could not observe adaptation of a moderately compatible partner to MOB (or vice versa) during repeated co-cultivation with a gammaproteobacterial MOB. Conversely, clear (though limited) adaptation was observed with an alphaproteobacterial MOB. Regardless of its initial compatibility with the MOB, a third partner nearly always completely obliterated the non-MOB partner in the existing MOB:non-MOB interactome. In PART 2b, we showed a clear partner selection where some of the persisting partners were “promiscuous” and could persist regardless of MOB type , whereas others were more specifically associated with either MOB type. Additionally, we observed that alpha- and gammaproteobacterial MOB differentially route CH4-derived carbon to the interactome. Finally, while repeated co-cultivation did not significantly impact the magnitude of overall methane oxidation rates (MOR), it did appear to stabilize the biological variability in MOR as compared to acenically grown MOB. In PART 3, the optimized cryopreservation protocol for storage of mixed microbial cultures adequately preserved both community structure and functionality of a methanotrophic interactome (among others) for 3 months at -80°C. These findings may be of significance for methanotrophic interactome Microbial Resource Management, if biotechnological application of non-MOB partners is the ultimate goal. Overall, unsupervised synthetic interactome assembly approaches should be preferred, as they specifically restrict only non-MOB partners that can persist with the MOB from other non-MOB partners. If specific biotechnological applications can be found for such an optimal combination of interactome partners, it is of great interest to preserve a reproducible sample of it for extended periods of time. Exploitation and engineering of these methanotrophic interactomes could lead to improved and sustainable mitigation and recovery of CH4 in the form of metabolic energy or CH4-derived carbon.
- Published
- 2016
37. Methanotrophic microbiomes as drivers for environmental biotechnology
- Author
-
van der Ha, David, Boon, Nico, and Verstraete, Willy
- Subjects
methane ,microbiology ,Biology and Life Sciences ,microbiome ,metabolic networking ,microbial ecology ,environmental ,mitigation ,MOB ,greenhouse gas ,carbon cycle ,methanotroph ,wastewater ,biotechnology - Abstract
Since the industrial revolution, the average temperature on Earth has risen considerably, mainly due to the enormous emissions of greenhouse gases. This doctoral research focused on microbial mitigation strategies for methane (CH4), the second most important greenhouse gas after CO2. Therefore, methanotrophic microbiomes were used, the latter being entire microbial communities depending on CH4 for their activity. In a first phase, the effects of external growth parameters on the activity and structure of such communities were evaluated. Thereafter, research was done on the interactions taking place within the methanotrophic microbiomes, thereby proving that carbon fluxes take place between methanotrophs and associated microorganisms. Lastly, the methalgae concept was developed; by cocultivation of methanotrophs and algae, it was possible to treat CO2 and CH4 simultaneously under anoxic conditions.
- Published
- 2013
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