Curriculum Vitae
Riks Laanbroek(1951)
Education
1975 MSc in Biology at the State University of Groningen (the Netherlands); subjects General, Medical and Biochemical Microbiology
1978 PhD in Science and Mathematics at the State University of Groningen: Physiology and ecology of amino acid-fermenting bacteria isolated from anoxic wastewater treatment plants (promotor Prof. Hans Veldkamp)
Professional appointments
2009 to date Senior Scientist NIOO - KNAW
2008 to date Research Associate Smithsonian Institute, Washington
2004 to date Professor in Microbial Ecology of Wetlands, Utrecht University
2001 - 2009 Director NIOO – Centre for Limnology, Nieuwersluis
1993 – 2001 Director of Science NIOO – Centre for Limnology, Nieuwersluis
1990 - 2005 Private chair in Soil Biology, Radboud University, Nijmegen
1985 – 1993 Head Department of Soil Biology, Institute of Ecological Research, Heteren
1983 – 1985 Scientist, Delta Institute for Hydrobiological Research, Yerseke
1980 – 1983 Post doc, State University of Groningen
1979 – 1980 Post doc, Georg August Universität, Göttingen, Germany
Services to the profession (selection)
Board member Centre for Wetland Ecology
Deputy chief editor FEMS Microbiology Ecology
Member Scientific Committee of the Dutch Society for Microbiology (NVvM)
Expertise
- The role of microbial diversity in geochemical cycles.
In this time period of growing awareness of a general loss of biodiversity, the discussion focuses on it’s meaning for the functioning of ecosystems. Notwithstanding the major role of microorganisms in many ecosystem processes, the biodiversity discussion is almost restricted to plant and animal diversity. Hence, a better insight in the meaning of microbial diversity is timely. A theme that focuses on the role of biodiversity in geochemical cycles is at the front in now-a-days microbial ecology. One of the most important functions of microbial communities is the recycling of carbon and nutrients. In this way microbial ecology is almost synonymous with geomicrobiology, which can be defined as the study of how microorganisms shape Earth’s geochemistry. How life responds from the perspective of both single organisms and communities in the face of environmental constraints and how it changes the environment in this process is perhaps the most fundamental topic in microbial ecology.
- Ammonia-oxidising bacteria
Aerobic ammonia-oxidising bacteria belong to two monophyletic groups of microorganisms within the class of the . They share the ability to oxidise ammonia to nitrite and hence link the reduced and oxidised parts of the global nitrogen cycle. Under oxic, neutral, non-marine conditions bacteria of the beta subclass of the are by far the most important organisms performing this reaction. Their diversity is restricted to only 6 lineages of a limited number of species. However, the species behave in different ways with respect to environmental conditions, which indicate niche differentiation between the species. In the Schelde estuary, for example, the dominant freshwater species is replaced by a salt-tolerant species. Surprisingly, the salt-tolerant species grows better under freshwater conditions compared to brackish circumstances, but are apparently overgrown by the others in the freshwater part of the estuary. It is not know if replacement of species has consequences for the rate of ammonia oxidation in the ecosystem. This question is tackled by studying the behaviour of isolated species in model systems in the laboratory. Changes in community composition are followed by tracing gene sequences belonging to specific species. In this way, chemolithotrophic ammonia-oxidising bacteria are good model organisms for studying a possible relation between species identity and ecosystem functioning.
PhD students
Frank Verhagen (1992), Willem Engelaar (1994), Paul Bodelier (1997), Ronald Kester (1997), Joke Nijburg (1998), Erik van Hannen (1999), Jaco van der Nat (2000), Arjen Speksnijder (2000), Monique de Bie (2002), Jody de Brouwer (2002), Nicole Wrage (2003), Marco Dignum (2003), Marc Staal (2003), Jolanda Verspagen (2006), Stefan Simis (2006), Martijn Antheunisse (2007), Marjolijn Tijdens (2007), Manuela Coci (2007), Marzia Miletto (2007), Juanjuan Wang (2011)
Co-Operation
Centre for Wetland Ecology
The Centre for Wetland Ecology (http://www.wetland-ecology.nl/) is a formal collaboration between the NIOO and the universities of Nijmegen, Amsterdam and Utrecht in which ecologists, ecophysiologists and biogeochemists work together for a better understanding of the functioning of wetlands. The research ranges from the functioning of individual animals, bacteria and plants in their natural wetland environment to the behaviour of ecosystems and landscapes.
Darwin Center for Geosciences
The Darwin Center for Biogeology aims at performing cutting-edge science in the central field of Biogeology where Biology and Earth Sciences meet. Its research mission is to understand the functioning of global, regional and local ecosystems, focussing on change and feedback at all time scales in and between biotic and abiotic components of a changing Earth.
Nitrification Network
The objectives of the Nitrification Network are to coordinate research activities of the participants where multi-investigator proposals and projects are called for and to coordinate meetings of interest to members of the Nitrification Network and others in the field.
Selected Publications
Most recent publications
Suwa Y, Norton J, Bollmann A, Klotz M, Stein L, Laanbroek HJ, Arp D, Goodwin L, Chertkov O, Held B, Bruce D, Detter J, Detter J, Tapia R, Han C (2011) Genome sequence of Nitrosomonas sp. AL212, an ammonia-oxidizing bacterium sensitive to high-levels of ammonia. Journal of Bacteriology 193 (2011) 50470
Abstract: Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) that was originally isolated in 1997 by Yuichi Suwa and colleagues. This organism belongs to the Nitrosomonas cluster 6A, which is characterized by sensitivity to high ammonia concentrations, higher substrate affinity (lower Km), and lower maximum growth rates than strains in Nitrosomonas cluster7, which includes Nitrosomonas europaea and Nitrosomonas eutropha. Genome-informed studies of this ammonia-sensitive cohort of AOB are needed, as these bacteria are found in freshwater environments, drinking water supplies, waste water treatment systems, and soils worldwide.
Wang JJ, Vollrath S, Behrends T, Bodelier PLE, Muyzer G, Meima-Franke M, Den Oudsten F, Van Cappellen P, Laanbroek HJ (2011) Distribution and Diversity of Gallionella-Like Neutrophilic Iron Oxidizers in a Tidal Freshwater Marsh. Applied and Environmental Microbiology 77: 2337-2344
Abstract: Microbial iron oxidation is an integral part of the iron redox cycle in wetlands, Nonetheless, relatively little is known about the composition and ecology of iron oxidizing communities in soils and sediments of wetlands. In this study, sediment cores were collected across a freshwater tidal marsh to characterize the iron-oxidizing bacteria (FeOB) and link their distributions to geochemical properties of the sediments. We applied recently designed 16S rRNA primers targeting Gallionella-related FeOB using a nested PCR-DGGE approach, combined with a novel quantitative PCR (qPCR) assay. The presence of Gallionella-related FeOB was detected in most of the samples. The diversity and abundance of the putative FeOB were generally higher in the upper 5-12 cm of sediment compared to deeper sediment, and higher in samples collected in April compared to July and October. Oxygen supply macrofauna appears to be a major forcing controlling the spatial and temporal variations in FeOB communities. The higher abundance of Gallionella-related FeOB in April coincided with elevated concentrations of extractable Fe(III) in the sediments. Despite this coincidence, the distributions of FeOB did not exhibit a simple relationship to the redox zonation inferred from the geochemical depth profiles.
Bollmann A, French A, Laanbroek HJ (2011) Isolation, cultivation, and characterization of ammonia-oxidizing bacteria and archaea adapted to low ammonium concentrations. Methods in Enzymology 468: 55-88
Coci M, Nicol G, Pilloni GN, Schmid M, Kamst-Agterveld, MP, Bodelier PLE, Laanbroek HJ (2010) Quantitative assessment of ammonia-oxidizing bacterial communities in the epiphyton of submerged macrophytes in shallow lakes. Applied and Environmental Microbiology 76: 1813-1821
Abstract: In addition to the benthic and pelagic habitats, the epiphytic compartment of submerged macrophytes in shallow freshwater lakes offers a niche to bacterial ammonia-oxidizing communities. However the diversity, numbers and activity of epiphytic ammonia-oxidizing bacteria has long been overlooked. In the present study we analyzed quantitatively the epiphytic communities of three shallow lakes by a potential nitrification assay and by quantitative PCR of 16S rRNA genes. On a volume base, gene copy numbers of epiphytic ammonia oxidizers were significantly lower than those of benthic bacteria. Stands with the submerged macrophyte Potamogeton pectinatus contained larger epiphytic gene numbers than pelagic numbers, which was significant in Lake Gooimeer but not in Lake Vossemeer. In Lake Nuldernauw, which contained only the submerged macrophyte Chara aspera, epiphytic numbers were significantly lower than pelagic gene numbers. In general, these trends were also found by measuring potential ammonia-oxidizing activities. The presence of ammonia-oxidizing bacterial cells in the epiphyton of P. pectinatus was also demonstrated by FISH microscopy images. By comparing community composition assessed by the 16S rRNA PCR-DGGE approach, it was concluded that the epiphytic ammonia-oxidizing communities consisted of cells that were also present in the benthic and pelagic compartments. Furthermore, the environmental variables associated with the shallow lakes affected significantly the numbers, activities and diversity of ammonia-oxidizing bacterial communities.
Laanbroek HJ, Bollmann A (2011) Nitrification in inland waters. In: Nitrification (B. Ward, D.J. Arp, M.G. Klotz, eds.), pp 385-403. American Society for Microbiology
Miletto M, Loeb R, Antheunisse AM, Bodelier PLE, Laanbroek HJ (2010). Response of the sulfate-reducing community to the re-establishment of estuarine conditions in two contrasting soils: a mesocosm approach. Microbial Ecology 59:109-120
Abstract: We studied the response of sulphate-reducing prokaryotic (SRPs) communities to the experimental variation of salinity and tide in an outdoor mesocosm set-up. Intact soil monoliths were collected at two areas of the Haringvliet lagoon (the Netherlands); one sampling location consisted of agricultural grassland, drained and fertilized for at least the last century, the other of a freshwater marshland, with more recent sea influence. Two factors, i.e. ‘salinity’ (freshwater/oligohaline) and ‘tide’ (stagnant/tidal), were tested in a full-factorial design. Soil samples were collected after five months (June-October). Dissimilatory (bi)sulphite reductase subunit-based denaturing gradient gel electrophoresis (dsrB-DGGE) analysis revealed that the SRPs community composition in the agricultural grassland and in the freshwater marshland was represented mainly by microorganisms related to the Desulfobulbaceae and the Desulfobacteraceae, respectively. Desulfovibrio- and Desulfomicrobium-related dsrB were detected only in the tidal treatments; Desulfomonile-related dsrB occurrence was related to the presence of oligohaline conditions. Treatments did have an effect on the overall SRPs community composition of both soils, but not on the sulphate depletion rates in sulphate-amended anoxic slurry incubations. However, initiation of sulphate reduction upon sulphate addition was clearly different between the two soils.
Smits NAC, Kamst-van Agterveld MP, Laanbroek HJ, Paalman AJ, Bobbink, R (2010) Nitrification along a grassland gradient: inhibition found in matgrass swards. Soil Biology Biochemistry 42: 635-641
Abstract: Measurements along a hill slope vegetation gradient in nutrient-poor grasslands from acid grasslands via matgrass swards to calcareous grasslands showed increased ammonium to nitrate ratios in the matgrass swards. These results generated the research question whether there might be a difference in nitrification activity or nitrifying community composition between the different zones in this hill slope gradient. In each of the vegetation types along the gradient, soil samples were taken in five grassland nature reserves. Potential nitrification rates have been determined as an indication of the size of the active ammonia-oxidising microbial communities. Additionally, the dominant ammonia-oxidising sequences related to the β-Proteobacteria have been determined by a Polymerase Chain Reaction (PCR) based on the 16S rRNA gene in combination with Denaturing Gradient Gel Electrophoresis (DGGE) at one of the nature reserves.
Compared to the top and lower zones of the vegetation gradient (i.e. acid grasslands and calcareous grasslands, respectively), potential nitrification rates were clearly repressed in the middle, matgrass swards zone. In contrast to the differences in potential nitrification activities observed in one of the nature reserves (Bemelerberg), no differences in dominant ammonia-oxidising sequences were observed at this location. One sequence belonging to cluster 3 of the Nitrosospira lineage appeared to be dominant among the sequences belonging to the ammonia-oxidising species of the β- Proteobacteria in all vegetation zones. Nitrification was apparently inhibited by the vegetation, whereas no shift in nitrifier populations could be shown. The possible role of repressed nitrification in the decline of this vegetation type is discussed.
Smits NAC, Bobbink R, Laanbroek HJ, Paalman AJ, Hefting MM (in press) Repression of potential nitrification activities by matgrass sward species. Plant and Soil
Abstract: Soil nitrification is a key process in regulating the relative availability of the various inorganic N forms to plants. In the current study, we investigated the effect of different plant species on numbers of ammonia-oxidizing microbial cells by measuring the potential nitrification activity (PAA). Soil from matgrass sward and from calcareous grassland was collected in the field and four characteristic plant species of each vegetation type were cultivated from seed. These plant species grew for four months in the two soil types in a cross-wise experiment. After those 4 months, PAA was significantly higher in calcareous soil compared to the matgrass sward soil and the presence of matgrass sward species had significantly decreased PAA in this soil. In soils from matgrass stands, PAA were much lower, and no effect of the different plant species could be detected. Plant biomass of the calcareous grassland species was overall positively correlated with PAA, whereas for matgrass plant species a negative trend was found. We conclude that matgrass sward plant species had a clear repressing effect on the potential ammonia-oxidizing activity in calcareous grassland soil within this four-month growth experiment. The observed repression of PAA is in accordance with earlier field observations of PAA in the different vegetation zones, where repressed PAA and significant higher ammonium to nitrate ratios were observed in the matgrass sward vegetation compared to the other vegetation zones (Smits et al. 2010).
Laanbroek HJ (2010) Methane emission from natural wetlands: Interplay between emergent macrophytes and soil microbial processes – A minireview. Annals Botany 105: 141-153
Abstract: Background According to IPCC 2007 natural wetlands contribute 20 – 39% to the global emission of methane. The range in the estimated percentage of the contribution of these systems to the total the release of this greenhouse gas is large due to differences in the nature of the emitting vegetation including the soil microbiota that interfere with the production and consumption of methane.
Scope Methane is a dominant end product of anaerobic mineralisation processes. When all electron acceptors except carbon dioxide are used by the microbial community, methanogenesis is the ultimate pathway to mineralise organic carbon compounds. Emergent wetlands plants play an important role in the emission of the methane to the atmosphere. They produce the carbon necessary for the production of methane, but also facilitate the release of methane by the possession of a system of interconnected internal gas lacunas. Aquatic macrophytes are commonly adapted to oxygen-limited conditions as they prevail in flooded or waterlogged soils. By this system, oxygen is transported to the underground parts of the plants. Part of the oxygen transported downwards is released in the root zone, where it sustains a number of beneficial oxidation processes. Through the pores from which oxygen escapes from the plant into the root zone, methane can enter the plant aerenchyma system and subsequently be emitted into the atmosphere. Part of the oxygen released into the root zone can be used to oxidise methane before it enters the atmosphere. However, the oxygen can also be used to regenerate alternative electron acceptors. The continuous supply of alternative electron acceptors will diminish the role of methanogenesis in the anaerobic mineralisation processes in the root zone and therefore repress the production and emission of methane. The role of alternative element cycles in the inhibition of methanogenesis is discussed.
Conclusions The role of the nitrogen cycle in repression of methane production is probably low. In contrast to wetlands particularly created for the purification of nitrogen-rich waste waters, concentrations of inorganic nitrogen compounds are low in the root zones in the growing season due to the nitrogen-consuming behaviour of the plant. Therefore nitrate competes hardly with other electron acceptors for reduced organic compounds and repression of methane oxidation by the presence of higher levels of ammonium will not be the case.
The role of the iron cycle is likely to be important with respect to the repression of methane production and oxidation. Iron-reducing and iron-oxidising bacteria are ubiquitous in the rhizosphere of wetland plants. The cycling of iron will largely be dependent on the size of the oxygen release in the root zone, which is likely to be different between different wetland plant species.
The role of the sulphur cycle in repression of methane production is important in marine, sulphate-rich ecosystems, but might also play a role in freshwater systems where sufficient sulphate is available. Sulphate-reducing bacteria are omnipresent in freshwater ecosystems, but do not always react immediately to the supply of fresh sulphate. Hence, their role in the repression of methanogenesis is still to be proven in freshwater marshes.
Vissers EW, Bodelier PLE, Muyzer G, Laanbroek HJ (2009)A nested PCR approach for improved recovery of Archaeal 16S rRNA gene fragments from freshwater samples. FEMS Microbiol Lett 298: 193-198
Abstract: In a survey on the presence of archaea in a number of European lakes, it was found that known archaeal primer sets for PCR were not suited for use in freshwater environment, as some lack selectivity, while others were too selective. A nested PCR was developed for DGGE with primer sets 21F-958R and Parch519f-Arch915r, respectively. After sequencing of the DGGE bands obtained by this nested method, 93% of the sequences were of archaeal origin. More diverse archaeal DGGE patterns were found as compared to other PCR methods. The nested PCR-DGGE method presented here is therefore a reliable tool to analyse the archaeal diversity in freshwater habitats, revealing even more of the wide spread of the archaea.
Wang J, Muyzer G, Bodelier PLE, Laanbroek HJ (2009) Diversity of iron oxidizers in wetland soils revealed by novel primers targeting Gallionella-related bacteria. ISME J. 3: 715-725
Abstract: Neutrophilic iron-oxidizing bacteria (FeOB) are important catalysts of iron cycling in wetland environments. However, little is known about their diversity and distribution in various environments. The aim of this study was to develop a PCR-DGGE assay enabling the detection of neutrophilic iron oxidizers in wetland habitats. Gradient tubes were used to enrich FeOB. From these enrichments, a clone library was established on the basis of the almost complete 16S rRNA gene using the universal bacterial primers 27f and 1492r. This clone library consisted of mainly - and -Proteobacteria, among which two major clusters were closely related to Gallionella spp. Specific probes and primers were developed on the basis of this 16S rRNA gene clone library. The newly designed Gallionella-specific 16S rRNA gene primer set 122f/998r was applied to community DNA obtained from three contrasting wetland environments, followed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis. A second 16S rRNA gene clone library was constructed using the PCR products from one of our sampling sites amplified with the newly developed primer set 122f/998r. The cloned 16S rRNA gene sequences all represented novel culturable iron oxidizers most closely related to Gallionella sp. On the basis of their nucleotide sequences, four groups could be identified that were comparable to the DGGE banding pattern obtained before with the same PCR products as used for the second clone library. Using these Gallionella-specific 16S rRNA gene-based primers, in combination with DGGE, first insights into the diversity and distribution of these bacteria in wetland soils were obtained.
Coci M, Bodelier PLE, Laanbroek HJ (2008) Epiphyton as a niche for ammonia-oxidizing bacteria: detailed comparison with the benthic and pelagic compartments in freshwater shallow lakes. Appl Environm Microbiol.74: 1963-1971
Abstract: Next to the benthic and pelagic compartments, the epiphyton of submerged macrophytes may offer an additional niche for ammonia-oxidizing bacteria in shallow freshwater lakes. In this study, we explored the potential activities and community compositions of ammonia-oxidizing bacteria of the epiphytic, benthic, and pelagic compartments of seven shallow freshwater lakes which differed in their trophic status, distribution of submerged macrophytes, and restoration history. PCR-denaturing gradient gel electrophoresis analyses demonstrated that the epiphytic compartment was inhabited by species belonging to cluster 3 of the Nitrosospira lineage and to the Nitrosomonas oligotropha lineage. Both the ammonia-oxidizing bacterial community compositions and the potential activities differed significantly between compartments. Interestingly, both the ammonia-oxidizing bacterial community composition and potential activity were influenced by the restoration status of the different lakes investigated.
Laanbroek HJ,Speksnijder AGCL (2008) Niche separation of ammonia-oxidising bacteria across a tidal freshwater marsh. Environm Microbiol 10 (2008) 3017-3025
Abstract: Like many functional groups or guilds of microorganisms, the group of ammonia-oxidizing bacteria (AOB) consists of a number of physiologically different species or lineages. These physiological differences suggest niche differentiation among these bacteria depending on the environmental conditions. Species of AOB might be adapted to different zones in the flooding gradient of a tidal marsh. This issue has been studied by sampling sediments from different sites and depths within a tidal freshwater marsh along the river Scheldt near the village of Appels in Belgium. Samples were taken in February, April, July and October 1998. Communities of AOB in the sediment were analysed on the basis of the 16S rRNA gene by application of polymerase chain reaction in combination with denaturing gradient gel electrophoresis (DGGE). In addition, moisture content and concentrations of ammonium and nitrate were determined as well as the potential ammonia-oxidizing activities. Six different DGGE bands belonging to the [beta]-subclass of the Proteobacteria were observed across the marsh. The community composition of AOB was determined by the elevation in the flooding gradient as well as by the sampling depth. The presence of plants was less important for the community composition of AOB. DGGE bands affiliated with the Nitrosospira lineage were mostly found in the upper part of the marsh and in the deeper layers of the sediment. Two of the three DGGE bands related to the Nitrosomonas oligotropha lineage were more broadly distributed over the marsh, but were predominantly found in the upper layers of the sediment. Members of the environmental Nitrosomonas lineage 5 were predominantly detected in the deeper layers in the lower parts of the marsh. Potential driving factors for niche differentiation are discussed.
Miletto M, Loy A, Antheunisse AM, Loeb R, Bodelier PLE, Laanbroek HJ (2008) Biogeography of sulphate-reducing bacteria in river floodplains. FEMS Microbiol Ecol 64: 395-406
Abstract: In this study we conducted a large scale field survey to describe the biogeography of sulfate-reducing prokaryotes (SRPs) communities in river floodplain soils. Twenty-nine soil samples were collected in tidal and non-tidal areas along the rivers Meuse, Rhine and Overijsselse Vecht (the Netherlands). The SRPs communities were examined using a polyphasic approach consisting of 16S rRNA gene-based oligonucleotide microarray, dsrB-based denaturing gradient gel electrophoresis (DGGE) and polar lipid-derived fatty acids (PLFAs) analyses. Fingerprints obtained with these three methods were used as a proxy to describe the SRPs diversity in the floodplain samples. The occurrence of known SRPs as suggested by microarray hybridizations was cross-confirmed by DGGE as well as PLFA analyses. Each set of profiles was subjected to a combined multivariate/correlation analysis, in order to compare SRPs community profiles and to highlight the environmental soil and pore water variables influencing the distribution of the SRPs communities along environmental gradients, as described by microarray/DGGE/PLFAs analyses.
Floodplain soils harbored diversified SRPs communities displaying biogeographic patterns. Nearly all profiles from the tidal sites consistently separated from the non-tidal sites, independently from the screening method and the multivariate statistics used. The distribution of the microarray/DGGE/PLFAs-based fingerprints in the principal component plots could be correlated to 8 soil variables, i.e. soil organic matter, total nitrogen, phosphorous and potassium, and extractable ammonium, nitrate, phosphate and sulfate, as well as 7 pore water variables, i.e. phosphate, sulfate, sulfide, chloride, sodium, potassium and magnesium ions. Indication of a salinity- and plant nutrient-dependent distribution of SRPs related to Desulfosarcina, Desulfomonile, and Desulfobacter was suggested by microarray, DGGE and PLFAs analyses.
Sekido T, Bodelier PLE, Shoji T, SuwaY, LaanbroekHJ (2008) Limitations of the use of group-specific primers in real-time PCR as appear from quantitative analyses of closely related ammonia-oxidising species. Water Res 42: 1093-1101
Abstract: To study the ecology of ammonia-oxidising bacteria (AOB), quantitative techniques are essential. Real-time PCR assays based on the 16S rRNA or on the structural amoA gene are routinely used. The CTO primer set rooted on the 16S rRNA gene has a number of mismatches with some of the cultures of AOB. To examine if these mismatches have an effect on the outcome of real-time PCR assays, the assay was tested with DNA from a number of closely related isolates of AOB. Standard curves of known amounts of initial DNA were similar among most of the tested cultures of AOB, except for the standard curves of Nitrosomonas strain AL212 and Nitrosospira strain NpAV. Nitrosomonas strain AL212 had 3 mismatches with the CTO primer set. Adaptation of the CTO primer set in order to perfectly match the Nitrosomonas strain AL212 gave a standard curve similar to the majority of the AOB tested. As Nitrosospira strain NpAV has no mismatches with the original CTO primer set, there must be another reason for the less efficient amplification than the sequence itself. Application of an existing sigmoidal mathematical model gave no other results with respect to the standard curves of Nitrosomonas europaea and Nitrosomonas strain AL212, but also demonstrated that primer mismatches can seriously underestimate the initial target concentration. It was concluded that in general correct interpretation of real-time PCR results requires knowledge of the target community composition, in particular of the target sequences of the dominant community members.
Tijdens M, Hoogveld HL, Kamst-van Agterveld MP, Simis SGH, Baudoux AC, Laanbroek HJ, Gons HJ (2008) Population dynamics and diversity of viruses, bacteria and phytoplankton in a shallow eutrophic lake. Microb Ecol 56: 29-42
Abstract: We have studied the temporal variation in viral abundances and community assemblage in the eutrophic Lake Loosdrecht through epifluorescence microscopy and pulsed field gel electrophoresis (PFGE). The virioplankton community was a dynamic component of the aquatic community, with abundances ranging between 5.5 × 107 and 1.3 × 108 virus-like particles ml−1 and viral genome sizes ranging between 30 and 200 kb. Both viral abundances and community composition followed a distinct seasonal cycle, with high viral abundances observed during spring and summer. Due to the selective and parasitic nature of viral infection, it was expected that viral and host community dynamics would covary both in abundances and community composition. The temporal dynamics of the bacterial and cyanobacterial communities, as potential viral hosts, were studied in addition to a range of environmental parameters to relate these to viral community dynamics. Cyanobacterial and bacterial communities were studied applying epifluorescence microscopy, flow cytometry, and denaturing gradient gel electrophoresis (DGGE). Both bacterial and cyanobacterial communities followed a clear seasonal cycle. Contrary to expectations, viral abundances were neither correlated to abundances of the most dominant plankton groups in Lake Loosdrecht, the bacteria and the filamentous cyanobacteria, nor could we detect a correlation between the assemblage of viral and bacterial or cyanobacterial communities during the overall period. Only during short periods of strong fluctuations in microbial communities could we detect viral community assemblages to co-vary with cyanobacterial and bacterial communities. Methods with a higher specificity and resolution are probably needed to detect the more subtle virus–host interactions. Viral abundances did however relate to cyanobacterial community assemblage and showed a significant positive correlation to Chl-a as well as prochlorophytes, suggesting that a significant proportion of the viruses in Lake Loosdrecht may be phytoplankton and more specific cyanobacterial viruses. Temporal changes in bacterial abundances were significantly related to viral community assemblage, and vice versa, suggesting an interaction between viral and bacterial communities in Lake Loosdrecht.
Top-ten most cited publications
1. Laanbroek HJ, Pfennig N (1981) Oxidation of short-chain fatty acids by sulphate-reducing bacteria in freshwater and in marine sediments. Arch. Microbiol. 128: 330-335
2. Van Hannen EJ, Zwart GJM, van Agterveld MP, Gons HJ, Ebert J, Laanbroek HJ (1999) Changes in the bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. Appl Environm Microbiol 65: 795-801
3. Speksnijder AGCL, Kowalchuk GA, de Jong S, Kline E, Stephen JR, Laanbroek HJ (2001) Micro-variation artefacts introduced by PCR and cloning of closely related 16S rDNA sequences. Appl Environm Microbiol 67: 469-472
4. Kowalchuk GA, Bodelier PLE, Heilig GHJ, Stephen JR, Laanbroek HJ (1998) Community analysis of ammonia-oxidising bacteria in relation to oxygen-availability in soils and root-oxygenated sediments, using PCR, DGGE and oligonucleotide probe hybridisation. FEMS Microbiol Ecol 27: 339-350
5. Van Hannen EJ, Mooij WM, Van Agterveld MP, Gons HJ, Laanbroek HJ (1999) Detritus-dependent development of the microbial community in an experimental system: A quantitative analysis using denaturing gradient gel electrophoresis. Appl Environm Microbiol 65: 2478-2484
6. Bodelier PLE, Laanbroek HJ (2004) Nitrogen as a regulatory factor of methane oxidation in soils and sediments. FEMS Microbiol. Ecol. 47: 265-277
7. Zwart G, Hiorns WD, Methé BA, van Agterveld MP, Huismans R, Nold SC, Zehr JP, Laanbroek HJ (1998) Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of freshwater bacteria with global distribution. Syst Appl Microbiol 21:546-556
8. Bodelier PLE, Libochant JA, Blom CWPM, Laanbroek HJ (1996) Dynamics of nitrification and denitrification in root-oxygenated sediments and adaptation of ammonia-oxidizing bacteria to low oxygen or anoxic habitats. Appl Environm Microbiol 62: 4100-4107
9. Laanbroek HJ, Abee T, Voogd IL (1982) Alcohol conversions by Desulfobulbus propionicus Lindhorst in the presence and absence of sulphate and hydrogen. Arch. Microbiol. 133: 178-184
10. Verhagen FJM, Laanbroek HJ (1991) Competition for ammonium between nitrifying and heterotrophic bacteria in energy limited chemostats. Appl Environm Microbiol 57: 3255-3263
Links
Centre for Wetland Ecology
http://www.wetland-ecology.nl/
Darwin Center for Biogeology
http://www.darwincenter.nl/organization.htm
Landscape Ecology, Utrecht University
http://www.bio.uu.nl/LandscapeEcology/
Nitrification Network
http://nitrificationnetwork.org/
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