Staff Publications

Staff Publications

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

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

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

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Influence of phenylacetic acid pulses on anaerobic digestion performance and archaeal community structure in WWTP sewage sludge digesters
Cabrol, L. ; Urra, J. ; Rosenkranz, F. ; Kroff, P.A. ; Plugge, C.M. ; Lesty, Y. ; Chamy, R. - \ 2015
Water Science and Technology 71 (2015)12. - ISSN 0273-1223 - p. 1790 - 1799.
rioolslib - anaërobe behandeling - anaërobe afbraak - sewage sludge - anaerobic treatment - anaerobic digestion - waste-water treatment - olive mill wastewaters - volatile fatty-acids - 16s ribosomal-rna - biogas production - degradation efficiency - microbial-populations - aromatic-compounds - phenolic-compounds - inhibition
The effect of phenylacetic acid (PAA) pulses on anaerobic digestion (AD) performance and archaeal community structure was evaluated in anaerobic digesters treating sewage sludge from a wastewater treatment plant (WWTP). Four pilot-scale continuous stirred tank reactors were set up at a full-scale municipal WWTP in Santiago de Chile, and fed with either primary or mixed sewage sludge. AD performance was evaluated by volatile fatty acid (VFA) and biogas production monitoring. Archaeal community structure was characterized by 16S rRNA denaturing gradient gel electrophoresis and band sequencing. In the primary sludge digester, a single PAA pulse at 200 mg L(-1) was sufficient to affect AD performance and archaeal community structure, resulting in long-term VFA accumulation, reduced biogas production and community shift from dominant acetoclastic (Methanosaeta concilii) to hydrogenotrophic (Methanospirillum hungatei) methanogens. By contrast, AD performance and archaeal community structure in the mixed sludge digester were stable and resistant to repeated PAA pulses at 200 and 600 mg L(-1). This work demonstrated that the effect of PAA pulses on methanogenic activity and archaeal community structure differed according to AD substrate, and suggests that better insights of the correlations between archaeal population dynamics and functional performance could help to better face toxic shocks in AD
Characterization of the bacterial community involved in the bioflocculation process of wastewater organic matter in high loaded MBRs
Faust, L. ; Szendy, M. ; Plugge, C.M. ; Brink, P.F. van den; Temmink, H. ; Rijnaarts, H.H.M. - \ 2015
Applied Microbiology and Biotechnology 99 (2015)12. - ISSN 0175-7598 - p. 5327 - 5337.
solids retention time - 16s ribosomal-rna - gradient gel-electrophoresis - improved energy recovery - in-situ hybridization - activated-sludge - microbial community - membrane bioreactor - identification - stability
High-loaded membrane bioreactors (HL-MBRs), i.e., bioreactors equipped with a membrane for biomass retention and operated at extremely short sludge and hydraulic retention times, can concentrate sewage organic matter to facilitate subsequent energy and chemical recovery from these organics. Bioflocculation, accomplished by microorganisms that produce extracellular polymers, is a very important mechanism in these reactors. Bacterial diversity of the sludge and supernatant fraction of HL-MBRs operated at very short sludge retention times (0.125, 0.5, and 1 day) were determined using a PCR-denaturing gradient gel electrophoresis (DGGE) and clone library approach and compared to the diversity in sewage. Already at a sludge retention time (SRT) of 0.125 day, a distinct bacterial community developed compared to the community in sewage. Bioflocculation, however, was low and the majority of the bacteria, especially Arcobacter, were present in the supernatant fraction. Upon increasing SRT from 0.125 to 1 day, a much stronger bioflocculation was accompanied by an increased abundance of Bacteroidetes in the (solid) sludge fraction: 27.5 % at an SRT of 0.5 day and 46.4 % at an SRT of 1 day. Furthermore, cluster analysis of DGGE profiles revealed that the bacterial community structure in the sludge was different from that in the supernatant. To localize specific bacterial classes in the sludge flocs, fluorescence in situ hybridization (FISH) was carried out with three different bacterial probes. This showed that Betaproteobacteria formed clusters in the sludge flocs whereas Alphaproteobacteria and Gammaproteobacteria were mainly present as single cells
Soil health indicators and Fusarium wilt suppression in organically managed greenhouse soils
Bruggen, A.H.C. van; Sharma, K. ; Kaku, E. ; Karfopoulos, S. ; Zelenev, V.V. ; Blok, W.J. - \ 2015
Applied Soil Ecology 86 (2015). - ISSN 0929-1393 - p. 192 - 201.
gradient gel-electrophoresis - escherichia-coli o157-h7 - wave-like dynamics - 16s ribosomal-rna - bacterial-populations - microbial-populations - pythium-ultimum - nutrient input - wheat roots - corky root
Soil health has been associated with internal cycling of nutrients, microbial activity and diversity as well as root disease suppression, which are frequently greater in organically than in conventionally managed soils. Resistance and resilience, measured as amplitude and frequency of oscillations in bacterial communities after a disturbance, were suggested as integral indicators of soil health, but until now there is little proof for this hypothesis. In this study, resistance and resilience of microbial communities and 24 soil chemical and biological parameters were analyzed and correlated to suppression of flax wilt (caused by Fusarium oxysporum f.sp. lini) in three experiments. Soil samples were collected on three different dates from a recently converted organic greenhouse and a similar, neighboring greenhouse under conventional management. The dynamics of copiotrophic and oligotrophic bacteria after a disturbance were monitored, and the resistance and resilience were calculated. The organic soil showed significantly higher water-holding capacity, organic matter content, total C and N contents, C: N ratio of the small particulate organic matter fraction, microbial biomass carbon, oxygen uptake rate, copiotrophic and oligotrophic bacterial communities and suppression of flax wilt incidence. After incorporation of a grass-clover mixture in both soils, the densities of copiotrophic and oligotrophic bacteria oscillated over time. The relative amplitudes of the oscillations (in grass-clover amended over non- amended soil) and the frequencies of the oscillations of both trophic groups were lower for the organic soil, indicating that the resistance and resilience of the microbial community were greater in this soil. These results support the hypothesis that the bacterial response to a disturbance can serve as an integral indicator for soil health, including disease suppressiveness. (C) 2014 Elsevier B.V. All rights reserved.
Growth of anaerobic methane oxidizing archaea and sulfate reducing bacteria in a high pressure membrane-capsule bioreactor
Timmers, P.H.A. ; Gieteling, J. ; Widjaja-Greefkes, H.C.A. ; Plugge, C.M. ; Stams, A.J.M. ; Lens, P.N.L. ; Meulepas, R.J.W. - \ 2015
Applied and Environmental Microbiology 81 (2015)4. - ISSN 0099-2240 - p. 1286 - 1296.
cold-seep sediments - 16s ribosomal-rna - gradient gel-electrophoresis - guaymas basin - hydrothermal sediments - microbial diversity - marine-sediments - population-dynamics - community structure - gene database
Anaerobic methane oxidizing communities of archaea (ANME) and sulfate reducing bacteria (SRB) grow slowly, which limits physiological studies. High methane partial pressure was previously successfully applied to stimulate growth, but it is not clear how different ANME subtypes and associated sulfate reducing bacteria (SRB) are affected by it. Here, we report growth of ANME/SRB in a membrane-capsule bioreactor inoculated with Eckernförde Bay sediment that combines high pressure incubation (10.1 MPa methane) and thorough mixing (100 rpm) with complete cell retention by a 0.2 µm membrane. Results were compared to previously obtained data from an ambient-pressure (0.101 MPa methane) bioreactor inoculated with the same sediment. Labelled-methane oxidation rates were not higher at 10.1 MPa, likely because measurements were done at ambient pressure. The subtype ANME-2a/b was abundant in both reactors, but subtype ANME-2c was only enriched at 10.1 MPa. SRB at 10.1 MPa mainly belonged to the SEEP-SRB2, Eel-1 group and Desulforomonadales and not to the typically found SEEP-SRB1. Increase of ANME-2a/b occurred in parallel with increase of SEEP-SRB2 which was previously only found associated with ANME-2c. Our results imply that the syntrophic association is flexible and that methane pressure and sulfide concentration influence growth of different ANME-SRB consortia. We also studied the effect of elevated methane pressure on methane production and oxidation by a mixture of methanogenic and sulfate-reducing sludge. Here, methane oxidation rates decreased and were not coupled to sulfide production, indicating trace methane oxidation during net methanogenesis and not anaerobic methane oxidation, even at high methane partial pressure.
Detection, identification and differentiation of Pectobacterium and Dickeya species causing potato blackleg and tuber soft rot: a review
Czajkowski, R.L. ; Pérombelon, M.C.M. ; Jafra, S. ; Lojkowska, E. ; Potrykus, M. ; Wolf, J.M. van der; Sledz, W. - \ 2015
Annals of Applied Biology 166 (2015)1. - ISSN 0003-4746 - p. 18 - 38.
carotovora subsp atroseptica - fragment-length-polymorphism - plant-pathogenic bacteria - erwinia-chrysanthemi strains - polymerase-chain-reaction - 16s ribosomal-rna - monoclonal-antibodies - genetic diversity - ssp-carotovorum - peel extracts
The soft rot Enterobacteriaceae (SRE) Pectobacterium and Dickeya species (formerly classified as pectinolytic Erwinia spp.) cause important diseases on potato and other arable and horticultural crops. They may affect the growing potato plant causing blackleg and are responsible for tuber soft rot in storage thereby reducing yield and quality. Efficient and cost-effective detection and identification methods are essential to investigate the ecology and pathogenesis of the SRE as well as in seed certification programmes. The aim of this review was to collect all existing information on methods available for SRE detection. The review reports on the sampling and preparation of plant material for testing and on over thirty methods to detect, identify and differentiate the soft rot and blackleg causing bacteria to species and subspecies level. These include methods based on biochemical characters, serology, molecular techniques which rely on DNA sequence amplification as well as several less-investigated ones.
Microbial dynamics during and after in situ chemical oxidation of chlorinated solvents
Sutton, N.B. ; Atashgahi, S. ; Wal, van der, J. ; Wijn, G. ; Grotenhuis, J.T.C. ; Smidt, H. ; Rijnaarts, H. - \ 2015
Groundwater 53 (2015)2. - ISSN 0017-467X - p. 261 - 270.
diesel-contaminated soil - 16s ribosomal-rna - real-time pcr - community structure - dnapl source - dechlorination - dehalococcoides - trichloroethene - bioremediation - genes
In situ chemical oxidation (ISCO) followed by a bioremediation step is increasingly being considered as an effective biphasic technology. Information on the impact of chemical oxidants on organohalide respiring bacteria (OHRB), however, is largely lacking. Therefore, we used quantitative PCR (qPCR) to monitor the abundance of OHRB (Dehalococcoides mccartyi, Dehalobacter, Geobacter, and Desulfitobacterium) and reductive dehalogenase genes (rdh; tceA, vcrA, and bvcA) at a field location contaminated with chlorinated solvents prior to and following treatment with sodium persulfate. Natural attenuation of the contaminants tetrachloroethene (PCE) and trichloroethene (TCE) observed prior to ISCO was confirmed by the distribution of OHRB and rdh genes. In wells impacted by persulfate treatment, a 1 to 3 order of magnitude reduction in the abundances of OHRB and complete absence of rdh genes was observed 21 days after ISCO. Groundwater acidification (pH500 mV) due to persulfate treatment were significant and contributed to disruption of the microbial community. In wells only mildly impacted by persulfate, a slight stimulation of the microbial community was observed, with more than 1 order of magnitude increase in the abundance of Geobacter and Desulfitobacterium 36 days after ISCO. After six months, regeneration of the OHRB community occurred, however, neither D. mccartyi nor any rdh genes were observed, indicating extended disruption of biological natural attenuation (NA) capacity following persulfate treatment. For full restoration of biological NA activity, additional time may prove sufficient; otherwise addition electron donor amendment or bioaugmentation may be required.
Determinants of the microbial community structure of eutrophic, hyporheic river sediments polluted with chlorinated aliphatic hydrocarbons
Hamonts, K. ; Ryngaert, A. ; Smidt, H. ; Springael, D. ; Dejonghe, W. - \ 2014
FEMS Microbiology Ecology 87 (2014)3. - ISSN 0168-6496 - p. 715 - 732.
16s ribosomal-rna - gradient gel-electrophoresis - sulfate-reducing bacteria - dehalococcoides sp strain - reductive dehalogenase genes - vinyl-chloride reductase - contaminated groundwater - seasonal dynamics - running waters - lake sediment
Chlorinated aliphatic hydrocarbons (CAHs) often discharge into rivers as contaminated groundwater baseflow. As biotransformation of CAHs in the impacted river sediments might be an effective remediation strategy, we investigated the determinants of the microbial community structure of eutrophic, CAH-polluted sediments of the Zenne River. Based on PCR-DGGE analysis, a high diversity of Bacteria, sulfate-reducing bacteria, Geobacteraceae, methanogenic archaea, and CAH-respiring Dehalococcoides was found. Depth in the riverbed, organic carbon content, CAH content and texture of the sediment, pore water temperature and conductivity, and concentrations of toluene and methane significantly contributed to the variance in the microbial community structure. On a meter scale, CAH concentrations alone explained only 6% of the variance in the Dehalococcoides and sulfate-reducing communities. On a cm-scale, however, CAHs explained 14.5-35% of the variation in DGGE profiles of Geobacteraceae, methanogens, sulfate-reducing bacteria, and Bacteria, while organic carbon content explained 2-14%. Neither the presence of the CAH reductive dehalogenase genes tceA, bvcA, and vcrA, nor the community structure of the targeted groups significantly differed between riverbed locations showing either no attenuation or reductive dechlorination, indicating that the microbial community composition was not a limiting factor for biotransformation in the Zenne sediments.
Comparison of Fecal Methanogenic Archaeal Community Between Erhualian and Landrace Pigs Using Denaturing Gradient Gel Electrophoresis and Real-Time PCR Analysis
Su, Y. ; Smidt, H. ; Zhu, W.Y. - \ 2014
Journal of Integrative Agriculture 13 (2014)6. - ISSN 2095-3119 - p. 1340 - 1348.
16s ribosomal-rna - methanobrevibacter-smithii - human gut - diversity analysis - mcra gene - quantification - populations - bacterial - methane - prevalence
Erhualian and Landrace breeds are typical genetically obese and lean pigs, respectively. To compare the fecal methanogenic Archaeal community between these two pig breeds, fecal samples from different growth phase pigs were collected and used for PCR-denaturing gradient gel electrophoresis (DGGE) with two primer pairs (344fGC/519r and 519f/915rGC) and real-time PCR analysis. Results showed that a better separation and higher quality of bands pattern were obtained in DGGE profiles using primers 344fGC/519r as compared with primers 519f/915rGC. Sequencing of DGGE bands showed that the predominant methanogens in the feces of Erhualian and Landrace pigs belonged to Methanobrevibacter spp. and Methanosphaera spp. Real-time PCR analysis revealed that there was no significant difference in the numbers of fecal total methanogens between Erhualian and Landrace pigs; however, pig growth phase affected the numbers of 16S rRNA genes of total methanogens and Methanobrevibacter smithii. Dissociation curves of methyl coenzyme-M reductase subunit A (mcrA) gene fragments amplified with real-time PCR showed all samples possessed a single peak at 82°C, which might be associated with M. smithii. Samples from the same growth phase of each breed showed good replicative dissociation curves. The results suggest that the growth phase (including diet factor) other than genotype of pig may affect the fecal methanogenic Archaeal community of pigs.
The Colonization Dynamics of the Gut Microbiota in Tilapia Larvae
Giatsis, C. ; Sipkema, D. ; Smidt, H. ; Verreth, J.A.J. ; Verdegem, M.C.J. - \ 2014
PLoS One 9 (2014)7. - ISSN 1932-6203 - 15 p.
gradient gel-electrophoresis - 16s ribosomal-rna - early-life stages - gadus-morhua - fish - populations - genes - determinant - communities - aquaculture
The gut microbiota of fish larvae evolves fast towards a complex community. Both host and environment affect the development of the gut microbiota; however, the relative importance of both is poorly understood. Determining specific changes in gut microbial populations in response to a change in an environmental factor is very complicated. Interactions between factors are difficult to separate and any response could be masked due to high inter-individual variation even for individuals that share a common environment. In this study we characterized and quantified the spatio-temporal variation in the gut microbiota of tilapia larvae, reared in recirculating aquaculture systems (RAS) or active suspension tanks (AS). Our results showed that variation in gut microbiota between replicate tanks was not significantly higher than within tank variation, suggesting that there is no tank effect on water and gut microbiota. However, when individuals were reared in replicate RAS, gut microbiota differed significantly. The highest variation was observed between individuals reared in different types of system (RAS vs. AS). Our data suggest that under experimental conditions in which the roles of deterministic and stochastic factors have not been precisely determined, compositional replication of the microbial communities of an ecosystem is not predictable.
The first 1000 cultured species of the human gastrointestinal microbiota
Rajilic-Stojanovic, M. ; Vos, W.M. de - \ 2014
FEMS Microbiology Reviews 38 (2014)5. - ISSN 0168-6445 - p. 996 - 1047.
irritable-bowel-syndrome - 16s ribosomal-rna - human gut microbiota - gradient gel-electrophoresis - human intestinal microbiota - human fecal samples - mucin-degrading bacterium - equol-producing bacterium - diet-induced obesity - bottle-fed infants
The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.
Effect of diet on the intestinal microbiota and its activity
Zoetendal, E.G. ; Vos, W.M. de - \ 2014
Current Opinion in Gastroenterology 30 (2014)2. - ISSN 0267-1379 - p. 189 - 195.
human gut microbiome - 16s ribosomal-rna - human colonic microbiota - metabolic syndrome - fecal samples - cancer-risk - obesity - ecology - enterotypes - health
AB Purpose of review: To summarize and discuss recent findings concerning diet-microbiota-health relations. Recent findings: Mouse and other model animal studies have provided detailed insight into host-microbiota interactions, but cannot be extrapolated easily to humans that have different dietary habits, intestinal architecture, and microbiota composition. In spite of the fact that all humans have a personalized microbiome, the discovery of the high-level clusters, such as enterotypes, offer great potential for stratifying individuals in intervention studies based on their intestinal microbiota. A highly diverse microbiota seems to be key to adult human health. Long-term dietary patterns have been found to be associated with specific microbiota compositions and in some cases enterotypes. Fecal transplantations indicate that homeostasis can be restored and indicate that diet-microbiota-induced disorders can be improved by therapeutic modification of the microbiota. The specificity of complex carbohydrate conversion is the driving ecological force in the colon, while competition for sugars with the host is the driver for the small intestinal ecosystem. At both locations, the microbial fermentation of dietary components occurs in trophic chains and insight into these multispecies conversions is essential to understand the impact of diet on health. Summary: There are clear associations between the microbiota, our diet and our health. However, as microbiota correlations with human health and diet are generally based on baseline comparisons between populations, there is a need for dedicated dietary intervention studies in humans to differentiate between correlation and causality.
Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage
Méndez-Garcia, C. ; Mesa, V. ; Sprenger, R.R. ; Richter, M. ; Suarez Diez, M. ; Solano, J. ; Bargiela, R. ; Golyshina, O.V. ; Manteca, A. ; Ramos, J.L. ; Gallego, J.R. ; Llorente, I. ; Martins Dos Santos, V.A.P. ; Jensen, O.N. ; Paláez, A.I. ; Sánchez, J. ; Ferrer, M. - \ 2014
ISME Journal 8 (2014). - ISSN 1751-7362 - p. 1259 - 1274.
acidophile acidithiobacillus-ferrivorans - community genomic analysis - 16s ribosomal-rna - rio-tinto - metal-rich - anaerobic sediments - oxidizing bacteria - fam. nov - diversity - biofilm
Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH ~2) in three distinct compartments: two from a stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) and one from a submerged anoxic non-stratified mat biofilm. The communities colonising pyrite and those in the mature formations appear to be populated by the greatest diversity of bacteria and archaea (including 'ARMAN' (archaeal Richmond Mine acidophilic nano-organisms)-related), as compared with the known AMD, with ~44.9% unclassified sequences. We propose that the thick polymeric matrix may provide a safety shield against the prevailing extreme condition and also a massive carbon source, enabling non-typical acidophiles to develop more easily. Only 1 of 39 species were shared, suggesting a high metabolic heterogeneity in local microenvironments, defined by the O2 concentration, spatial location and biofilm architecture. The suboxic mats, compositionally most similar to each other, are more diverse and active for S, CO2, CH4, fatty acid and lipopolysaccharide metabolism. The oxic stratum of the streamer, displaying a higher diversity of the so-called 'ARMAN'-related Euryarchaeota, shows a higher expression level of proteins involved in signal transduction, cell growth and N, H2, Fe, aromatic amino acids, sphingolipid and peptidoglycan metabolism. Our study is the first to highlight profound taxonomic and functional shifts in single AMD formations, as well as new microbial species and the importance of H2 in acidic suboxic macroscopic growths
Effects of the antibiotic enrofloxacin on the ecology of tropical eutrophic freshwater microcosms
Rico, A. ; Rocha Dimitrov, M. ; Wijngaarden, R.P.A. van; Satapornvanit, K. ; Smidt, H. ; Brink, P.J. van den - \ 2014
Aquatic Toxicology 147 (2014). - ISSN 0166-445X - p. 92 - 104.
16s ribosomal-rna - risk-assessment - fluoroquinolone antibiotics - microbial-populations - veterinary medicines - aquatic microcosms - primary producers - ciprofloxacin - community - toxicity
The main objective of the present study was to assess the ecological impacts of the fluoroquinolone antibiotic enrofloxacin on the structure and functioning of tropical freshwater ecosystems. Enrofloxacin was applied at a concentration of 1, 10, 100 and 1000µg/L for 7 consecutive days in 600-L outdoor microcosms in Thailand. The ecosystem-level effects of enrofloxacin were monitored on five structural (macroinvertebrates, zooplankton, phytoplankton, periphyton and bacteria) and two functional (organic matter decomposition and nitrogen cycling) endpoint groups for 4 weeks after the last antibiotic application. Enrofloxacin was found to dissipate relatively fast from the water column (half-dissipation time: 11.7h), and about 11% of the applied dose was transformed into its main by-product ciprofloxacin after 24h. Consistent treatment-related effects on the invertebrate and primary producer communities and on organic matter decomposition could not be demonstrated. Enrofloxacin significantly affected the structure of leaf-associated bacterial communities at the highest treatment level, and reduced the abundance of ammonia-oxidizing bacteria and ammonia-oxidizing archaea in the sediments, with calculated NOECs of 10 and
Denitrification in restored and unrestored Danish streams
Veraart, A.J. ; Audet, J. ; Rocha Dimitrov, M. ; Hoffmann, C.C. ; Gillissen, F. ; Klein, J.J.M. de - \ 2014
Ecological Engineering 66 (2014). - ISSN 0925-8574 - p. 129 - 140.
16s ribosomal-rna - denitrifying bacteria - headwater streams - nosz genes - nutrient-uptake - restoration - water - sediments - nirk - pcr
Stream restoration often aims at mitigating nutrient pollution in aquatic ecosystems. However, despite recent research efforts, effects of restoration practices on in-stream nitrogen removal remain unclear. In this study, denitrification rates as well as factors controlling denitrification in unrestored and restored sections of two Danish streams (S1 and S2) were compared. The 15N isotope pairing technique was used to measure denitrification in situ. Denitrifier presence was analyzed by denaturing gradient gel electrophoresis (DGGE) and quantitative PCR of nitrite reductase (nirK and nirS) and nitrous oxide reductase (nosZ) genes. Denitrification rates were highly variable, with denitrification rates of 3106 µmol N m-2 h-1 in the unrestored section of S1, but no detectable denitrification in the restored section of S1, whereas in S2 restored and unrestored sections had similar denitrification rates of around 250 µmol N m-2 h-1. These large differences in denitrification rates were mainly due to differences in hydrologic conditions and sediment characteristics. High nitrate fluxes from upwelling groundwater created denitrification hotspots in the unrestored section of S1. Moreover, a lack of organic matter in the restored section of S1 likely caused a low abundance of denitrifiers and consequently no detectable denitrification. Our results indicate the importance of hydrology and sediment organic matter for stream nitrogen dynamics, which should be considered in restoration design
Normal Operating Range of Bacterial Communities in Soil Used for Potato Cropping
Inceoglu, O. ; Overbeek, L.S. van; Salles, J.F. ; Elsas, J.D. van - \ 2013
Applied and Environmental Microbiology 79 (2013)4. - ISSN 0099-2240 - p. 1160 - 1170.
16s ribosomal-rna - gradient gel-electrophoresis - microbial communities - rhizosphere bacteria - plant genotype - diversity - dynamics - ecology - growth - populations
In this study, the impacts of six potato (Solanum tuberosum) cultivars with different tuber starch allocations (including one genetically modified [GM] line) on the bacterial communities in field soil were investigated across two growth seasons interspersed with 1 year of barley cultivation, using quantitative PCR, clone library, and PCR-denaturing gradient gel electrophoresis (DGGE) analyses. It was hypothesized that the modifications in the tuber starch contents of these plants, yielding changed root growth rates and exudation patterns, might have elicited altered bacterial communities in the soil. The data showed that bacterial abundances in the bulk soil varied over about 2 orders of magnitude across the 3 years. As expected, across all cultivars, positive potato rhizosphere effects on bacterial abundances were noted in the two potato years. The bulk soil bacterial community structures revealed progressive shifts across time, and moving-window analysis revealed a 60% change over the total experiment. Consistent with previous findings, the community structures in the potato rhizosphere compartments were mainly affected by the growth stage of the plants and, to a lesser extent, by plant cultivar type. The data from the soil under the non-GM potato lines were then taken to define the normal operating range (NOR) of the microbiota under potatoes. Interestingly, the bacterial communities under the GM potato line remained within this NOR. In regard to the bacterial community compositions, particular bacterial species in the soil appeared to be specific to (i) the plant species under investigation (barley versus potato) or, with respect to potatoes, (ii) the plant growth stage. Members of the genera Arthrobacter, Streptomyces, Rhodanobacter, and Dokdonella were consistently found only at the flowering potato plants in both seasons, whereas Rhodoplanes and Sporosarcina were observed only in the soil planted to barley
Faecalibacterium prausnitzii and human intestinal health
Miquel, S. ; Martin, R. ; Rossi, O. ; Bermudez-Humaran, L.G. ; Chatel, J.M. ; Sokol, H. ; Thomas, M. ; Wells, J.M. ; Langella, P. - \ 2013
Current Opinion in Microbiology 16 (2013)3. - ISSN 1369-5274 - p. 255 - 261.
16s ribosomal-rna - irritable-bowel-syndrome - mucosa-associated microbiota - butyrate-producing bacteria - active crohns-disease - gut microbiota - ulcerative-colitis - fecal microbiota - fusobacterium-prausnitzii - gastrointestinal-tract
Faecalibacterium prausnitzii is the most abundant bacterium in the human intestinal microbiota of healthy adults, representing more than 5% of the total bacterial population. Over the past five years, an increasing number of studies have clearly described the importance of this highly metabolically active commensal bacterium as a component of the healthy human microbiota. Changes in the abundance of F. prausnitzii have been linked to dysbiosis in several human disorders. Administration of F. prausnitzii strain A2-165 and its culture supernatant have been shown to protect against 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced colitis in mice. Here, we discuss the role of F. prausnitzii in balancing immunity in the intestine and the mechanisms involved.
Fame and future of faecal transplantations - developing next-generation therapies with synthetic microbiomes
Vos, W.M. de - \ 2013
Microbial Biotechnology 6 (2013)4. - ISSN 1751-7907 - p. 316 - 325.
recurrent clostridium-difficile - gastrointestinal-tract microbiota - 16s ribosomal-rna - human gut - intestinal microbiota - ulcerative-colitis - narrow-spectrum - bowel-syndrome - bacteriotherapy - diversity
While practised for over thousand years, there is presently a renaissance in the interest of using of faecal transplantations to modify the intestinal microbiota of patients. This clinical practice consists of delivering large amounts of bowel microbes in various forms into the intestinal tract of the recipient that usually has been cleared previously. The major reason for the popularity of faecal transplantations is their effectiveness in treating a variety of diseases. Hence, there is a need to develop this procedure to the next level. While there are various developments to select, standardize and store the donor microbiota, it is more challenging to understand the intestinal microbial communities and develop ways to deliver these via robust biotechnological processes. The various approaches that have been followed to do so are discussed in this contribution that is also addressing the concept of the minimal microbiome as well as the production of the synthetic communities that can be instrumental in new therapeutic avenues to modify the intestinal microbiota.
Microbial diversity and dynamics of microbial communities during black-slop soaking of soybeans as determined by PCR-DGGE and molecular cloning
Yan, Y.Z. ; Wolkers-Rooijackers, J.C.M. ; Nout, M.J.R. ; Han, B.Z. - \ 2013
World Journal of Microbiology and Biotechnology 29 (2013)10. - ISSN 0959-3993 - p. 1969 - 1974.
gradient gel-electrophoresis - 16s ribosomal-rna - polymerase-chain-reaction - tempe production - temperature - water
Tempe is a traditional fermented food in Indonesia. The manufacture process is quite complex, which comprises two stages, preparatory soaking of soybeans and fungal solid state fermentation. Daily addition of previous soak water (back-slopping) during the soybean soaking step is considered to be crucial in the manufacture of high quality tempe. The microbial diversity and dynamics of the microbial communities evolving during back-slop soaking of soybeans for tempe making was investigated by culture-independent PCR–DGGE and molecular cloning. Both DNA and total RNA were isolated and included in this study, to obtain a view on the succession of total and viable bacteria in the complex microbiota. DGGE profiles indicated that Enterobacter sp., Enterococcus sp., Pseudomonas putida, Leuconostoc fallax, Pediococcus pentosaceus, and Weissella cibaria, were the predominant bacteria. Their occurrence shifted dramatically during the back-slop soaking procedure. This study combined with previous culture-dependent studies could gain a better understanding of the complex microbiota of traditional fermented food and give useful information for its quality control.
Activity and viability of methanogens in anaerobic digestion of unsaturated and saturated long-chain fatty acids
Sousa, D.Z. ; Salvador, A.F. ; Ramos, J. ; Guedes, A.P. ; Barbosa, S. ; Stams, A.J.M. ; Alves, M.M. ; Pereira, M.A. - \ 2013
Applied and Environmental Microbiology 79 (2013)14. - ISSN 0099-2240 - p. 4239 - 4245.
16s ribosomal-rna - microbial communities - calcium addition - waste-water - oleic-acid - bacteria - inhibition - sludge - bioreactors - diversity
Lipids can be anaerobically digested to methane, but methanogens are often considered to be highly sensitive to the long-chain fatty acids (LCFA) deriving from lipids hydrolysis. In this study, the effect of unsaturated (oleate [C18:1]) and saturated (stearate [C18:0] and palmitate [C16:0]) LCFA toward methanogenic archaea was studied in batch enrichments and in pure cultures. Overall, oleate had a more stringent effect on methanogens than saturated LCFA, and the degree of tolerance to LCFA was different among distinct species of methanogens. Methanobacterium formicicum was able to grow in both oleate- and palmitate-degrading enrichments (OM and PM cultures, respectively), whereas Methanospirillum hungatei only survived in a PM culture. The two acetoclastic methanogens tested, Methanosarcina mazei and Methanosaeta concilii, could be detected in both enrichment cultures, with better survival in PM cultures than in OM cultures. Viability tests using live/dead staining further confirmed that exponential growth-phase cultures of M. hungatei are more sensitive to oleate than are M. formicicum cultures; exposure to 0.5 mM oleate damaged 99% ± 1% of the cell membranes of M. hungatei and 53% ± 10% of the cell membranes of M. formicicum. In terms of methanogenic activity, M. hungatei was inhibited for 50% by 0.3, 0.4, and 1 mM oleate, stearate, and palmitate, respectively. M. formicicum was more resilient, since 1 mM oleate and >4 mM stearate or palmitate was needed to cause 50% inhibition on methanogenic activity
The rhizosphere selects for particular groups of acidobacteria and verrucomicrobia
Nunes da Rocha, U. ; Plugge, C.M. ; George, I. ; Elsas, J.D. van; Overbeek, L.S. van - \ 2013
PLoS One 8 (2013)12. - ISSN 1932-6203
16s ribosomal-rna - bacterial community structure - hitherto-uncultured bacteria - allium-porrum rhizosphere - soil microbial community - phylum acidobacteria - gen. nov. - subdivision 1 - forest soils - diversity
There is a lack in our current understanding on the putative interactions of species of the phyla of Acidobacteria and Verrucomicrobia with plants. Moreover, progress in this area is seriously hampered by the recalcitrance of members of these phyla to grow as pure cultures. The purpose of this study was to investigate whether particular members of Acidobacteria and Verrucomicrobia are avid colonizers of the rhizosphere. Based on previous work, rhizosphere competence was demonstrated for the Verrucomicrobia subdivision 1 groups of Luteolibacter and Candidatus genus Rhizospheria and it was hypothesized that the rhizosphere is a common habitat for Acidobacteria subdivision 8 (class Holophagae). We assessed the population densities of Bacteria, Verrucomicrobia subdivision 1 groups Luteolibacter and Candidatus genus Rhizospheria and Acidobacteria subdivisions 1, 3, 4, 6 and Holophagae in bulk soil and in the rhizospheres of grass, potato and leek in the same field at different points in time using real-time quantitative PCR. Primers of all seven verrucomicrobial, acidobacterial and holophagal PCR systems were based on 16S rRNA gene sequences of cultivable representatives of the different groups. Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres. In particular, the Holophaga 16S rRNA gene number were more abundant in the leek rhizosphere than in bulk soil and the rhizospheres of grass and potato. Attraction to, and colonization of, leek roots by Holophagae strain CHC25 was further shown in an experimental microcosm set-up. In the light of this remarkable capacity, we propose to coin strain CHC25 Candidatus Porrumbacterium oxyphilus (class Holophagae, Phylum Acidobacteria), the first cultured representative with rhizosphere competence
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