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0000-0003-3900-5522
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INRAE
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Publisher: Informa UK Limited
Date: 10-2012
DOI: 10.1080/00071668.2012.723802
Abstract: 1. Changes in bacterial and fungal communities in chicken litter with high and low moisture content over a five week period during a single chicken grow out cycle in a poultry shed in subtropical Australia were investigated to study the association between specific microbes and odour production. 2. Microbial biomass, as indicated by DNA yields, was higher and community composition was more dynamic over time in moist compared with dry chicken litter. 3. Bacillus, Atopostipes and Aspergillus species increased in relative abundance in moist chicken litter s les over time reflecting the relatively high fitness and hence activity of these specific bacteria and this specific fungus in this environment.
Publisher: Springer Science and Business Media LLC
Date: 03-08-2012
DOI: 10.1007/S00216-012-6268-0
Abstract: Capillary electrophoresis (CE) has been the principle system for nucleic acid analysis since the early 1990s due to its inherent advantages such as fast analysis time, high resolution and efficiency, minimal s le requirement, high detection sensitivity, and automation. In the past few decades, microbial community fingerprinting methods such as terminal restriction fragment length polymorphism and single-stranded conformation polymorphism (SSCP) have migrated to CE to utilize its advantages over conventional slab gel electrophoresis. Recently, a gel-based direct rRNA fingerprint method was demonstrated. Different from other existing microbial community characterization approaches, this novel approach is polymerase chain reaction free and capable of providing information on the relative abundance of rRNA from in idual phylotypes in low- ersity s les. As a gel-based method, it has a long analysis time and relatively large reagent and s le requirements. Here, we addressed these limitations by transferring the RNA fingerprint approach to the CE platform. Analysis time significantly improved from 24 h to 60 min, and the use of a fluorescently labeled hybridization probe as the detection strategy decreased the s le requirement by ten-fold. The combination of fast analysis time, low s le requirement, and sensitive fluorescence detection makes CE-RNA-SSCP an appealing new approach for characterizing low- ersity microbial communities.
Publisher: Wiley
Date: 08-03-2006
DOI: 10.1111/J.1462-2920.2005.00950.X
Abstract: The exact extent of microbial ersity remains unknowable. Nevertheless, fingerprinting patterns [denaturing gradient electrophoresis (DGE), single-strand conformation polymorphism (SSCP)] provide an image of a microbial ecosystem and contain ersity data. We generated numerical simulation fingerprinting patterns based on three types of distribution (uniform, geometric and lognormal) with a range of units from 10 to 500,000. First, simulated patterns containing a ersity of around 1000 units or more gave patterns similar to those obtained in experiments. Second, the number of bands or peaks saturated quickly to about 35 and were unrelated to the degree of ersity. Finally, assuming lognormal distribution, we used an estimator of ersity on in silico and experimental fingerprinting patterns. Results on in silico patterns corresponded to the simulation inputs. Diversity results in experimental patterns were in the same range as those obtained from the same DNA s le in molecular inventories. Thus, fingerprinting patterns contain extractable data about ersity although not on the basis of a number of bands or peaks, as is generally assumed to be the case.
Publisher: Cold Spring Harbor Laboratory
Date: 18-11-2021
DOI: 10.1101/2021.11.15.468583
Abstract: In pigs, the gut microbiota composition plays a major role in the process of digestion, but is influenced by many external factors, especially diet. To be used in breeding applications, genotype by diet interactions on microbiota composition have to be quantified, as well as their impact on genetic covariances with feed efficiency (FE) and digestive efficiency (DE) traits. This study aimed at determining the impact of an alternative diet on variance components of microbiota traits (genera and alpha ersity indices), and estimating genetic correlations between microbiota and efficiency traits for pigs fed a conventional (CO) or a high fiber (HF) diet. Fecal microbes of 812 full-siblings fed a CO diet and 752 pigs fed the HF diet were characterized at 16 weeks of age by sequencing the V3-V4 region of the 16S rRNA gene. A total of 231 genera were identified. Digestibility coefficients of nitrogen, organic matter and energy were predicted analyzing the same fecal s les with near infrared spectrometry. Daily feed intake, feed conversion ratio, residual feed intake and average daily gain (ADG) were also recorded. The 71 genera with less than 20% of zeros were retained for genetic analyses. Heritability (h 2 ) of microbiota traits were similar between diets (from null to 0.38 ± 0.12 in the CO diet and to 0.39 ± 0.12 in the HF diet). Only three out of the 24 genera and two alpha ersity indices with significant h 2 in both diets had genetic correlations across diets significantly different from 0.99 ( P 0.05), indicating limited genetic by diet interactions for these traits. When both diets were analyzed jointly, 59 genera had h 2 significantly different from zero. Based on the genetic correlations between these genera and ADG, FE and DE traits, three groups of genera could be identified. A group of 29 genera was favorably correlated with DE and FE traits, 14 genera were unfavorably correlated with DE traits, and the last group of 16 genera had correlations close to zero with production traits. However, genera favorably correlated with DE and FE traits were unfavorably correlated with ADG, and vice versa. Alpha ersity indices had correlation patterns similar to the first group. In the end, genetic by diet interactions on gut microbiota composition of growing pigs were limited in this study. Based on this study, microbiota-based traits could be used as proxies to improve FE and DE in growing pigs.
Publisher: Elsevier BV
Date: 05-2013
DOI: 10.1016/J.JVIROMET.2013.02.007
Abstract: The addition of sodium chloride to freshwater or diluted minimal salt medium increases the adsorption of T2 phages on Escherichia coli. For the first time the adsorption in diluted minimal salt medium was measured by counting unadsorbed phages (i.e. free particles) using flow cytometry, allowing a gentle separation between adsorbed and unadsorbed phages. Flow cytometry was able to detect weakly adsorbed phage that remained undetected using classical centrifugation-based methods and this allowed us to show that increasing ionic strength enhances the phage adsorption to its bacterial host with an extremely low detection limit. A key result was that the adsorption in high ionic strength (i.e. 100 mM) reached 4.5±0.1×10⁻⁵ mL/min which is 1400 fold higher than previously reported values. In order to understand the mechanism underpinning such a weak phage adsorption, the zeta potentials and the diffusion coefficient of the particles were measured by dynamic light scattering. The bacterial cells and the phages had zeta potentials between -60 mV and -10 mV and -30 mV and -10 mV, respectively. The diffusion coefficient of the phage was 2.8±0.4×10⁻¹² m² s⁻¹ corresponding to a hydrodynamic radius of 104±15 nm. However significant adsorption occurs in conditions where the DLVO theory predicts that minimal encounter, suggesting that forces other that electrostatic repulsion and Van der Waals interaction (e.g. potential impurities, particle shape and other biological characteristics) are likely to interplay.
Publisher: Oxford University Press (OUP)
Date: 16-08-2010
DOI: 10.1111/J.1365-2672.2010.04706.X
Abstract: To evaluate the importance of the bacterial composition on the resilience of the organic matter assimilation in the sea. Chemostats were inoculated with coastal and offshore bacterial communities. Bacterial density and protein synthesis increased before stabilizing, and this response to confinement was more marked in the offshore chemostats. Before the toluene perturbation the community structure in the coastal chemostats remained complex whereas the offshore chemostats became dominated by Alteromonas sp. After the perturbation, bacterial protein synthesis was inhibited before peaking briefly at a level fivefold to that observed before the perturbation and then stabilizing at a level comparable to that before the perturbation. Alteromonas dominated both the coastal and the offshore communities immediately after the perturbation and the coastal communities did not recover their initial complexity. Cell lysis induced by the toluene perturbation favoured the growth of Alteromonas which could initiate growth rapidly in response to the nutrient pulse. Despite their different community structure in situ, the resilience of protein synthesis of coastal and offshore bacterial communities was dependent on Alteromonas, which dominated in the chemostats. Here we show that although Alteromonas sp. dominated in artificial offshore and coastal communities in chemostats, their response time to the shock was different. This suggests that future perturbation studies on resilience in the marine environment should take account of ecosystem history.
Publisher: Universitat Politecnica de Valencia
Date: 28-09-2023
Publisher: Wiley
Date: 22-06-2007
Publisher: Springer Science and Business Media LLC
Date: 07-07-2010
DOI: 10.1007/S00253-010-2740-Y
Abstract: A reactive iron barrier in a contaminated aquifer with low pH was found to dechlorinate 1,2-dichloroethane (1,2-DCA) in situ. This chlorinated ethane is known to resist abiotic reduction by zero valent iron. S les taken up-gradient and within the barrier were used to inoculate anaerobic batch cultures amended with various electron donors. Cultures inoculated with groundwater from within the reactive iron barrier reduced 1,2-DCA to ethene. The same effect could be achieved by simultaneously supplying hydrogen while neutralising pH. The presence of iron or hydrogen at neutral pH had negligible effects on 1,2-DCA reduction in cultures inoculated with groundwater s led up-gradient of the barrier. Molecular microbial community characterisation revealed that Dehalobacter species were more abundant in groundwater s led from within the barrier. These findings suggest reactive iron barriers represent a remediation technology for 1,2-DCA degradation acting through in situ recruitment of 1,2-DCA reducing bacteria such as Dehalobacter.
Publisher: Cold Spring Harbor Laboratory
Date: 29-11-2019
DOI: 10.1101/859215
Abstract: This study describes the response of piglet microbiota to weaning in various environments, and investigates whether microbiota composition is associated with the robustness of piglets. Faecal s les and growth data were collected just before and 7 days after weaning in 288 piglets from 16 commercial farms characterised by their pathogenic status and antimicrobial use. The effect of weaning on the most abundant microbial families of faecal microbiota was roughly the same in all farms and in agreement with previous findings. Four enterotypes, ubiquitous in all farms, were identified, for which the most discriminating genera were Prevotella , Faecalibacterium , Roseburia , and Lachnospira. They corresponded to a gradual maturational shift from pre to post-weaning microbiota. Besides antimicrobial use, the pathogenic status of the farm had a major influence on the post-weaning microbial evolution of apparently healthy piglets. Regarding in idual characteristics, piglets whose growth was less perturbed by weaning had more Bacteroidetes (P 0.01) and less Proteobacteria (P 0.001). In response to weaning, they showed a greater increase in Prevotella (P 0.01), Coprococcus (P 0.01) and Lachnospira (P 0.05) than piglets that grew more slowly. Thus, the microbiota of robust piglets shares common characteristics regardless the living environment of animals.
Publisher: Wiley
Date: 26-02-2021
DOI: 10.1111/JBG.12539
Abstract: This study aimed to evaluate the genetic relationship between faecal microbial composition and five feed efficiency (FE) and production traits, residual feed intake (RFI), feed conversion ratio (FCR), daily feed intake (DFI), average daily gain (ADG) and backfat thickness (BFT). A total of 588 s les from two experimental pig lines developed by ergent selection for RFI were sequenced for the 16 rRNA hypervariable V3‐V4 region. The 75 genera with less than 20% zero values (97% of the counts) and two α‐ ersity indexes were analysed. Line comparison of the microbiota traits and estimations of heritability (h 2 ) and genetic correlations ( r g ) were analysed. A non‐metric multidimensional scaling showed line differences between genera. The α‐ ersity indexes were higher in the LRFI line than in the HRFI line ( p .01), with h 2 estimates of 0.19 ± 0.08 (Shannon) and 0.12 ± 0.06 (Simpson). Forty‐eight genera had a significant h 2 ( .125). The r g of the α‐ ersities indexes with production traits were negative. Some r g of genera belonging to the Lachnospiraceae , Ruminococcaceae , Prevotellaceae , Lactobacillaceae , Streptococcaceae , Rikenellaceae and Desulfovibrionaceae families significantly differed from zero ( p .05) with FE traits, RFI (3), DFI (7) and BFT (11). These results suggest that a sizable part of the variability of the gut microbial community is under genetic control and has genetic relationships with FE, including ersity indicators. It offers promising perspectives for selection for feed efficiency using gut microbiome composition in pigs.
Publisher: Elsevier BV
Date: 2014
Publisher: Springer Science and Business Media LLC
Date: 27-07-2022
DOI: 10.1186/S12711-022-00742-6
Abstract: Breeding pigs that can efficiently digest alternative diets with increased fiber content is a viable strategy to mitigate the feed cost in pig production. This study aimed at determining the contribution of the gut microbiota and host genetics to the phenotypic variability of digestive efficiency (DE) traits, such as digestibility coefficients of energy, organic matter and nitrogen, feed efficiency (FE) traits (feed conversion ratio and residual feed intake) and growth traits (average daily gain and daily feed intake). Data were available for 791 pigs fed a conventional diet and 735 of their full-sibs fed a high-fiber diet. Fecal s les were collected at 16 weeks of age to sequence the V3–V4 regions of the 16S ribosomal RNA gene and predict DE with near-infrared spectrometry. The proportions of phenotypic variance explained by the microbiota (microbiability) were estimated under three OTU filtering scenarios. Then, microbiability and heritability were estimated independently (models Micro and Gen) and jointly (model Micro+Gen) using a Bayesian approach for all traits. Breeding values were estimated in models Gen and Micro+Gen. Differences in microbiability estimates were significant between the two extreme filtering scenarios (14,366 and 803 OTU) within diets, but only for all DE. With the intermediate filtering scenario (2399 OTU) and for DE, microbiability was higher ( 0.44) than heritability ( 0.32) under both diets. For two of the DE traits, microbiability was significantly higher under the high-fiber diet (0.67 ± 0.06 and 0.68 ± 0.06) than under the conventional diet (0.44 ± 0.06). For growth and FE, heritability was higher (from 0.26 ± 0.06 to 0.44 ± 0.07) than microbiability (from 0.17 ± 0.05 to 0.35 ± 0.06). Microbiability and heritability estimates obtained with the Micro+Gen model did not significantly differ from those with the Micro and Gen models for all traits. Finally, based on their estimated breeding values, pigs ranked differently between the Gen and Micro+Gen models, only for the DE traits under both diets. The microbiota explained a significant proportion of the phenotypic variance of the DE traits, which was even larger than that explained by the host genetics. Thus, the use of microbiota information could improve the selection of DE traits, and to a lesser extent, of growth and FE traits. In addition, our results show that, at least for DE traits, filtering OTU is an important step and influences the microbiability.
Publisher: Wiley
Date: 28-11-2011
DOI: 10.1111/J.1462-2920.2011.02656.X
Abstract: Chloroform (CF, CHCl(3)) is a recalcitrant and toxic environmental pollutant. In this communication we report for the first time a microbial community capable of complete CF dechlorination by metabolic processes. Cultures derived from subsurface soil (3.5 m) could sustain complete dechlorination of CF at levels of least 360 µM at a rate of 40 µM per day. Scrutiny of CF dechlorination revealed two metabolic processes at work. First, CF was respired to dichloromethane (DCM, CH(2) Cl(2)), which was then fermented to acetate, hydrogen and carbon dioxide. Elevated hydrogen partial pressures were found to inhibit the fermentation process. Interspecies hydrogen transfer was observed in the form of methanogenesis and acetogenesis. This suggests that the dechlorination process required syntrophic partners to maintain low hydrogen partial pressures. (13)C-labelled DCM was employed to help elucidate the chemistry of the process and identify bacterial community members involved. CF respiring cultures, where emulsified vegetable oil was supplied as the electron donor and DCM fermenting cultures, where DCM was supplied as the sole organic carbon source were studied separately. Pyrosequencing of these cultures revealed Dehalobacter lineages as a predominant community member in both. Subsequent growth experiments confirmed that the proliferation of Dehalobacter was linked directly to both the dehalorespiration and dehalofermentation processes.
Publisher: Oxford University Press (OUP)
Date: 07-2008
Publisher: MDPI AG
Date: 28-07-2020
DOI: 10.3390/MICROORGANISMS8081141
Abstract: In poultry, the selection of broilers for growth performance has induced a deterioration in the health of the parental hens associated with poor reproductive efficiency. To improve these parameters, we administered to laying parental broiler hens a regular diet supplemented or not (Control) with a moderate (1%) or a high level (2%) of grape seed extract (GSE). The 1% GSE diet was administered from a young age (from 4 to 40 weeks of age) and the high level of 2% GSE was administered only during a 2-week period (from 38 to 40 weeks of age) in the laying period. The analysis of 40-week-old hens showed that 2% GSE displayed a reduction in the fat tissue and an improvement in fertility with heavier and more resistant eggs. Seven monomer phenolic metabolites of GSE were significantly measured in the plasma of the 2% GSE hens. GSE supplementation increased the relative abundance of the following bacteria populations: Bifidobacteriaceae, Lactobacilliaceae and Lachnospiraceae. In conclusion, a supplementation period of only 2 weeks with 2% GSE is sufficient to improve the metabolic and laying parameters of breeder hens through a modification in the microbiota.
Publisher: MDPI AG
Date: 31-08-2021
DOI: 10.3390/MICROORGANISMS9091852
Abstract: The bacterial consumption of viruses not been reported on as of yet even though bacteria feed on almost anything. Viruses are widely distributed but have no acknowledged active biocontrol. Viral biomass undoubtedly reintegrates trophic cycles however, the mechanisms of this phase still remain unknown. 13C-labelled T4 phages monitor the increase of the density of the bacterial DNA concomitant with the decrease of plaque forming units. We used 12C T4 phages as a control. T4 phage disappearance in wastewater sludge was found to occur mainly through predation by Aeromonadacea. Phage consumption also favours significant in situ bacterial growth. Furthermore, an isolated strain of Aeromonas was observed to grow on T4 phages as sole the source of carbon, nitrogen, and phosphorus. Bacterial species are capable of consuming bacteriophages in situ, which is likely a widespread and underestimated type of biocontrol. This assay is anticipated as a starting point for harnessing the bacterial potential in limiting the diffusion of harmful viruses within environments such as in the gut or in water.
Publisher: Elsevier BV
Date: 03-2012
DOI: 10.1016/J.WATRES.2011.10.047
Abstract: Nonylphenols (NP) have estrogenic potential because of their phenolic ring, but the organisms involved in the degradation of this alkylated phenol remain unidentified. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP) and a new method based on pyrosequencing, we identified the bacteria involved in the degradation of the aromatic ring of [U-ring-(13)C] 4-n-NP in aerobic sludge. The first order degradation rate of 4-n-NP was 5.5d(-1). Single strand conformation polymorphism of density-separated labeled and unlabeled 16S rRNA showed significant differences and enabled selection of four representative fractions for pyrosequencing. Nineteen phylotypes showed a significant enrichment in the heavy fraction in the labeled pulse. The relative abundances of these phylotypes were combined with the RNA concentration of each fraction to yield a simple model of the distribution of each phylotype across the gradient. This model was used to estimate the percentage of labeling for each phylotype. The sequences showing the highest labeling (11%) were closely related to Afipia sp. but represented only 2 % of the RNA in the heavy fraction of the labeled pulse. The sequences representing the largest proportion of the RNA in the heavy fraction were related to Propionibacterium acnes and Frateuria aurantia, which are known to possess enzymes for phenol degradation. The model shows that despite Afipia having the highest (13)C enrichment, other species encoding phenol degradation pathways are responsible for more (13)C incorporation. Last, we showed that some species represent 12% of the total RNA but contain only 1% (13)C above natural abundance.
Publisher: The Company of Biologists
Date: 2019
DOI: 10.1242/JEB.202879
Abstract: The interaction between the gut microbiota (GM) and the brain has led to the concept of the microbiota-gut-brain axis but data in birds remain scarce. We tested the hypothesis that colonization of germ-free chicks from a quail line selected for a high emotional reactivity (E+) with GM from a line with low emotional reactivity (E-) would reduce their emotional behaviour in comparison with germ-free chicks from E+ line colonized with GM from the same E+ line. The GM composition analysis of both groups revealed a shift in term of microbial ersity and richness between Day 21 and Day 35 and the GM of the two groups of quails were closer to each other at Day 35 than at Day 21 at a phylum level. Quails that received GM from the E- line expressed a lower emotional reactivity than the quails colonized by GM from the E+line in the tonic immobility and the novel environment tests proceeded during the second week of age. This result was reversed in a second tonic immobility test and an open-field run two weeks later. These behavioural and GM modifications over time could be the consequence of the resilience of the GM to recover its equilibrium present in the E+ host, which is in part driven by the host genotype. This study shows for the first time that a gut microbiota transfer can influence emotional reactivity in Japanese quails strengthening the existence of a microbiota-gut-brain axis in this species of bird.
Publisher: Research Square Platform LLC
Date: 09-06-2021
DOI: 10.21203/RS.3.RS-580088/V1
Abstract: Background: Bacterial consumption of viruses has never yet been reported, even though bacteria feed on almost anything. Viruses are omnipresent predators for all organisms, but have no acknowledged active biocontrol. The viral biomass undoubtedly reintegrates the trophic cycles, however the mechanisms of this phase still remain unknown. Methods: Here, we used stable isotope probing with 13C labelled T4 phages to monitor the increase of density of the bacterial DNA concomitant with the decrease of plaque forming units. We used 12C T4 phages as control. Results: T4 phage disappearance in wastewater sludge was found to occur mainly through predation by Aeromonadacea. Phage consumption also favours significant in situ bacterial growth. Furthermore, an isolated strain of Aeromonas was observed to grow on T4 phages as sole source of carbon, nitrogen and phosphorus. Conclusions: bacterial species are capable of consuming bacteriophages in situ, which is likely a widespread and underestimated type of biocontrol. This assay is anticipated as a starting point for harnessing the bacterial potential in limiting the diffusion of harmful viruses within environments such as gut or water.
Publisher: Cold Spring Harbor Laboratory
Date: 06-2021
DOI: 10.1101/2021.06.01.446436
Abstract: Bacterial consumption of viruses has never yet been reported, even though bacteria feed on almost anything. Viruses are omnipresent predators for all organisms, but have no acknowledged active biocontrol. The viral biomass undoubtedly reintegrates the trophic cycles, however the mechanisms of this phase still remain unknown. Here, we used stable isotope probing with 13 C labelled T4 phages to monitor the increase of density of the bacterial DNA concomitant with the decrease of plaque forming units. We used 12 C T4 phages as control. T4 phage disappearance in wastewater sludge was found to occur mainly through predation by Aeromonadacea . Phage consumption also favours significant in situ bacterial growth. Furthermore, an isolated strain of Aeromonas was observed to grow on T4 phages as sole source of carbon, nitrogen and phosphorus. bacterial species are capable of consuming bacteriophages in situ , which is likely a widespread and underestimated type of biocontrol.This assay is anticipated as a starting point for harnessing the bacterial potential in limiting the diffusion of harmful viruses within environments such as gut or water.
Publisher: Informa UK Limited
Date: 30-04-2020
Publisher: Elsevier BV
Date: 03-2008
DOI: 10.1016/J.MBS.2008.01.002
Abstract: Hubbell's neutral model has become a major paradigm in ecology. Whereas the steady-state structure is well understood, results about the dynamical aspects of the model are scarce. Here we derive dynamical equations for the Simpson ersity index. Both mean and variance of the ersity are proven to satisfy stable linear system dynamics. We show that in the stationary limit we indeed recover previous results, and we supplement this with numerical simulations to validate the dynamical part of our analytical computations. These findings are especially relevant for experiments in microbial ecology, where the Simpson ersity index can be accurately measured as a function of time.
Publisher: Wiley
Date: 11-01-2020
DOI: 10.1002/MBO3.977
Abstract: Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here, we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental s le using a synthetic standard in minuscule amounts (100 ppm to 1% of the 16S rRNA sequences) that is added to the s le before DNA extraction and quantified by two quantitative polymerase chain reaction (qPCR) reactions. This allows normalizing by the initial microbial density, taking into account the DNA recovery yield. We quantified the internal standard and the total load of 16S rRNA genes by qPCR. The qPCR for the latter uses the exact same primers as those used for Illumina sequencing of the V3‐V4 hypervariable regions of the 16S rRNA gene to increase accuracy. We are able to calculate the absolute concentration of the species per gram of s le, taking into account the DNA recovery yield. This is crucial for an accurate estimate as the yield varied between 40% and 84%. This method avoids sacrificing a high proportion of the sequencing effort to quantify the internal standard. If sacrificing a part of the sequencing effort to the internal standard is acceptable, we however recommend that the internal standard accounts for 30% of the environmental 16S rRNA genes to avoid the PCR bias associated with rare phylotypes. The method proposed here was tested on a feces s le but can be applied more broadly on any environmental s le. This method offers a real improvement of metabarcoding of microbial communities since it makes the method quantitative with limited efforts.
Publisher: Springer Science and Business Media LLC
Date: 26-05-2011
DOI: 10.1007/S00248-011-9877-9
Abstract: In the past decade, an increasing number of methods in microbial ecology have been developed that address the questions of which microbes exist in the environment, what their roles are and, to some extent, what their abundance is. In the present paper, we propose and describe the proof of principle of a novel method for analysing shifts in microbial community composition that uses small RNA fragments directly derived from 16S rRNA. Community fingerprints are generated on the basis of sequence-dependent conformational differences of rRNA fragments. We applied this method to profile artificial and natural communities and to detect changes in community structure in enrichment cultures. This method constitutes a PCR-free alternative to microbial community characterisation and can provide information on the relative abundance of rRNA from in idual phylotypes in low ersity s les.
Publisher: Wiley
Date: 25-01-2008
DOI: 10.1111/J.1462-2920.2007.01497.X
Abstract: One of the first comparisons of a natural iron fertilized bloom with a high-nutrient low-chlorophyll (HNLC) site was undertaken during the Kerguelen ocean and plateau compared study (KEOPS) cruise. To understand better the bacteria-phytoplankton relationship in the context of natural iron fertilization, bacterial ersity and activity was investigated in the bloom and in the adjacent HNLC region by 16S rDNA clone libraries and by single strand conformation polymorphism (SSCP) analysis. Both libraries were dominated by Alphaproteobacteria, Gammaproteobacteria and the Cytophaga-Flavobacteria-Bacteroides group. Cluster analysis at 99% sequence similarity yielded several micro erse clusters and revealed striking differences between the two libraries. In the bloom, the dominant operational taxonomic units (OTUs) were the Roseobacter NAC11-7 cluster, SAR92 and a Cytophaga-Flavobacteria-Bacteroides cluster related to the agg58 group, whereas in the HNLC region, SAR11, Roseobacter RCA and Polaribacter dominated. SSCP analysis of 16S rDNA and 16S rRNA revealed contrasting dynamics of three different Roseobacter OTUs. Roseobacter NAC11-7 and NAC11-6 had higher relative abundances and activities in the bloom compared with the HNLC site and NAC11-6 was only detected at the decline of the bloom concomitant with a shift in phytoplankton composi tion. In contrast, Roseobacter RCA was relatively abundant and active both inside and outside of the bloom. These results suggest that the different OTUs within the Roseobacter group represent functional groups that each play an important role in the cycling of carbon.
Location: France
No related grants have been discovered for olivier zemb.