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1.
Environ Microbiol ; 22(3): 1141-1153, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-31867821

RESUMEN

Some temperate tree species are associated with very low soil nitrification rates, with important implications for forest N dynamics, presumably due to their potential for biological nitrification inhibition (BNI). However, evidence for BNI in forest ecosystems is scarce so far and the nitrifier groups controlled by BNI-tree species have not been identified. Here, we evaluated how some tree species can control soil nitrification by providing direct evidence of BNI and identifying the nitrifier group(s) affected. First, by comparing 28 year-old monocultures of several tree species, we showed that nitrification rates correlated strongly with the abundance of the nitrite oxidizers Nitrobacter (50- to 1000-fold changes between tree monocultures) and only weakly with the abundance of ammonia oxidizing archaea (AOA). Second, using reciprocal transplantation of soil cores between low and high nitrification stands, we demonstrated that nitrification changed 16 months after transplantation and was correlated with changes in the abundance of Nitrobacter, not AOA. Third, extracts of litter or soil collected from the low nitrification stands of Picea abies and Abies nordmanniana inhibited the growth of Nitrobacter hamburgensis X14. Our results provide for the first time direct evidence of BNI by tree species directly affecting the abundance of Nitrobacter.


Asunto(s)
Ecosistema , Interacciones Huésped-Patógeno/fisiología , Nitrificación , Nitrobacter/fisiología , Microbiología del Suelo , Suelo/química , Árboles/microbiología , Archaea/crecimiento & desarrollo , Oxidación-Reducción
2.
Antonie Van Leeuwenhoek ; 110(11): 1453-1465, 2017 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-28608318

RESUMEN

Considering the great agronomic and environmental importance of denitrification, the aim of the present study was to study the temporal and spatial factors controlling the abundance and activity of denitrifying bacterial communities in a range of eight agricultural soils over 2 years. Abundance was quantified by qPCR of the nirS, nirK and nosZ genes, and the potential denitrification enzyme activity (DEA) was estimated. Our data showed a significant temporal variation considerably high for the abundance of nirK-harboring communities, followed by nosZ and nirS communities. Regarding soil parameters, the abundances of nosZ, nirS and nirK were mostly influenced by organic material, pH, and slightly by NO3-, respectively. Soil texture was the most important factor regulating DEA, which could not be explained by the abundance of denitrifiers. Analyses of general patterns across lands to understand the soil functioning is not an easy task because the multiple factors influencing processes such as denitrification can skew the data. Careful analysis of atypical sites are necessary to classify the soils according to trait similarity and in this way reach a better predictability of the denitrifiers dynamics.


Asunto(s)
Bacterias/enzimología , Desnitrificación/fisiología , Nitrito Reductasas/metabolismo , Microbiología del Suelo , Suelo/química , Agricultura , Genes Bacterianos/genética , Países Bajos , Nitrito Reductasas/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Análisis de Regresión , Análisis Espacio-Temporal
3.
Environ Microbiol ; 18(2): 644-55, 2016 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-26411284

RESUMEN

Nitrogen (N) is considered as a main limiting factor in plant growth, and nitrogen losses through denitrification can be responsible for severe decreases in plant productivity. Recently, it was demonstrated that Fallopia spp. is responsible for biological denitrification inhibition (BDI) through the release of unknown secondary metabolites. Here, we investigate the secondary metabolites involved in the BDI of Fallopia spp. The antioxidant, protein precipitation capability of Fallopia spp. extracts was measured in relation to the aerobic respiration and denitrification of two bacteria (Gram positive and Gram negative). Proanthocyanidin concentrations were estimated. Proanthocyanidins in extracts were characterized by chromatographic analysis, purified and tested on the bacterial denitrification and aerobic respiration of two bacterial strains. The effect of commercial procyanidins on denitrification was tested on two different soil types. Denitrification and aerobic respiration inhibition were correlated with protein precipitation capacity and concentration of proanthocyanidins but not to antioxidant capacity. These proanthocyanidins were B-type procyanidins that inhibited denitrification more than the aerobic respiration of bacteria. In addition, procyanidins also inhibited soil microbial denitrification. We demonstrate that procyanidins are involved in the BDI of Fallopia spp. Our results pave the way to a better understanding of plant-microbe interactions and highlight future applications for a more sustainable agriculture.


Asunto(s)
Biflavonoides/metabolismo , Catequina/metabolismo , Desnitrificación/fisiología , Fallopia/metabolismo , Nitrógeno/metabolismo , Proantocianidinas/metabolismo , Agricultura , Antioxidantes/fisiología , Biflavonoides/farmacología , Catequina/farmacología , Fallopia/genética , Proantocianidinas/farmacología , Suelo/química , Microbiología del Suelo
4.
Microbiology (Reading) ; 162(7): 1173-1184, 2016 07.
Artículo en Inglés | MEDLINE | ID: mdl-27082768

RESUMEN

Alnus glutinosa has been shown previously to synthesize, in response to nodulation by Frankia sp. ACN14a, an array of peptides called Alnus symbiotic up-regulated peptides (ASUPs). In a previous study one peptide (Ag5) was shown to bind to Frankia nitrogen-fixing vesicles and to modify their porosity. Here we analyse four other ASUPs, alongside Ag5, to determine whether they have different physiological effects on in vitro grown Frankia sp. ACN14a. The five studied peptides were shown to have different effects on nitrogen fixation, respiration, growth, the release of ions and amino acids, as well as on cell clumping and cell lysis. The mRNA abundance for all five peptides was quantified in symbiotic nodules and one (Ag11) was found to be more abundant in the meristem part of the nodule. These findings point to some peptides having complementary effects on Frankia cells.


Asunto(s)
Alnus/metabolismo , Adhesión Bacteriana/efectos de los fármacos , Defensinas/farmacología , Frankia/crecimiento & desarrollo , Consumo de Oxígeno/efectos de los fármacos , Proteínas de Plantas/farmacología , Simbiosis/efectos de los fármacos , Frankia/efectos de los fármacos , Frankia/metabolismo , Fijación del Nitrógeno/efectos de los fármacos , Nodulación de la Raíz de la Planta/fisiología , Raíces de Plantas/metabolismo , Raíces de Plantas/microbiología , Microbiología del Suelo
5.
Proc Biol Sci ; 283(1845)2016 12 28.
Artículo en Inglés | MEDLINE | ID: mdl-28003453

RESUMEN

Adaptation to local resource availability depends on responses in growth rate and nutrient acquisition. The growth rate hypothesis (GRH) suggests that growing fast should impair competitive abilities for phosphorus and nitrogen due to high demand for biosynthesis. However, in microorganisms, size influences both growth and uptake rates, which may mask trade-offs and instead generate a positive relationship between these traits (size hypothesis, SH). Here, we evolved a gradient of maximum growth rate (µmax) from a single bacterium ancestor to test the relationship among µmax, competitive ability for nutrients and cell size, while controlling for evolutionary history. We found a strong positive correlation between µmax and competitive ability for phosphorus, associated with a trade-off between µmax and cell size: strains selected for high µmax were smaller and better competitors for phosphorus. Our results strongly support the SH, while the trade-offs expected under GRH were not apparent. Beyond plasticity, unicellular populations can respond rapidly to selection pressure through joint evolution of their size and maximum growth rate. Our study stresses that physiological links between these traits tightly shape the evolution of competitive strategies.


Asunto(s)
Adaptación Fisiológica/genética , Evolución Biológica , Pseudomonas fluorescens/citología , Pseudomonas fluorescens/genética , Nitrógeno/fisiología , Fenotipo , Fósforo/fisiología
6.
Environ Sci Technol ; 50(1): 338-48, 2016 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-26651080

RESUMEN

Microbial communities have a key role for the performance of engineered ecosystems such as waste gas biofilters. Maintaining constant performance despite fluctuating environmental conditions is of prime interest, but it is highly challenging because the mechanisms that drive the response of microbial communities to disturbances still have to be disentangled. Here we demonstrate that the bioprocess performance and stability can be improved and reinforced in the face of disturbances, through a rationally predefined strategy of microbial resource management (MRM). This strategy was experimentally validated in replicated pilot-scale nitrifying gas-biofilters, for the two steps of nitrification. The associated biological mechanisms were unraveled through analysis of functions, abundances and community compositions for the major actors of nitrification in these biofilters, that is, ammonia-oxidizing bacteria (AOB) and Nitrobacter-like nitrite-oxidizers (NOB). Our MRM strategy, based on the application of successive, transient perturbations of increasing intensity, enabled to steer the nitrifier community in a favorable way through the selection of more resistant AOB and NOB sharing functional gene sequences close to those of, respectively, Nitrosomonas eutropha and Nitrobacter hamburgensis that are well adapted to high N load. The induced community shifts resulted in significant enhancement of nitrification resilience capacity following the intense perturbation.


Asunto(s)
Ecosistema , Consorcios Microbianos , Nitritos/metabolismo , Nitrobacter/metabolismo , Nitrosomonas/metabolismo , Amoníaco/metabolismo , Nitrificación
7.
Oecologia ; 181(3): 919-30, 2016 07.
Artículo en Inglés | MEDLINE | ID: mdl-27038993

RESUMEN

Plant diversity effects on ecosystem functioning can potentially interact with global climate by altering fluxes of the radiatively active trace gases nitrous oxide (N2O) and methane (CH4). We studied the effects of grassland species richness (1-16) in combination with application of fertilizer (nitrogen:phosphorus:potassium = 100:43.6:83 kg ha(-1) a(-1)) on N2O and CH4 fluxes in a long-term field experiment. Soil N2O emissions, measured over 2 years using static chambers, decreased with species richness unless fertilizer was added. N2O emissions increased with fertilization and the fraction of legumes in plant communities. Soil CH4 uptake, a process driven by methanotrophic bacteria, decreased with plant species numbers, irrespective of fertilization. Using structural equation models, we related trace gas fluxes to soil moisture, soil inorganic N concentrations, nitrifying and denitrifying enzyme activity, and the abundance of ammonia oxidizers, nitrite oxidizers, and denitrifiers (quantified by real-time PCR of gene fragments amplified from microbial DNA in soil). These analyses indicated that plant species richness increased soil moisture, which in turn increased N cycling-related activities. Enhanced N cycling increased N2O emission and soil CH4 uptake, with the latter possibly caused by removal of inhibitory ammonium by nitrification. The moisture-related indirect effects were surpassed by direct, moisture-independent effects opposite in direction. Microbial gene abundances responded positively to fertilizer but not to plant species richness. The response patterns we found were statistically robust and highlight the potential of plant biodiversity to interact with climatic change through mechanisms unrelated to carbon storage and associated carbon dioxide removal.


Asunto(s)
Óxido Nitroso , Suelo/química , Atmósfera , Metano , Plantas
8.
Ecology ; 96(4): 915-26, 2015 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-26230013

RESUMEN

The roles of species richness, resource use, and resource availability are central to many hypotheses explaining the diversity-invasion phenomenon but are generally not investigated together. Here, we created a large diversity gradient of soil microbial communities by either assembling communities of pure bacterial strains or removing the diversity of a natural soil. Using data on the resource-use capacities of the soil communities and an invader that were gathered from 71 carbon sources, we quantified the niches available to both constituents by using the metrics community niche and remaining niche available to the invader. A strong positive relationship between species richness and community niche across both experiments indicated the presence of resource complementarity. Moreover, community niche and the remaining niche available to the invader predicted invader abundance well. This suggested that increased competition in communities of higher diversity limits community invasibility and underscored the importance of resource availability as a key mechanism through which diversity hinders invasions. As a proof of principle, we subjected selected invaded communities to a resource pulse, which progressively uncoupled the link between soil microbial diversity and invasion and allowed the invader to rebound after nearly being eliminated in some communities. Our results thus show that (1) resource competition suppresses invasion, (2) biodiversity increases resource competition and decreases invasion through niche preemption, and (3) resource pulses that cannot be fully used, even by diverse communities, are favorable to invasion.


Asunto(s)
Bacterias/clasificación , Biodiversidad , Microbiología del Suelo , Bacterias/metabolismo , Galactosa/metabolismo
9.
Ecology ; 96(3): 788-99, 2015 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-26236874

RESUMEN

It has long been recognized that plant species and soil microorganisms. are tightly linked, but understanding how different species vary in their effects on soil is currently limited. In this study, we identified those. plant characteristics (identity, specific functional traits, or resource acquisition strategy) that were the best predictors of nitrification and denitrification processes. Ten plant populations representing eight species collected from three European grassland sites were chosen for their contrasting plant trait values and resource acquisition strategies. For each individual plant, leaf and root traits and the associated potential microbial activities (i.e., potential denitrification rate [DEA], maximal nitrification rate [NEA], and NH4+ affinity of the microbial community [NHScom]) were measured at two fertilization levels under controlled growth conditions. Plant traits were powerful predictors of plant-microbe interactions, but relevant plant traits differed in relation to the microbial function studied. Whereas denitrification was linked to the relative growth rate of plants, nitrification was strongly correlated to root trait characteristics (specific root length, root nitrogen concentration, and plant affinity for NH4+) linked to plant N cycling. The leaf economics spectrum (LES) that commonly serves as an indicator of resource acquisition strategies was not correlated to microbial activity. These results suggest that the LES alone is not a good predictor of microbial activity, whereas root traits appeared critical in understanding plant-microbe interactions.


Asunto(s)
Achillea/fisiología , Nitrógeno/metabolismo , Poaceae/fisiología , Microbiología del Suelo , Austria , Desnitrificación , Inglaterra , Francia , Nitrificación , Suelo/química
10.
Microb Ecol ; 70(3): 809-18, 2015 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-25877793

RESUMEN

Many studies have assessed the responses of soil microbial functional groups to increases in atmospheric CO2 or N deposition alone and more rarely in combination. However, the effects of elevated CO2 and N on the (de)coupling between different microbial functional groups (e.g., different groups of nitrifiers) have been barely studied, despite potential consequences for ecosystem functioning. Here, we investigated the short-term combined effects of elevated CO2 and N supply on the abundances of the four main microbial groups involved in soil nitrification: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (belonging to the genera Nitrobacter and Nitrospira) in grassland mesocosms. AOB and AOA abundances responded differently to the treatments: N addition increased AOB abundance, but did not alter AOA abundance. Nitrobacter and Nitrospira abundances also showed contrasted responses to the treatments: N addition increased Nitrobacter abundance, but decreased Nitrospira abundance. Our results support the idea of a niche differentiation between AOB and AOA, and between Nitrobacter and Nitrospira. AOB and Nitrobacter were both promoted at high N and C conditions (and low soil water content for Nitrobacter), while AOA and Nitrospira were favored at low N and C conditions (and high soil water content for Nitrospira). In addition, Nitrobacter abundance was positively correlated to AOB abundance and Nitrospira abundance to AOA abundance. Our results suggest that the couplings between ammonia and nitrite oxidizers are influenced by soil N availability. Multiple environmental changes may thus elicit rapid and contrasted responses between and among the soil ammonia and nitrite oxidizers due to their different ecological requirements.


Asunto(s)
Bacterias/metabolismo , Dióxido de Carbono/metabolismo , Nitrificación , Nitrógeno/metabolismo , Microbiología del Suelo , Amoníaco/metabolismo , Dactylis/crecimiento & desarrollo , Pradera , Nitritos/metabolismo , Oxidación-Reducción
11.
New Phytol ; 204(2): 408-23, 2014 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-24995955

RESUMEN

Plant-soil feedbacks can influence plant growth and community structure by modifying soil biota and nutrients. Because most research has been performed at the species level and in monoculture, our ability to predict responses across species and in mixed communities is limited. As plant traits have been linked to both soil properties and plant growth, they may provide a useful approach for an understanding of feedbacks at a generic level. We measured how monocultures and mixtures of grassland plant species with differing traits responded to soil that had been conditioned by model grassland plant communities dominated by either slow- or fast-growing species. Soils conditioned by the fast-growing community had higher nitrogen availability than those conditioned by the slow-growing community; these changes influenced future plant growth. Effects were stronger, and plant traits had greater predictive power, in mixtures than in monocultures. In monoculture, all species produced more above-ground biomass in soil conditioned by the fast-growing community. In mixtures, slow-growing species produced more above-ground biomass, and fast-growing species produced more below-ground biomass, in soils conditioned by species with similar traits. The use of a plant trait-based approach may therefore improve our understanding of differential plant species responses to plant-soil feedbacks, especially in a mixed-species environment.


Asunto(s)
Retroalimentación Fisiológica , Desarrollo de la Planta , Microbiología del Suelo , Suelo/química , Biomasa , Ecosistema , Nitrógeno/metabolismo , Fenotipo , Brotes de la Planta , Especificidad de la Especie
12.
New Phytol ; 204(3): 620-630, 2014 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-25059468

RESUMEN

Previous studies on the effect of secondary metabolites on the functioning of rhizosphere microbial communities have often focused on aspects of the nitrogen (N) cycle but have overlooked biological denitrification inhibition (BDI), which can affect plant N-nutrition. Here, we investigated the BDI by the compounds of Fallopia spp., an invasive weed shown to be associated with a low potential denitrification of the soil. Fallopia spp. extracts were characterized by chromatographic analysis and were used to test the BDI effects on the metabolic and respiratory activities of denitrifying bacteria, under aerobic and anaerobic (denitrification) conditions. The BDI of Fallopia spp. extracts was tested on a complex soil community by measuring denitrification enzyme activity (DEA), substrate induced respiration (SIR), as well as abundances of denitrifiers and total bacteria. In 15 strains of denitrifying bacteria, extracts led to a greater BDI (92%) than respiration inhibition (50%). Anaerobic metabolic activity reduction was correlated with catechin concentrations and the BDI was dose dependent. In soil, extracts reduced the DEA/SIR ratio without affecting the denitrifiers: total bacteria ratio. We show that secondary metabolite(s) from Fallopia spp. inhibit denitrification. This provides new insight into plant-soil interactions and improves our understanding of a plant's ability to shape microbial soil functioning.


Asunto(s)
Desnitrificación/fisiología , Extractos Vegetales/química , Polygonaceae/metabolismo , Pseudomonas/efectos de los fármacos , Aerobiosis , Anaerobiosis , Bioensayo , Especies Introducidas , Cinética , Estructura Molecular , Consumo de Oxígeno , Malezas , Pseudomonas/clasificación , Pseudomonas/genética , Suelo/química
13.
Oecologia ; 173(1): 223-37, 2013 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-23386044

RESUMEN

In order to predict which ecosystem functions are most at risk from biodiversity loss, meta-analyses have generalised results from biodiversity experiments over different sites and ecosystem types. In contrast, comparing the strength of biodiversity effects across a large number of ecosystem processes measured in a single experiment permits more direct comparisons. Here, we present an analysis of 418 separate measures of 38 ecosystem processes. Overall, 45 % of processes were significantly affected by plant species richness, suggesting that, while diversity affects a large number of processes not all respond to biodiversity. We therefore compared the strength of plant diversity effects between different categories of ecosystem processes, grouping processes according to the year of measurement, their biogeochemical cycle, trophic level and compartment (above- or belowground) and according to whether they were measures of biodiversity or other ecosystem processes, biotic or abiotic and static or dynamic. Overall, and for several individual processes, we found that biodiversity effects became stronger over time. Measures of the carbon cycle were also affected more strongly by plant species richness than were the measures associated with the nitrogen cycle. Further, we found greater plant species richness effects on measures of biodiversity than on other processes. The differential effects of plant diversity on the various types of ecosystem processes indicate that future research and political effort should shift from a general debate about whether biodiversity loss impairs ecosystem functions to focussing on the specific functions of interest and ways to preserve them individually or in combination.


Asunto(s)
Biodiversidad , Plantas/clasificación , Ciclo del Carbono , Ecosistema , Cadena Alimentaria , Modelos Lineales , Modelos Teóricos , Ciclo del Nitrógeno , Fenómenos Fisiológicos de las Plantas
14.
Microb Ecol ; 62(1): 69-79, 2011 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-21584756

RESUMEN

Bacteria inhabiting crystalline rocks from two terrestrial Icelandic volcanic lava flows of similar age and from the same geographical region, but differing in porosity and mineralogy, were characterised. Microarray (PhyloChip) and clone library analysis of 16S rRNA genes revealed the presence of a diverse assemblage of bacteria in each lava flow. Both methods suggested a more diverse community at the Dómadalshraun site (rhyolitic/andesitic lava flow) than that present at the Hnausahraun site (basaltic lava flow). Proteobacteria dominated the clone library at the Dómadalshraun site, while Acidobacteria was the most abundant phylum in the Hnausahraun site. Although analysis of similarities of denaturing gradient gel electrophoresis profiles suggested a strong correlation of community structure with mineralogy, rock porosity may also play an important role in shaping the bacterial community in crystalline volcanic rocks. Clone sequences were most similar to uncultured microorganisms, mainly from soil environments. Of these, Antarctic soils and temperate rhizosphere soils were prominent, as were clones retrieved from Hawaiian and Andean volcanic soils. The novel diversity of these Icelandic microbial communities was supported by the finding that up to 46% of clones displayed <85% sequence identities to sequences currently deposited in the RDP database.


Asunto(s)
Bacterias/aislamiento & purificación , Biodiversidad , Sedimentos Geológicos/microbiología , Erupciones Volcánicas/análisis , Bacterias/clasificación , Bacterias/genética , Sedimentos Geológicos/química , Islandia , Datos de Secuencia Molecular , Filogenia
15.
Appl Microbiol Biotechnol ; 85(3): 779-790, 2010 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-19826809

RESUMEN

In this study, we explored methodological aspects of nucleic acid recovery from microbial communities involved in a gas biofilter filled with pine bark woodchips. DNA was recovered indirectly in two steps, comparing different methods: cell dispersion (crushing, shaking, and sonication) and DNA extraction (three commercial kits and a laboratory protocol). The objectives were (a) to optimize cell desorption from the packing material and (b) to compare the 12 combinations of desorption and extraction methods, according to three relevant criteria: DNA yield, DNA purity, and community structure representation by denaturing gradient gel electrophoresis (DGGE). Cell dispersion was not influenced by the operational parameters tested for shaking and blending, while it increased with time for sonication. DNA extraction by the laboratory protocol provided the highest DNA yields, whereas the best DNA purity was obtained by a commercial kit designed for DNA extraction from soil. After successful PCR amplification, the 12 methods did not generate the same bias in microbial community representation. Eight combinations led to high diversity estimation, independently of the experimental procedure. Among them, six provided highly similar DGGE profiles. Two protocols generated a significantly dissimilar community profile, with less diversity. This study highlighted the crucial importance of DNA recovery bias evaluation.


Asunto(s)
Dermatoglifia del ADN/métodos , ADN/genética , ADN/aislamiento & purificación , Metagenómica/métodos , Madera/microbiología , Biodiversidad , Análisis por Conglomerados , Electroforesis en Gel de Poliacrilamida , Filtración/métodos , Desnaturalización de Ácido Nucleico , Reacción en Cadena de la Polimerasa
16.
Ecology ; 90(12): 3324-32, 2009 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-20120802

RESUMEN

Predicting biodiversity effects on ecosystem functioning requires adequate evaluation of the mechanisms explaining why more diverse systems could perform better than less diverse ones. In this context, tackling functional diversity has become an important issue. Even though the aggregation of species into functional groups supposes niche differences among groups, the concept of niche has not been fully exploited in the context of the biodiversity-ecosystem functioning research. Here we report the results of microcosm experiments where we used bacteria as a model to explore whether niche differences among species provide a good estimation of community functioning. For that we used experimental communities of denitrifying bacterial species and investigated the effects of bacterial diversity on two community processes, denitrification and anaerobic CO2-production. We first measured the activities of 16 bacterial species grown individually on six different carbon sources. We then used the same set of species to assemble communities varying in both species richness and composition in microcosms containing a mixture of all six carbon sources. The performances of individual species on individual carbon sources were used to calculate, for each process measured, an a priori index called "community niche" that accounted for the performances of the species present in a given community across the entire range of the six resources. We found that species richness had a positive but small effect on both community processes whereas community niche explained a much larger proportion of the variation. According to the results of a path analysis, community niche was the main driver for the corresponding community process, but species richness affected community niche and thus had an indirect effect on denitrification and CO2 production. In addition to community niche, the presence of particular bacterial species also influenced community functioning, indicating that other effects than the capacity to use carbon sources played a, albeit minor, role in our experiment. Our study provides evidence for the importance of resource niches in shaping biodiversity-ecosystem functioning relationships of bacterial communities.


Asunto(s)
Bacterias/crecimiento & desarrollo , Bacterias/metabolismo , Biodiversidad , Dióxido de Carbono/metabolismo , Ecosistema , Nitrógeno/metabolismo , Dióxido de Carbono/análisis , Modelos Biológicos , Nitrógeno/análisis , Filogenia , Densidad de Población , Dinámica Poblacional , Crecimiento Demográfico , Especificidad de la Especie
17.
Biotechnol Bioeng ; 102(3): 714-24, 2009 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-18846553

RESUMEN

Addition of hydroxylamine (NH2OH) to autotrophic biomass in nitrifying bioreactors affected the activity, physical structure, and microbial ecology of nitrifying aggregates. When NH2OH is added to nitrifying cultures in 6-h batch experiments, the initial NH3-N uptake rates were physiologically accelerated by a factor of 1.4-13. NH2OH addition caused a 20-40% decrease in the median aggregate size, broadened the shape of the aggregate size distribution by up to 230%, and caused some of the microcolonies to appear slightly more dispersed. Longer term NH2OH addition in fed batch bioreactors decreased the median aggregate size, broadened the aggregate size distribution, and decreased NH3-N removal from >90% to values ranging between 75% and 17%. This altered performance is explained by quantitative fluorescence in situ hybridization (FISH) results that show inhibition of nitrifying populations, and by qPCR results showing that the copy numbers of amoA and nxrA genes gradually decreased by up to an order-of-magnitude. Longer term NH2OH addition damaged the active biomass. This research clarifies the effect of NH2OH on nitrification and demonstrates the need to incorporate NH2OH-related dynamics of the nitrifying biomass into mathematical models, accounting for both ecophysiological and structural responses.


Asunto(s)
Procesos Autotróficos/efectos de los fármacos , Bacterias/metabolismo , Reactores Biológicos , Hidroxilamina/farmacología , Amoníaco/metabolismo , Bacterias/enzimología , Bacterias/genética , Biomasa , Técnicas de Cultivo de Célula , Regulación Bacteriana de la Expresión Génica/efectos de los fármacos , Hidroxilamina/metabolismo , Hibridación Fluorescente in Situ , Nitrito Reductasas/genética , Nitrito Reductasas/metabolismo , Nitrosomonas/enzimología , Nitrosomonas/genética , Nitrosomonas/metabolismo , Oxidorreductasas/genética , Oxidorreductasas/metabolismo , Reacción en Cadena de la Polimerasa
18.
FEMS Microbiol Ecol ; 63(2): 261-71, 2008 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-18199085

RESUMEN

A new PCR-denaturing gel gradient electrophoresis (DGGE) tool based on the functional gene nxrA encoding the catalytic subunit of the nitrite oxidoreductase in nitrite-oxidizing bacteria (NOB) has been developed. The first aim was to determine if the primers could target representatives of NOB genera: Nitrococcus and Nitrospira. The primers successfully amplified nxrA gene sequences from Nitrococcus mobilis, but not from Nitrospira marina. The second aim was to develop a PCR-DGGE tool to characterize NOB community structure on the basis of Nitrobacter-like partial nrxA gene sequences (Nb-nxrA). We tested (1) the ability of this tool to discriminate between Nitrobacter strains, and (2) its ability to reveal changes in the community structure of NOB harbouring Nb-nrxA sequences induced by light grazing or intensive grazing in grassland soils. The DGGE profiles clearly differed between the four Nitrobacter strains tested. Differences in the structure of NOB community were revealed between grazing regimes. Phylogenetic analysis of the sequences corresponding to different DGGE bands showed that Nb-nxrA sequences did not group in management-specific clusters. Most of the nxrA sequences obtained from soils differed from nxrA sequences of NOB strains. Along with existing tools for characterizing the community structure of nitrifiers, this new approach is a significant step forward to performing comprehensive studies on nitrification.


Asunto(s)
Electroforesis en Gel de Poliacrilamida , Genes Bacterianos/genética , Nitrito Reductasas/genética , Reacción en Cadena de la Polimerasa , Microbiología del Suelo , Bacterias/genética , Secuencia de Bases , Biodiversidad , ADN Bacteriano/genética , Datos de Secuencia Molecular , Filogenia , Análisis de Secuencia de ADN
19.
FEMS Microbiol Ecol ; 63(1): 132-40, 2008 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-18031541

RESUMEN

Nitrite oxidoreductase (NXR) is the key enzyme responsible for the oxidation of NO(2)(-) to NO(3)(-) in nitrite-oxidizing bacteria. For the first time a molecular approach for targeting the nxrA gene was developed, encoding the catalytic subunit of the NXR, to study diversity of Nitrobacter-like organisms based on the phylogeny of nxrA gene sequences in soils. NxrA sequences of the Nitrobacter strains analysed (Nitrobacter hamburgensis, Nitrobacter vulgaris, Nitrobacter winogradskyi, Nitrobacter alkalicus) by PCR, cloning and sequencing revealed the occurrence of multiple copies of nxrA genes in these strains. The copy number and similarity varied among strains. The diversity of Nitrobacter-like nxrA sequences was explored in three soils (a French permanent pasture soil, a French fallow soil, and an African savannah soil) using a cloning and sequencing approach. Most nxrA sequences found in these soils (84%) differed from nxrA sequences obtained from Nitrobacter strains. Moreover, the phylogenetic distribution and richness of nxrA-like sequences was extremely variable depending on soil type. This nxrA tool extends the panel of functional genes available for studying bacteria involved in the nitrogen cycle.


Asunto(s)
Clonación Molecular , Nitritos/metabolismo , Nitrobacter/clasificación , Oxidorreductasas , Reacción en Cadena de la Polimerasa/métodos , Análisis de Secuencia de ADN , Microbiología del Suelo , África , Francia , Variación Genética , Datos de Secuencia Molecular , Nitrobacter/enzimología , Nitrobacter/genética , Oxidación-Reducción , Oxidorreductasas/genética , Oxidorreductasas/metabolismo , Filogenia , Suelo/análisis
20.
J Hazard Mater ; 331: 226-234, 2017 Jun 05.
Artículo en Inglés | MEDLINE | ID: mdl-28273572

RESUMEN

The persistent organochlorine pesticides (OCPs) in soils are suspected to disturb soil biogeochemical cycles. This study addressed the dynamic changes in soil functionality under lindane and chlordecone exposures with or without maize plant. Decreases in soil ammonium concentration, potential nitrogen mineralization and microbial biomass were only OCP-influenced in bulk soils. OCPs appeared to inhibit the ammonification step. With plants, soil functionality under OCP stress was similar to controls demonstrating the plant influence to ensure the efficiency of C- and N-turnover in soils. Moreover, OCPs did not impact the microbial community physiological profile in all tested conditions. However, microbial community structure was OCP-modified only in the presence of plants. Abundances of gram-negative and saprophytic fungi increased (up to +93% and +55%, respectively) suggesting a plant stimulation of nutrient turnover and rhizodegradation processes. Nevertheless, intimate microbial/plant interactions appeared to be OCP-impacted with depletions in mycorrhizae and micro/meso-fauna abundances (up to -53% and -56%, respectively) which might have adverse effects on more long-term plant growth (3-4 months). In short-term experiment (28days), maize growth was similar to the control ones, indicating an enhanced plasticity of the soil functioning in the presence of plants, which could efficiently participate to the remediation of OCP-contaminated soils.


Asunto(s)
Clordecona/toxicidad , Hexaclorociclohexano/toxicidad , Raíces de Plantas/efectos de los fármacos , Microbiología del Suelo , Contaminantes del Suelo/toxicidad , Biomasa , Carbono/análisis , Nitrógeno/análisis , Suelo/química , Zea mays
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