Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils.

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.

IncP-1 and PromA group plasmids are major providers of horizontal gene transfer capacities across bacteria in the mycosphere of different soil fungi.

Plasmids of the IncP-1ß group have been found to be important carriers of accessory genes that enhance the ecological fitness of bacteria, whereas plasmids of the PromA group are key agents of horizontal gene transfer in particular soil settings. However, there is still a paucity of knowledge with respect to the diversity, abundance, and involvement in horizontal gene transfer of plasmids of both groups in the mycosphere. Using triparental exogenous isolation based on the IncQ tracer plasmid pSUP104 as well as direct molecular detection, we analyzed the pool of mobilizer and self-transferable plasmids in mycosphere soil. Replicate mushroom types that were related to Russula, Inocybe, Ampulloclitocybe, and Galerina spp. were sampled from a forest soil area, and bulk soil was used as the control. The data showed that the levels of IncP-1ß plasmids are significantly raised across several of the mycospheres analyzed, whereas those of PromA group plasmids were similar across the mycospheres and corresponding bulk soil. Moreover, the frequencies of triparental exogenous isolation of mobilizer plasmids into a Pseudomonas fluorescens recipient strain were significantly elevated in communities from several mycospheres as compared with those from bulk soil. Molecular analysis of selected transconjugants, as well as from directly isolated strains, revealed the presence of plasmids of three size groups, i.e., (1) 40-45, (2) 50-60, and (3) ≥60 kb, across all isolations. Replicon typing using IncN, IncW and IncA/C proxies revealed no positive signals. In contrast, a suite of plasmids produced signals with IncP-1ß as well as PromA type replicon typing systems. Moreover, a selected subset of plasmids, obtained from the Inocybe and Galerina isolates, was transferred out further, revealing their capacities to transfer and mobilize across a broad host range.

IncP-1ß Plasmids Are Important Carriers of Fitness Traits for Variovorax Species in the Mycosphere--Two Novel Plasmids, pHB44 and pBS64, with Differential Effects Unveiled.

The Laccaria proxima mycosphere strongly selects Variovorax paradoxus cells. Fifteen independent V. paradoxus strains, isolated from mycospheres sampled at two occasions, were investigated with respect to the occurrence of plasmids of sizes <60-100 kb. Two V. paradoxus strains, HB44 and BS64, were found to contain such plasmids, which were coined pHB44 and pBS64. Replicon typing using a suite of plasmid-specific PCR systems indicated that both plasmids belong to the IncP-1ß group. Also, both were able to mobilize selectable IncQ group plasmids into Escherichia coli as well as Pseudomonas fluorescens. Moreover, they showed stable replication in these organisms, confirming their broad host range. Strain BS64 was cured of pBS64 and plasmid pHB44 was subsequently moved into this cured strain by making use of the IncQ group tracer plasmid pSUP104, which was then removed at elevated temperature. Thus, both plasmids could be screened for their ability to confer a phenotype upon strain BS64. No evidence for the presence of genes for xenobiotic degradation and/or antibiotic or heavy metal resistances was found for either of the two plasmids. Remarkably, both could stimulate the production of biofilm material by strain BS64. Also, the population densities of pBS64-containing strain BS64 were temporarily raised in liquid as well as soil systems (versus the plasmid-cured strain), both in the presence of the fungal host Lyophyllum sp. strain Karsten. Strikingly, plasmid pHB44 significantly enhanced the fitness of strain BS64 in soil containing Lyophyllum sp. strain Karsten, but decreased its fitness in soil supplemented with extra FeCl3. The effect was noted both in separate (no inter-strain competition) and joint (competition) inoculations.

Temporal dynamics of abundance and composition of nitrogen-fixing communities across agricultural soils.

BACKGROUND: Despite the fact that the fixation of nitrogen is one of the most significant nutrient processes in the terrestrial ecosystem, a thorough study of the spatial and temporal patterns in the abundance and distribution of N-fixing communities has been missing so far. METHODOLOGY/PRINCIPAL FINDINGS: In order to understand the dynamics of diazotrophic communities and their resilience to external changes, we quantified the abundance and characterized the bacterial community structures based on the nifH gene, using real-time PCR, PCR-DGGE and 454-pyrosequencing, across four representative Dutch soils during one growing season. In general, higher nifH gene copy numbers were observed in soils with higher pH than in those with lower pH, but lower numbers were related to increased nitrate and ammonium levels. Results from nifH gene pyrosequencing confirmed the observed PCR-DGGE patterns, which indicated that the N fixers are highly dynamic across time, shifting around 60%. Forward selection on CCA analysis identified N availability as the main driver of these variations, as well as of the evenness of the communities, leading to very unequal communities. Moreover, deep sequencing of the nifH gene revealed that sandy soils (B and D) had the lowest percentage of shared OTUs across time, compared with clayey soils (G and K), indicating the presence of a community under constant change. Cosmopolitan nifH species (present throughout the season) were affiliated with Bradyrhizobium, Azospirillum and Methylocistis, whereas other species increased their abundances progressively over time, when appropriate conditions were met, as was notably the case for Paenibacilus and Burkholderia. CONCLUSIONS: Our study provides the first in-depth pyrosequencing analysis of the N-fixing community at both spatial and temporal scales, providing insights into the cosmopolitan and specific portions of the nitrogen fixing bacterial communities in soil.

Fluctuations in Ammonia Oxidizing Communities Across Agricultural Soils are Driven by Soil Structure and pH.

The milieu in soil in which microorganisms dwell is never constant. Conditions such as temperature, water availability, pH and nutrients frequently change, impacting the overall functioning of the soil system. To understand the effects of such factors on soil functioning, proxies (indicators) of soil function are needed that, in a sensitive manner, reveal normal amplitude of variation. Thus, the so-called normal operating range (NOR) of soil can be defined. In this study we determined different components of nitrification by analyzing, in eight agricultural soils, how the community structures and sizes of ammonia oxidizing bacteria and archaea (AOB and AOA, respectively), and their activity, fluctuate over spatial and temporal scales. The results indicated that soil pH and soil type are the main factors that influence the size and structure of the AOA and AOB, as well as their function. The nitrification rates varied between 0.11 ± 0.03 µgN h(-1) gdw(-1) and 1.68 ± 0.11 µgN h(-1) gdw(-1), being higher in soils with higher clay content (1.09 ± 0.12 µgN h(-1) gdw(-1)) and lower in soils with lower clay percentages (0.27 ± 0.04 µgN h(-1) gdw(-1)). Nitrifying activity was driven by soil pH, mostly related to its effect on AOA but not on AOB abundance. Regarding the influence of soil parameters, clay content was the main soil factor shaping the structure of both the AOA and AOB communities. Overall, the potential nitrifying activities were higher and more variable over time in the clayey than in the sandy soils. Whereas the structure of AOB fluctuated more (62.7 ± 2.10%) the structure of AOA communities showed lower amplitude of variation (53.65 ± 3.37%). Similar trends were observed for the sizes of these communities. The present work represents a first step toward defining a NOR for soil nitrification. The sensitivity of the process and organisms to impacts from the milieu support their use as proxies in the NOR of agricultural soils. Moreover, the clear effect of soil texture established here suggests that the NOR should be defined in a soil type-specific manner.

Spatial and temporal variation of archaeal, bacterial and fungal communities in agricultural soils.

BACKGROUND: Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal ß-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal ß-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers. CONCLUSIONS: Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.

Seasonal variations in the diversity and abundance of diazotrophic communities across soils.

The nitrogen (N)-fixing community is a key functional community in soil, as it replenishes the pool of biologically available N that is lost to the atmosphere via anaerobic ammonium oxidation and denitrification. We characterized the structure and dynamic changes in diazotrophic communities, based on the nifH gene, across eight different representative Dutch soils during one complete growing season, to evaluate the amplitude of the natural variation in abundance and diversity, and identify possible relationships with abiotic factors. Overall, our results indicate that soil type is the main factor influencing the N-fixing communities, which were more abundant and diverse in the clay soils (n=4) than in the sandy soils (n=4). On average, the amplitude of variation in community size as well as the range-weighted richness were also found to be higher in the clay soils. These results indicate that N-fixing communities associated with sandy and clay soil show a distinct amplitude of variation under field conditions, and suggest that the diazotrophic communities associated with clay soil might be more sensitive to fluctuations associated with the season and agricultural practices. Moreover, soil characteristics such as ammonium content, pH and texture most strongly correlated with the variations observed in the diversity, size and structure of N-fixing communities, whose relative importance was determined across a temporal and spatial scale.

Exposição alergênica em cinemas na cidade de Goiânia, GO / Allergen exposure in cinemas of Goiânia, Brazil

Objetivo: Avaliar a presença e nível dos alérgenos de Dermatophagoides pteronyssinus (Der p 1), Dermatophagoides farinae (Der f 1), Canis familiares (Can f 1), Felis domesticus (Fel d 1) e Blattella germanica (Bla g 2) em cinemas na cidade de Goiânia, GO, Brasil. Métodos: Foram coletadas amostras de poeira do chão e dos assentos da frente, do meio e do fundo de salas de cinemas, num total de 30 amostras após consentimento informado dos proprietários. A detecção dos alérgenos foi realizada pelo método ELISA.Resultados: As concentrações médias de alérgenos encontradas nos cinemas em 1g/g foram 0,35, 6,87, 0,65 e 0,07, respectivamente para Der p 1, Der f 1, Can f 1 e Fel d 1. Em nenhuma amostra foi possível a detecção de alérgenos de barata. Níveis sensibilizantes de alergénos foram observados em 76,6 per cent das amostras de Der f 1, mas também ocorreram para Der p 1 (3,33 per cent) e Can f 1 (10,0 per cent). Em 20 per cent das amostras, osníveis de Der f 1 encontrado foram superiores os considerados de risco para exacerbações das doenças alérgicas. Conclusões: As salas de cinema são ambientes fechados nas quais indivíduos susceptíveis podem entrar em contato com alérgenos e desencadearem exacerbações. Medidas para a redução dos níveis de alérgenos em locais públicos devem ser adotadas como estratégia global de controle ambiental para a melhoria da qualidade de vida em indivíduos atópicos.