38 research outputs found
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Assessment of the bimodality in the distribution of bacterial genome sizes
Bacterial genome sizes have previously been shown to exhibit a bimodal distribution. This phenomenon has prompted discussion regarding evolutionary forces driving genome size in bacteria and its ecological significance. We investigated the level of inherent redundancy in the public database and the effect it has on the shape of the apparent bimodal distribution. Our study reveals that there is a significant bias in the genome sequencing efforts towards a certain group of species, and that correcting the bias using species nomenclature and clustering of the 16S rRNA gene, results in a unimodal rather than the previously published bimodal distribution. The true genome size distribution and its wider ecological implications will soon emerge as we are currently witnessing rapid growth in the number of sequenced genomes from diverse environmental niches across a range of habitats at an unprecedented rate
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Sequence and organization of the complete mitochondrial genome of the blackfly Simulium variegatum (Diptera: Simuliidae)
The complete mitochondrial genome of the European blackfly, Simulium variegatum Meigen, 1818 was sequenced using a combined Illumina and Sanger sequencing approach. Using the known sequence of Chironomus tepperi Skuse, 1889 (Chironomidae) homologous NGS reads were identified and assembled. The genome is 15,367 bp in length and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. Gene order resembles that of the ancestral dipteran gene arrangement. The base composition of the genome is A (37.6%), T (35.3%), C (15.8%) and G (11.3%). The control region between 12S rRNA and tRNAIle is composed of 362 bp with no obvious repetitive motifs
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PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform
1. Studying fungal biodiversit y using data generated from Illumina MiSeq sequencing platforms poses a number of bioinformatic challenges with the analysis typically involving a large number of tools for each analytical step from quality ïŹltering to generating identiïŹed operational taxonomic unit (OTU) abundance tables. 2. Here, we introduce PIPITS, an o pen-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS e xploits a number of state of the art applications to process paired-end reads from quality ïŹltering to producing OTU abundance tables. 3. We pro vide detailed descriptions of the pipeline and show its utility in the analysis of 9 396 092 sequences generated on the MiSeq platform from Illumina MiSeq. 4. PIPITS is the ïŹrst automated bioinformatics pipeline dedicated for fungal ITS sequences which incorporates ITSx to extract subregions of ITS and exploits the latest RDP ClassiïŹer to classify sequences against the curatedUNITE fungal data set
Catchment-scale biogeography of riverine bacterioplankton
Lotic ecosystems such as rivers and streams are unique in that they represent a continuum of both space and time during the transition from headwaters to the river mouth. As microbes have very different controls over their ecology, distribution and dispersion compared with macrobiota, we wished to explore biogeographical patterns within a river catchment and uncover the major drivers structuring bacterioplankton communities. Water samples collected across the River Thames Basin, UK, covering the transition from headwater tributaries to the lower reaches of the main river channel were characterised using 16S rRNA gene pyrosequencing. This approach revealed an ecological succession in the bacterial community composition along the river continuum, moving from a community dominated by Bacteroidetes in the headwaters to Actinobacteria-dominated downstream. Location of the sampling point in the river network (measured as the cumulative water channel distance upstream) was found to be the most predictive spatial feature; inferring that ecological processes pertaining to temporal community succession are of prime importance in driving the assemblages of riverine bacterioplankton communities. A decrease in bacterial activity rates and an increase in the abundance of low nucleic acid bacteria relative to high nucleic acid bacteria were found to correspond with these downstream changes in community structure, suggesting corresponding functional changes. Our findings show that bacterial communities across the Thames basin exhibit an ecological succession along the river continuum, and that this is primarily driven by water residence time rather than the physiochemical status of the river
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Mapping and validating predictions of soil bacterial biodiversity using European and national scale datasets
Recent research has highlighted strong correlations between soil edaphic parameters and bacterial biodiversity. Here we seek to explore these relationships across the European Union member states with respect to mapping bacterial biodiversity at the continental scale. As part of the EU FP7 EcoFINDERs project, bacterial communities from 76 soil samples taken across Europe were assessed from eleven countries encompassing Arctic to Southern Mediterranean climes, representing a diverse range of soil types and land uses (grassland, forest and arable land). We found predictable relationships between community biodiversity (ordination site scores) and land use factors as well as soil properties such as pH. Based on the modelled relationship between soil pH and bacterial biodiversity found for the surveyed soils, we were able to predict biodiversity in âŒ1000 soils for which soil pH data had been collected as part of national scale monitoring. We then performed interpolative mapping utilising existing EU wide soil pH data to present the first map of bacterial biodiversity across the EU member states. The predictive accuracy of the map was assessed again using the national scale data, but this time contrasting the EU wide spatial predictions with point data on bacterial communities. Generally the maps were useful at predicting broad extremes of biodiversity reflective of low or high pH soils, though predictive accuracy was limited for Britain particularly for organic/acidic soil communities. Spatial accuracy could however be increased by utilising published maps of soil pH calculated using geostatistical approaches at both global and national scales. These findings will contribute to wider efforts to predict and understand the spatial distribution of soil biodiversity at global scales. Further work should focus on enhancing the predictive power of such maps, by harmonising global datasets on soil conditioning parameters, soil properties and biodiversity; and the continued efforts to advance the geostatistical modelling of specific components of soil biodiversity at local to global scales
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Gut and faecal bacterial community of the terrestrial isopod porcellionides pruinosus: potential use for monitoring exposure scenarios
This work aimed to characterize the gut and faeces bacterial communities (BC) of Porcellionides pruinosus using high-throughput
sequencing. Isopods were collected from the field and kept in laboratory conditions similar to those normally applied in
ecotoxicology tests. Faeces and purged guts of isopods (n=3 Ă 30) were analysed by pyrosequencing the V3-V4 region of 16 S
rRNA encoding gene. Results showed that gut and faecal BCs were dominated by Proteobacteria, particularly by an OTU
(Operational Taxonomic Unit) affiliated to genus Coxiella. Diversity and richness values were statistically higher for faecal BC,
mainly due to the occurrence of several low-abundance phylotypes. These results may reflect faecal carriage of bacterial groups that
cannot settle in the gut. BCs of P. pruinosus comprised: (1) common members of the soil microbiota, (2) bacterial symbionts, (3)
bacteria related to host metabolic/ecological features, and (4) bacterial etiological agents. Comparison of BC of this isopod species
with the BC from other invertebrates revealed common bacterial groups across taxa. The baseline information provided by this
work will assist the design and data interpretation of future ecotoxicological or biomonitoring assays where the analysis of P.
pruinosus BC should be included as an additional indicator.publishe
Mycobial community assemblages in sink drains across a university campus
Multiple fungal species, including potential opportunistic pathogens have been previously identified in water systems. Here, we investigated over 250 restroom sink fungal communities across a university campus and evaluated their diversity and core taxa present. Remarkable similarity in mycobial community composition was observed across buildings with Ascomycota consistently dominating. We found a core mycobiome independent of the building sampled, that included Exophiala species, potential opportunistic pathogenic black yeasts. Other prevalent and dominant taxa included Saccharomyces and Fusarium, common built environment fungi. The frequent presence of Malassezia, a common skin commensal, showed the external influence of human activities as a source of fungi to sinks. The study represents a novel exploration of sink P-traps mycobial communities from a public area and highlights their importance as reservoirs of possible pathogenic fungi, as well as emphasizing the relevance of further research in this understudied ecosystem within the built environment
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The interactions and hierarchical effects of long-term agricultural stressors on soil bacterial communities
Soils are subjected to multiple anthropogenic modifications, but the synergistic impacts of simultaneous environmental stressors on below-ground communities are poorly understood. We used a large-scale (1152 plots), long-term (26âyears), multi-factorial grassland experiment to assess the impact of five common agricultural practises (pesticides, herbicide, liming, fertilizers and grazing exclusion) and their interactive effects on the composition and activity of soil microbial communities. We confirmed that pH strongly impacts belowground communities, but further demonstrate that pH strongly mediates the impacts of other management factors. Notably, there was a significant interaction between liming and the effect of pesticide application, with only half of the taxa responding to pesticide being shared in both limed and unlimed treatments. Likewise, nutrient amendments significantly altered bacterial community structure in acidic soils. Not only do these results highlight an hierarchy of effect of commonly used agricultural practices but also the widespread interactions between treatments: many taxa were significantly affected by interactions between treatments, even in the absence of significant main effects. Furthermore, the results demonstrated that chemical amendments may not percolate deeply into physically unperturbed soils with effects concentrated between 0 and 30âcm, despite 20+ years of treatment. The research shows that future changes to agricultural practices will need to consider interactions among multiple factors
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Rhizosphere bacteria are more strongly related to plant root traits than fungi in temperate montane forests: insights from closed and open forest patches along an elevational gradient
Heterogeneous canopies in temperate montane forests affect microclimate and soil characteristics, with important effects on soil microbial communities and related processes. Here, we studied the interactions between plant root traits and soil bacterial and fungal communities in closed forest and gaps in a mixed forest along an elevational gradient in the French Alps (1400, 1700 and 2000 m).
Samples were separated into three fractions (plant root endosphere, rhizosphere and bulk soil), to further investigate the influence of plant zones on microbial communities. Bacterial (16S) and fungal (ITS) biodiversity was determined using high throughput sequencing, along with standard measures of soil, litter and root traits.
We found that (i) microbial community diversity was higher in gaps than in closed forest because of increased root trait diversity and density; (ii) open versus closed forest patches affected phylogenetic dispersion despite differences in elevations with phylogenetic clustering in closed forest; (iii) the interaction between root traits and microbial communities was stronger for rhizosphere and endosphere compartments than for bulk soil and (iv) bacterial community composition was better explained by root traits than for fungi.
Our findings highlight the importance of open gaps versus closed forest patches and associated root traits affecting microbial community structure, particularly for bacterial assemblages that exhibited a stronger interaction with root traits than for fungi
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Interacting effects of land use type, soil microbes and plant traits on aggregate stability
Soil aggregates are critical to soil functionality, but there remain many uncertainties with respect to the role of biotic factors in forming aggregates. Understanding the interacting effects of soil, land use type, vegetation and microbial communities is a major challenge that needs assessment in both field and controlled laboratory conditions, as well as in bulk and rhizosphere soils. To address these effects and their feedbacks, we first examined the influence of soil, root and litter characteristics along a land use gradient (ancient woodland, secondary woodland, grassland, pasture and arable land) on microbial community structure (in both bulk and rhizosphere soil), as well as on aggregate stability. Then, we performed an inoculation experiment where we extracted soil columns from the arable and secondary woodland and used a third unstructured loamy soil as a control. We sterilized these three soils to remove microbial communities, and then either inoculated the tops of sterilized soil columns with soil from the secondary woodland or the arable field sites. Control columns of all soil types were not inoculated. In a fully-crossed design, we planted two species possessing distinct root system morphological traits: Brachypodium sylvaticum (fibrous system with many thin and fine roots) and Urtica dioica (taproot system with few fine roots). After four months, microbial communities (in bulk and rhizospheric soil) and aggregate stability were measured, along with root traits. In both the field and laboratory experiments, bacterial (16S) and fungal (ITS) biodiversity was determined using high throughput sequencing. In the field study we found that: i) there were strong relationships between aggregate stability and microbial community composition that were driven by land use, ii) the relationship between aggregate stability along the land use gradient and the trophic nature of bacterial communities was not significant, but that certain soil, root and litter parameters shaped bacterial phyla, with oligotrophic bacteria conditioned by the rhizosphere niche, and copiotrophic phyla more dependent on bulk soil conditions, iii) land use gradient (from woodland to arable), reduced the relative abundance of saprotrophic and ectomycorrhizal fungi with an increase in the relative abundance of Ascomycota and a reduction in the relative abundance of Basidiomycota. In the laboratory experiment we found that: i) the inoculation of sterilized soils with soils from the field significantly increased aggregate stability in control soil that was initially poorly structured, ii) the effects of inoculation on aggregate stability were similar when either secondary woodland or arable soils were used as inoculums and iii) these effects were affected significantly by root length density. Our results show that microbial communities influence soil structure and that bacterial communities are intimately associated to rhizospheric conditions and root traits (of which root length density was the most pertinent)