ThermoPhyl : a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples

The ability to specifically and sensitively target genotypes of interest is critical for the success of many PCR-based analyses of environmental or clinical samples that contain multiple templates.Next-generation sequence data clearly show that such samples can harbour hundreds to thousands of operational taxonomic units; a richness which precludes the manual evaluation of candidate assay specificity and sensitivity using multiple sequence alignments. To solve this problem we have developed and validated a free software tool which automates the identification of PCR assays targeting specific genotypes in complex samples. ThermoPhyl uses user-defined target and non-target sequence databases to assess the phylogenetic sensitivity and specificity of thermodynamically optimised candidate assays derived from primer design software packages. ThermoPhyl takes its name from its central premise of testing Thermodynamically optimal assays for Phylogenetic specificity and sensitivity and can be used for two primer (traditional PCR) or two primers with an internal probe (e.g. TaqMan® qPCR) applications and potentially for oligonucleotide probes.Here we describe the use of ThermoPhyl for traditional PCR and qPCR assays. PCR assays selected using ThermoPhyl were validated using 454 pyrosequencing of a traditional specific PCR assay and with a set of four genotype-specific qPCR assays applied to estuarine sediment samples

The effects of fire on soil nitrogen associated with patches of the actinorhizal shrub Ceanothus cordulatus

Nitrogen is a limiting resource in many temperate forests and nitrogen-fixing plants are usually limited to the early stages of post-disturbance succession. In fire-dependent Sierra Nevada forests, however, Ceanothus cordulatus is relatively abundant even in old-growth forest conditions which are at least partly maintained by fire.We conducted a field experiment to determine if soil beneath Ceanothus patches represent ‘resource islands’ of available N which persist after fire. Nine plots containing discrete patches of Ceanothus, Arctostaphylos patula (manzanita; chosen as a non N-fixing reference species), and bare forest floor were subjected to either a low-intensity (n = 3) or highintensity (n = 3) bum treatment, or remained unburned as controls (n = 3). Soil temperatures during the bum were monitored by a network of thermocouples placed at the surface of the mineral soil and at ca. 10 cm depths. Soil samples were collected from the organic horizon, 0-10 cm and 15-25 cm depths within each patch type immediately before burning and 2 days, and 6, and 11 months after. Soil moisture, total C and N, and ammonium and nitrate concentrations were determined in the laboratory. Before the burn, Ceanothus patches were significantly enriched in total and inorganic N in the organic horizon relative to the other patch types. A sharp increase in inorganic N was observed in all patch types and depths immediately following burning, but by 6 months after the burn, Ceanothus patches were significantly enriched relative to the surrounding patch types and remained so at months. Resprouting Ceanothus patches will continue to be an important source of a limiting nutrient in this fire-prone ecosystem.Keywords: Frankia, Sierra Nevada, Fire, Ceanothus, Nitroge

Facilitative and competitive effecs of a N-fixing shrub on white fir saplings

In Sierra Nevada forests, shrubs are considered strong soil moisture competitors with regenerating trees, reducing seedling establishment, and slowing growth. Recent studies, however, suggest that in some circumstances shrubs can facilitate tree establishment and growth by modifying harsh microclimate conditions; increasing acquisition of water, carbon, and/or nutrients via shared mycorrhizal connections; or enhancing soil fertility, particularly under nitrogen-fixing shrubs such as Ceanothus spp. We examined the establishment dates and growth rates and patterns of white fir saplings growing in greenleaf manzanita, whitethorn ceanothus, and bare patches to examine whether establishment was correlated with past wet years, whether saplings growing in ceanothus had nitrogen-enriched foliage or faster growth rates than in the other two patches, and whether saplings in shrub patches experienced competition for light. Sapling establishment was not correlated with high precipitation or heavy snowpack years, suggesting shade-tolerant saplings do not need wet years to become established. Soils under ceanothus were nitrogen enriched, but white fir sapling foliage did not have higher nitrogen concentrations and saplings did not grow faster in ceanothus than in the other two patches. Because growth rates of saplings were comparable in all patch types examined despite significantly different edaphic and abiotic conditions, we inferred that the various competitive and facilitative interactions affecting tree growth are in net balance across the patch types examined. However, competition for light is important—a significant percentage of growth release events occurred after saplings emerged above their host shrubs. Where shrubs are present, shade-tolerant species (i.e., white fir) are favored over drought-tolerant (pine) species. Our results may help interpret changes in understory conditions that are contributing to mixed conifer’s compositional shift toward more shade-tolerant species after a century of fire-suppression.Keywords: shade tolerance, soil fertility, forest regeneration, fire suppression, nitrogen fixation, mixed conifer, plant competitio

Facilitative and competive effects of a N-fixing shrub on white fir saplings

In Sierra Nevada forests, shrubs are considered strong soil moisture competitors with regenerating trees, reducing seedling establishment, and slowing growth. Recent studies, however, suggest that in some circumstances shrubs can facilitate tree establishment and growth by modifying harsh microclimate conditions; increasing acquisition of water, carbon, and/or nutrients via shared mycorrhizal connections; or enhancing soil fertility, particularly under nitrogen-fixing shrubs such as Ceanothus spp. We examined the establishment dates and growth rates and patterns of white fir saplings growing in greenleaf manzanita, whitethorn ceanothus, and bare patches to examine whether establishment was correlated with past wet years, whether saplings growing in ceanothus had nitrogen-enriched foliage or faster growth rates than in the other two patches, and whether saplings in shrub patches experienced competition for light. Sapling establishment was not correlated with high precipitation or heavy snowpack years, suggesting shade-tolerant saplings do not need wet years to become established. Soils under ceanothus were nitrogen enriched, but white fir sapling foliage did not have higher nitrogen concentrations and saplings did not grow faster in ceanothus than in the other two patches. Because growth rates of saplings were comparable in all patch types examined despite significantly different edaphic and abiotic conditions, we inferred that the various competitive and facilitative interactions affecting tree growth are in net balance across the patch types examined. However, competition for light is important—a significant percentage of growth release events occurred after saplings emerged above their host shrubs. Where shrubs are present, shade-tolerant species (i.e., white fir) are favored over drought-tolerant (pine) species. Our results may help interpret changes in understory conditions that are contributing to mixed conifer’s compositional shift toward more shade-tolerant species after a century of fire-suppression.Keywords: Nitrogen fixation, Shade tolerance, Forest regeneration, Plant competition, Fire suppression, Soil fertility, Mixed conife

Metabolic flexibility as a major predictor of spatial distribution in microbial communities

A better understand the ecology of microbes and their role in the global ecosystem could be achieved if traditional ecological theories can be applied to microbes. In ecology organisms are defined as specialists or generalists according to the breadth of their niche. Spatial distribution is often used as a proxy measure of niche breadth; generalists have broad niches and a wide spatial distribution and specialists a narrow niche and spatial distribution. Previous studies suggest that microbial distribution patterns are contrary to this idea; a microbial generalist genus (Desulfobulbus) has a limited spatial distribution while a specialist genus (Methanosaeta) has a cosmopolitan distribution. Therefore, we hypothesise that this counter-intuitive distribution within generalist and specialist microbial genera is a common microbial characteristic. Using molecular fingerprinting the distribution of four microbial genera, two generalists, Desulfobulbus and the methanogenic archaea Methanosarcina, and two specialists, Methanosaeta and the sulfate-reducing bacteria Desulfobacter were analysed in sediment samples from along a UK estuary. Detected genotypes of both generalist genera showed a distinct spatial distribution, significantly correlated with geographic distance between sites. Genotypes of both specialist genera showed no significant differential spatial distribution. These data support the hypothesis that the spatial distribution of specialist and generalist microbes does not match that seen with specialist and generalist large organisms. It may be that generalist microbes, while having a wider potential niche, are constrained, possibly by intrageneric competition, to exploit only a small part of that potential niche while specialists, with far fewer constraints to their niche, are more capable of filling their potential niche more effectively, perhaps by avoiding intrageneric competition. We suggest that these counter-intuitive distribution patterns may be a common feature of microbes in general and represent a distinct microbial principle in ecology, which is a real challenge if we are to develop a truly inclusive ecology

A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain

Research into the chemical biology of bromodomains has been driven by the development of acetyl-lysine mimetics. The ligands are typically anchored by binding to a highly conserved asparagine residue. Atypical bromodomains, for which the asparagine is mutated, have thus far proven elusive targets, including PHIP(2) whose parent protein, PHIP, has been linked to disease progression in diabetes and cancers. The PHIP(2) binding site contains a threonine in place of asparagine, and solution screening have yielded no convincing hits. We have overcome this hurdle by combining the sensitivity of X-ray crystallography, used as the primary fragment screen, with a strategy for rapid follow-up synthesis using a chemically-poised fragment library, which allows hits to be readily modified by parallel chemistry both peripherally and in the core. Our approach yielded the first reported hit compounds of PHIP(2) with measurable IC50 values by an AlphaScreen competition assay. The follow-up libraries of four poised fragment hits improved potency into the sub-mM range while showing good ligand efficiency and detailed structural data

Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies

Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common in recent years as sequencing costs continue to fall and bioinformatic tools become more powerful and user-friendly. The combination of molecular biology, microbiology, microbial ecology, computer science, and bioinformatics—in addition to the traditional considerations when conducting an animal science study—makes microbiome studies sometimes intimidating due to the intersection of different fields. The objective of this review is to serve as a jumping-off point for those animal scientists less familiar with 16S rRNA gene sequencing and analyses and to bring up common issues and concerns that arise when planning an animal microbiome study from design through analysis. This review includes an overview of 16S rRNA gene sequencing, its advantages, and its limitations; experimental design considerations such as study design, sample size, sample pooling, and sample locations; wet lab considerations such as field handing, microbial cell lysis, low biomass samples, library preparation, and sequencing controls; and computational considerations such as identification of contamination, accounting for uneven sequencing depth, constructing diversity metrics, assigning taxonomy, differential abundance testing, and, finally, data availability. In addition to general considerations, we highlight some special considerations by species and sample type

Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity

Background: Environmental mycobacteria (EM) include species commonly found in various terrestrial and aquatic environments, encompassing animal and human pathogens in addition to saprophytes. Approximately 150 EM species can be separated into fast and slow growers based on sequence and copy number differences of their 16S rRNA genes. Cultivation methods are not appropriate for diversity studies; few studies have investigated EM diversity in soil despite their importance as potential reservoirs of pathogens and their hypothesized role in masking or blocking M. bovis BCG vaccine. Methods: We report here the development, optimization and validation of molecular assays targeting the 16S rRNA gene to assess diversity and prevalence of fast and slow growing EM in representative soils from semi tropical and temperate areas. New primer sets were designed also to target uniquely slow growing mycobacteria and used with PCR-DGGE, tag-encoded Titanium amplicon pyrosequencing and quantitative PCR. Results: PCR-DGGE and pyrosequencing provided a consensus of EM diversity; for example, a high abundance of pyrosequencing reads and DGGE bands corresponded to M. moriokaense, M. colombiense and M. riyadhense. As expected pyrosequencing provided more comprehensive information; additional prevalent species included M. chlorophenolicum, M. neglectum, M. gordonae, M. aemonae. Prevalence of the total Mycobacterium genus in the soil samples ranged from 2.3×107 to 2.7×108 gene targets g−1; slow growers prevalence from 2.9×105 to 1.2×107 cells g−1. Conclusions: This combined molecular approach enabled an unprecedented qualitative and quantitative assessment of EM across soil samples. Good concordance was found between methods and the bioinformatics analysis was validated by random resampling. Sequences from most pathogenic groups associated with slow growth were identified in extenso in all soils tested with a specific assay, allowing to unmask them from the Mycobacterium whole genus, in which, as minority members, they would have remained undetected

Ovine pedomics : the first study of the ovine foot 16S rRNA-based microbiome

We report the first study of the bacterial microbiome of ovine interdigital skin based on 16S rRNA by pyrosequencing and conventional cloning with Sanger-sequencing. Three flocks were selected, one a flock with no signs of footrot or interdigital dermatitis, a second flock with interdigital dermatitis alone and a third flock with both interdigital dermatitis and footrot. The sheep were classified as having either healthy interdigital skin (H), interdigital dermatitis (ID) or virulent footrot (VFR). The ovine interdigital skin bacterial community varied significantly by flock and clinical condition. The diversity and richness of operational taxonomic units was greater in tissue from sheep with ID than H or VFR affected sheep. Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria were the most abundant phyla comprising 25 genera. Peptostreptococcus, Corynebacterium and Staphylococcus were associated with H, ID and VFR respectively. Sequences of Dichelobacter nodosus, the causal agent of ovine footrot, were not amplified due to mismatches in the 16S rRNA universal forward primer (27F). A specific real time PCR assay was used to demonstrate the presence of D. nodosus which was detected in all samples including the flock with no signs of ID or VFR. Sheep with ID had significantly higher numbers of D. nodosus (104-109 cells/g tissue) than those with H or VFR feet