DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences

DECIPHER is a new method for finding 16S rRNA chimeric sequences by the use of a search-based approach. The method is based upon detecting short fragments that are uncommon in the phylogenetic group where a query sequence is classified but frequently found in another phylogenetic group. The algorithm was calibrated for full sequences (fs_DECIPHER) and short sequences (ss_DECIPHER) and benchmarked against WigeoN (Pintail), ChimeraSlayer, and Uchime using artificially generated chimeras. Overall, ss_DECIPHER and Uchime provided the highest chimera detection for sequences 100 to 600 nucleotides long (79% and 81%, respectively), but Uchime's performance deteriorated for longer sequences, while ss_DECIPHER maintained a high detection rate (89%). Both methods had low false-positive rates (1.3% and 1.6%). The more conservative fs_DECIPHER, benchmarked only for sequences longer than 600 nucleotides, had an overall detection rate lower than that of ss_DECIPHER (75%) but higher than those of the other programs. In addition, fs_DECIPHER had the lowest false-positive rate among all the benchmarked programs (<0.20%). DECIPHER was outperformed only by ChimeraSlayer and Uchime when chimeras were formed from closely related parents (less than 10% divergence). Given the differences in the programs, it was possible to detect over 89% of all chimeras with just the combination of ss_DECIPHER and Uchime. Using fs_DECIPHER, we detected between 1% and 2% additional chimeras in the RDP, SILVA, and Greengenes databases from which chimeras had already been removed with Pintail or Bellerophon. DECIPHER was implemented in the R programming language and is directly accessible through a webpage or by downloading the program as an R package (http://DECIPHER.cee.wisc.edu).     

Diversity surveys and evolutionary relationships of aoxB genes in aerobic arsenite-oxidizing bacteria

A new primer set was designed to specifically amplify ca. 1,100 bp of aoxB genes encoding the As(III) oxidase catalytic subunit from taxonomically diverse aerobic As(III)-oxidizing bacteria. Comparative analysis of AoxB protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. AoxB phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16S rRNA phylogeny. Alphaproteobacteria-, Betaproteobacteria-, and Gammaproteobacteria-related sequences were retrieved from environmental surveys, demonstrating their prevalence in mesophilic As-contaminated soils. Our study underlines the usefulness of the aoxB gene as a functional marker of aerobic As(III) oxidizers.     

Critical biophysical properties in the Pseudomonas aeruginosa efflux gene regulator MexR are targeted by mutations conferring multidrug resistance

The self‐assembling MexA‐MexB‐OprM efflux pump system, encoded by the mexO operon, contributes to facile resistance of Pseudomonas aeruginosa by actively extruding multiple antimicrobials. MexR negatively regulates the mexO operon, comprising two adjacent MexR binding sites, and is as such highly targeted by mutations that confer multidrug resistance (MDR). To understand how MDR mutations impair MexR function, we studied MexR‐wt as well as a selected set of MDR single mutants distant from the proposed DNA‐binding helix. Although DNA affinity and MexA‐MexB‐OprM repression were both drastically impaired in the selected MexR‐MDR mutants, MexR‐wt bound its two binding sites in the mexO with high affinity as a dimer. In the MexR‐MDR mutants, secondary structure content and oligomerization properties were very similar to MexR‐wt despite their lack of DNA binding. Despite this, the MexR‐MDR mutants showed highly varying stabilities compared with MexR‐wt, suggesting disturbed critical interdomain contacts, because mutations in the DNA‐binding domains affected the stability of the dimer region and vice versa. Furthermore, significant ANS binding to MexR‐wt in both free and DNA‐bound states, together with increased ANS binding in all studied mutants, suggest that a hydrophobic cavity in the dimer region already shown to be involved in regulatory binding is enlarged by MDR mutations. Taken together, we propose that the biophysical MexR properties that are targeted by MDR mutations—stability, domain interactions, and internal hydrophobic surfaces—are also critical for the regulation of MexR DNA binding.     

Depth gradients in food‐web processes linking habitats in large lakes: Lake Superior as an exemplar ecosystem

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Strongyloidiasis and Infective Dermatitis Alter Human T Lymphotropic Virus-1 Clonality in vivo

Human T-lymphotropic Virus-1 (HTLV-1) is a retrovirus that persists lifelong by driving clonal proliferation of infected T-cells. HTLV-1 causes a neuroinflammatory disease and adult T-cell leukemia/lymphoma. Strongyloidiasis, a gastrointestinal infection by the helminth Strongyloides stercoralis, and Infective Dermatitis associated with HTLV-1 (IDH), appear to be risk factors for the development of HTLV-1 related diseases. We used high-throughput sequencing to map and quantify the insertion sites of the provirus in order to monitor the clonality of the HTLV-1-infected T-cell population (i.e. the number of distinct clones and abundance of each clone). A newly developed biodiversity estimator called “DivE” was used to estimate the total number of clones in the blood. We found that the major determinant of proviral load in all subjects without leukemia/lymphoma was the total number of HTLV-1-infected clones. Nevertheless, the significantly higher proviral load in patients with strongyloidiasis or IDH was due to an increase in the mean clone abundance, not to an increase in the number of infected clones. These patients appear to be less capable of restricting clone abundance than those with HTLV-1 alone. In patients co-infected with Strongyloides there was an increased degree of oligoclonal expansion and a higher rate of turnover (i.e. appearance and disappearance) of HTLV-1-infected clones. In Strongyloides co-infected patients and those with IDH, proliferation of the most abundant HTLV-1⁺ T-cell clones is independent of the genomic environment of the provirus, in sharp contrast to patients with HTLV-1 infection alone. This implies that new selection forces are driving oligoclonal proliferation in Strongyloides co-infection and IDH. We conclude that strongyloidiasis and IDH increase the risk of development of HTLV-1-associated diseases by increasing the rate of infection of new clones and the abundance of existing HTLV-1⁺ clones.     

Selection on trait combinations along environmental gradients

Plant species are sorted into communities along environmental gradients. In this issue of the Journal of Vegetation Science, Schellenberger Costa et al. report how the means and dispersion of community trait distributions change with temperature, precipitation, soil nutrients and anthropogenic disturbance. We highlight the value of existing trait metrics for understanding habitat filtering and describe a new approach using trait covariance.     

Differential Binding of IgG and IgA to Mucus of the Female Reproductive Tract

Cells of the endocervix are responsible for the secretion of mucins, which provide an additional layer of protection to the female reproductive tract (FRT). This barrier is likely fortified with IgA as has previously been shown in the gastrointestinal tract and lungs of mice. Mucus associated IgA can facilitate clearance of bacteria. While a similar function for IgG has been proposed, an association with mucus has not yet been demonstrated. Here we find that IgA and IgG are differentially associated with the different types of mucus of the FRT. We observed that while both IgA and IgG are stably associated with cervical mucus, only IgG is associated with cervicovaginal mucus. These findings reveal that antibodies can bind tightly to mucus, where they can play a significant role in the fortification of the mucus barriers of the FRT. It may be possible to harness this interaction in the development of vaccines designed to protect the FRT mucosal barriers from sexually transmitted diseases such as HIV.     

Comparison of a Thermoanaerobium sp. from a New Zealand hot spring with Thermoanaerobium brockii

Abstract An anaerobic ethanologenic strain of extremely thermophilic bacteria isolated from a New Zealand hot spring resembled Thermoanaerobium brockii in morphology and cell-wall ultrastructure. However, antibodies produced against the New Zealand isolate did not crossreact with the type strain of T. brockii . The New Zealand isolate strain Tok6-B1 fermented a wider range of carbohydrate substrates, including pentoses, and was less inhibited by a hydrogen atmosphere. Ethanol and acetate were major end-products and lactate a minor product of glucose fermentation. Under a hydrogen atmosphere, these 3 end-products were formed in approximately equal amounts.     

Vegetation change following removal of keystone herbivores from desert grasslands in New Mexico

Abstract. Responses of plant communities to mammalian herbivores vary widely, due to variation in plant species composition, herbivore densities, forage preferences, soils, and climate. In this study, we evaluated vegetation changes on 30 sites within and adjacent to the Sevilleta National Wildlife Refuge (SNWR) in central New Mexico, USA, over a 20‐yr period following removal of the major herbivores (livestock and prairie dogs) in 1972–1975. The study sites were established in 1976, and were resampled in 1986 and 1996 using line transect methods. At the landscape scale, repeated measures ANOVA of percentage cover measurements showed no significant overall net changes in total perennial plant basal cover, either with or without herbivores present; however, there was an overall increase in annual forbs and plant litter from 1976 to 1996. At the site scale, significant changes in species composition and dominance were observed both through time and across the SNWR boundary. Site histories varied widely, with sites dominated by Bouteloua eriopoda being the most dynamic and sites dominated by Scleropogon brevifolius being the most persistent. Species‐specific changes also were observed across multiple sites: B. eriopoda cover increased while Gutierrezia sarothrae greatly decreased. The non‐uniform, multi‐directional changes of the sites' vegetation acted to prevent detection of overall changes in perennial vegetation at the landscape level. Some sites displayed significant changes after removal of herbivores, while others appeared to respond primarily to climate dynamics. Certain species that were not preferred by livestock or prairie dogs, showed overall declines during drought periods, while other preferred species exhibited widespread increases during wetter periods regardless of herbivore presence. Therefore, the vegetation dynamics cannot be attributed solely to removal of herbivores, and in some cases can be explained by short‐ and long‐term fluctuations in climate. These results emphasize the variety of responses of sites with differences in vegetation to mammalian herbivores under otherwise similar climatic conditions, and illustrate the value of site‐ and landscape‐scale approaches to understanding the impacts of plant‐herbivore interactions.