We identify key environmental and geochemical factors that shape the arid soil microbiome along aridity and vegetation gradients spanning over 300 km of the Atacama Desert, Chile. Decreasing average soil relative humidity and increasing temperature explain significant reductions in the diversity and connectivity of these desert soil microbial communities and lead to significant reductions in the abundance of key taxa typically associated with fertile soils. This finding is important because it suggests that predicted climate change-driven increases in aridity may compromise the capacity of the arid-soil microbiome to sustain necessary nutrient cycling and carbon sequestration functions as well as vegetative cover in desert ecosystems, which comprise one-third of the terrestrial biomes on Earth.

Periodontal disease affects the majority of adults worldwide and has been linked to numerous systemic diseases. Despite decades of research, the reasons for the substantial differences among periodontitis patients in disease incidence, progressivity, and response to treatment remain poorly understood. While deep sequencing of oral bacterial communities has greatly expanded our comprehension of the microbial diversity of periodontal disease and identified associations with healthy and disease states, predicting treatment outcomes remains elusive. Our results suggest that combining multiple omics approaches enhances the ability to differentiate among disease states and determine differential effects of treatment, particularly with the addition of metabolomic information. Furthermore, multi-omics analysis of biofilm community instability indicated that these approaches provide new tools for investigating the ecological dynamics underlying the progressive periodontal disease process.

Hematodinium is a genus of parasitic dinoflagellates that infects crustaceans worldwide including Tanner crabs Chionoecetes bairdi and snow crabs C. opilio in the Northeast Pacific Ocean. The present study describes the optimization of a PCR-based assay for the detection and monitoring of Hematodinium sp. in snow and Tanner crabs. Two fragments, 1682 and 187 bp, were amplified from the 18S ribosomal DNA region of the parasite. The assay performed well in 6 additional decapod species (1 lobster and 5 crabs) infected with Hematodinium spp., suggesting that it could be used to detect Hematodinium spp. in other decapods. We also report Hematodinium spp. infections in the majid crab, Hyas coarctatus, and the lithodid crab, Lithodes couesi. Sequencing of 18S rDNA and the adjacent internal transcribed spacer 1 (ITS1) region of Hematodinium spp. isolated from 7 host species in the present study revealed the presence of 2 Hematodinium clades, one in the blue crab Callinectes sapidus and a second in all other host species. The ITS1 sequences of the 2 clades could not be aligned, but showed a conserved secondary structure that may be related to a functional diversification during a host switch. Comparison of our data with 18S and ITS1 sequence data available in GenBank placed the north Pacific Hematodinium sp. in a clade separate from the Hematodinium sp. infecting the portunoids, C. sapidus, Liocarcinus depurator and Scylla serrata, and within a second clade that infected all other decapod hosts located in the North Pacific and North Atlantic Oceans.KEY WORDS: ITS1 · Secondary structure · 18S rDNA · Parasite · PCR · Crustacean · Parasitic · Dinoflagellate · Disease Resale or republication not permitted without written consent of the publisher OPEN PEN ACCESS CCESSDis Aquat Org 89: [155][156][157][158][159][160][161][162][163][164][165][166] 2010 including Portunus pelagicus, Norway lobsters Nephrops norvegicus and blue crabs Callinectes sapidus (reviewed in Stentiford & Shields 2005, Small et al. 2006, 2007b. Despite the potential economic and ecological impact of Hematodinium-related mortality on affected populations, little is known about the method of infection, the life history of the parasite outside the host and the underlying causes for the recent worldwide increase in frequency of Hematodiniumassociated disease.Traditional techniques of disease detection involve macroscopic examination of pleopods that generally result in detection of only relatively advanced infections (Stentiford et al. 2001) or microscopic examination of hemolymph smears. More sensitive, immunological methods for Hematodinium detection (Field & Appleton 1996, Stentiford et al. 2001, Small et al. 2002 are of insufficient specificity or may not recognize life stages of Hematodinium absent in the original inoculum or in alternate hosts (Bushek et al. 2002, Small et al. 2006. Use of the PCR has become increasingly widespread in pathogen identification and disease detection and monitoring and is particularly useful in the diagnosis of c...

Burkholderia pseudomallei is the causative agent of melioidosis and a potential bioterrorism agent. In the development of medical countermeasures against B. pseudomallei infection, the US Food and Drug Administration (FDA) animal Rule recommends using well-characterized strains in animal challenge studies. In this study, whole genome sequence data were generated for 6 B. pseudomallei isolates previously identified as candidates for animal challenge studies; an additional 5 isolates were sequenced that were associated with human inhalational melioidosis. A core genome single nucleotide polymorphism (SNP) phylogeny inferred from a concatenated SNP alignment from the 11 isolates sequenced in this study and a diverse global collection of isolates demonstrated the diversity of the proposed Animal Rule isolates. To understand the genomic composition of each isolate, a large-scale blast score ratio (LS-BSR) analysis was performed on the entire pan-genome; this demonstrated the variable composition of genes across the panel and also helped to identify genes unique to individual isolates. In addition, a set of ~550 genes associated with pathogenesis in B. pseudomallei were screened against the 11 sequenced genomes with LS-BSR. Differential gene distribution for 54 virulence-associated genes was observed between genomes and three of these genes were correlated with differential virulence observed in animal challenge studies using BALB/c mice. Differentially conserved genes and SNPs associated with disease severity were identified and could be the basis for future studies investigating the pathogenesis of B. pseudomallei. Overall, the genetic characterization of the 11 proposed Animal Rule isolates provides context for future studies involving B. pseudomallei pathogenesis, differential virulence, and efficacy to therapeutics.

Surprising social complexity and variability have recently been documented in several mammalian species once believed to be strictly solitary, and variation in resource abundance may drive this variation in sociality. Wagner et al. (Wagner, A. P., S. Creel, L. G. Frank, and S. T. Kalinowski. 2007. Patterns of relatedness and parentage in an asocial, polyandrous striped hyena population. Molecular Ecology 16:4356–4369) reported unusual space-use patterns among female striped hyenas (Hyaena hyaena) in central Kenya, where pairwise relatedness among females increased with the geographic distance separating them. The authors suggested that this pattern, very rare among mammals, might reflect attempts by females to avoid competition with close relatives for scarce resources in areas of range overlap. Here, we compare those data to new data, documenting genetic relatedness and space use in a previously unstudied wild population of striped hyenas in southern Kenya. We tested hypotheses suggesting that resource abundance and population density affect patterns of genetic relatedness and geographic distance in this species. Our results suggest that higher per capita prey density results in relaxed competition for food, and greater social tolerance among female striped hyenas. A hypothesis suggesting lower population density in the southern population was not supported. Relaxed resource competition also may lead to female–female cooperation in the southern population; we documented for the first time behavioral evidence of den sharing by adult female striped hyenas. Our data indicate that different populations of this little-studied species exhibit behavioral plasticity; in this case, markedly different space-use patterns and patterns of spatial relatedness under different ecological conditions.