Biology subjects

Barry, A.

Publications and source records attributed to Barry, A..

2 recordsLinked to original sources

bioRxiv2018

Biogeography and Edaphic Factors Structure Coastal Sediment Microbial Communities More than Vegetation Removal by Sudden Vegetation Dieback

Development of sudden vegetation dieback (SVD), a phenomenon that causes the rapid mortality of salt marsh plants, specifically Spartina alterniflora, has affected large-scale alterations in Atlantic coastal systems, through the often-complete removal of vegetation. In this study, two wetlands that differ in the time since development of SVD were compared in order to study biogeographic and temporal patterns that structure coastal wetland microbial communities and their response to disturbance.\n\nBiogeographic and edaphic factors that distinguished the two wetlands, such as differing salinity, water content, and soil carbon and nitrogen between the sites were more strongly associated with sediment microbial community structure than either sampling date or SVD development. In fact, no OTUs differed in abundance due to the season samples were collected, or vegetation loss due to SVD. This is not to say that SVD did not alter the composition of the microbial communities. The taxonomic composition of sediment communities in SVD-affected sediments was more heterogeneous between samples and a small number of OTUs were enriched in the vegetated sediments. Yet, these data suggest that coastal wetland sediment communities are predominantly shaped by environmental conditions and are generally resilient to temporal cycles or ecosystem disturbances.\n\nImportanceOne of the challenges of microbial ecology is predicting how microbial communities will respond to ecosystem change. Yet, few studies have addressed whether microbial responses to disturbance are consistent over space or time. In this study we employ SVD as a natural vegetation removal experiment and compare the sediment microbial communities between two geographically separated wetlands (ca 125 km). In this manner, we uncover a hierarchical structuring of the microbial communities, being predominantly governed by biogeography, with lesser effects due to disturbance, or temporal dynamics.

microbiology↗

bioRxiv2016

Detecting Selection Signals In Plasmodium falciparum Using Identity-By-Descent Analysis

Identification of genomic regions that are identical by descent (IBD) has proven useful for human genetic studies where analyses have led to the discovery of familial relatedness and fine-mapping of disease critical regions. Unfortunately however, IBD analyses have been underutilized inanalysis of other organisms, including human pathogens. This is in part due to the lack of statistical methodologies for non-diploid genomes in addition to the added complexity of multiclonal infections. As such, we have developed an IBD methodology, called isoRelate, for analysis of haploid recombining microorganisms in the presence of multiclonal infections. Using the inferred IBD status at genomic locations, we have also developed a novel statistic for identifying loci under positive selection and propose relatedness networks as a means of exploring shared haplotypes within populations. We evaluate the performance of our methodologies for detecting IBD and selection, including comparisons with existing tools, then perform an exploratory analysis of whole genome sequencing data from a global Plasmodium falciparum dataset of more than 2500 genomes. This analysis identifies Southeast Asia as havingmany highly related isolates, possibly as a result of both reduced transmission from intensified control efforts and population bottlenecks following the emergence of antimalarial drug resistance. Many signals of selection are also identified, most of which overlap genes that are known to be associated with drug resistance, in addition to two novel signals observed in multiple countries that have yet to be explored in detail. Additionally, we investigate relatedness networks over the selected loci and determine that one of these sweeps has spread between continents while the other has arisen independently in different countries. IBD analysis of microorganisms using isoRelate can be used for exploring population structure, positive selection and haplotype distributions, and will be a valuable tool for monitoring disease control and elimination efforts of many diseases.

bioinformatics↗