Ecological and Evolutionary Science
Research Article | Ecological and Evolutionary ScienceBacterial Stabilization of a Panel of PicornavirusesRecent studies have shown that bacteria promote infection and stabilization of poliovirus particles, but the breadth of these effects on other members of the Picornaviridae family is unknown. Here, we compared the effects of bacteria on four distinct members of the Picornaviridae family. We found that bacteria reduced inactivation of all of the viruses during bleach treatment, but not all viral strains were stabilized...
Research Article | Ecological and Evolutionary ScienceLoss and Gain in the Evolution of the Salmonella enterica Serovar Gallinarum Biovar Pullorum GenomePullorum disease, an acute poultry septicemia caused by Salmonella Gallinarum biovar Pullorum, is fatal for young chickens and is a heavy burden on poultry industry. The pathogen is rare in most developed countries but still extremely difficult to eliminate in China. Efficient epidemiological surveillance necessitates clarifying the origin of the isolates from different regions and their phylogenic relationships. Genomic...
Research Article | Ecological and Evolutionary ScienceNative and Invading Yellow Starthistle (Centaurea solstitialis) Microbiomes Differ in Composition and Diversity of BacteriaPrevious studies have found that introduced plants commonly experience more favorable microbial interactions in their non-native range, suggesting that changes to the microbiome could be an important contributor to invasion success. Little is known about microbiome variation across native and invading populations, however, and the potential sources of more favorable interactions are undescribed. Here, we report one of the first...
Research Article | Ecological and Evolutionary ScienceMicrobial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater AquariaSaltwater aquaria are living systems that support a complex biological community of fish, invertebrates, and microbes. The health and maintenance of saltwater tanks are pressing concerns for home hobbyists, zoos, and professionals in the aquarium trade; however, we do not yet understand the underlying microbial species interactions and community dynamics which contribute to tank setup and conditioning. This report provides a detailed...
Editor's Pick Research Article | Ecological and Evolutionary ScienceCharacterizing the Pathogenic, Genomic, and Chemical Traits of Aspergillus fischeri, a Close Relative of the Major Human Fungal Pathogen Aspergillus fumigatusAspergillus fumigatus is the primary cause of aspergillosis, a devastating ensemble of diseases associated with severe morbidity and mortality worldwide. A. fischeri is a close relative of A. fumigatus but is not generally...
Research Article | Ecological and Evolutionary ScienceGene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic ConditionsBy combining a genome-centric metagenomic approach with a culture-based approach, we investigated the genomic adaptations of prevalent populations in an engineered oligotrophic freshwater system. We found evidence for widespread positive selection on genes involved in phosphorus and carbon scavenging pathways and for gene expansions in motility and environmental sensing to be important genomic adaptations of the abundant taxon in this...
Research Article | Ecological and Evolutionary ScienceThe Phylogenomic Diversity of Herbivore-Associated Fibrobacter spp. Is Correlated to Lignocellulose-Degrading PotentialThe herbivore gut microbiome is incredibly diverse, and a functional understanding of this diversity is needed to more reliably manipulate this community for specific gain, such as increased production in ruminant livestock. Microbial degraders of plant cell wall polysaccharides in the herbivore gut, particularly Fibrobacter spp., are of fundamental importance to their hosts for digestion of a diet consisting primarily of...
Editor's Pick Research Article | Ecological and Evolutionary ScienceIdentification of an Exceptionally Long Intron in the HAC1 Gene of Candida parapsilosisThe unfolded protein response (UPR) responds to the build-up of misfolded proteins in the endoplasmic reticulum. The UPR has wide-ranging functions from fungal pathogenesis to applications in biotechnology. The UPR is regulated through the splicing of an unconventional intron in the HAC1 gene. This intron has been described in many fungal species and is of variable length. Until now it was believed that some members of the CTG-...
Research Article | Ecological and Evolutionary ScienceThe Enterococcus Cassette Chromosome, a Genomic Variation Enabler in EnterococciEnterococcus faecium is a bacterium found in a great variety of environments, ranging from the clinic as a nosocomial pathogen to natural habitats such as mammalian intestines, water, and soil. They are known to exchange genetic material through horizontal gene transfer and recombination, leading to great variability of accessory genes and aiding environmental...
Research Article | Ecological and Evolutionary ScienceTaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic ResolutionMicrobial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or...