Ecological and Evolutionary Science
Research Article | Ecological and Evolutionary ScienceQuantitative Models of Phage-Antibiotic Combination TherapyThis work develops and analyzes a novel model of phage-antibiotic combination therapy, specifically adapted to an in vivo context. The objective is to explore the underlying basis for clinical application of combination therapy utilizing bacteriophage that target antibiotic efflux pumps in Pseudomonas aeruginosa. In doing so, the paper addresses three key...
Research Article | Ecological and Evolutionary ScienceAdaptation of Lactobacillus plantarum to Ampicillin Involves Mechanisms That Maintain Protein HomeostasisAntibiotic resistance acquired by adaptation to certain antibiotics has led to growing public concerns. Here, a long-term evolution experiment was used together with proteomic analysis to identify genes/proteins responsible for the adaptive phenotype. This work has provided novel insights into the biosafety of new probiotics with high tolerance to antibiotics.
Research Article | Ecological and Evolutionary ScienceHorizontally Acquired Quorum-Sensing Regulators Recruited by the PhoP Regulatory Network Expand the Host Adaptation Repertoire in the Phytopathogen Pectobacterium brasilienseIn this study, we examine the impact of transcriptional network rearrangements driven by horizontal gene acquisition in PhoP and SlyA regulons using as a case study a phytopathosystem comprised of potato tubers and the soft-rot pathogen Pectobacterium brasiliense 1692 (Pb1692).
Editor's Pick Research Article | Ecological and Evolutionary ScienceDiatoms Are Selective Segregators in Global Ocean Planktonic CommunitiesDiatoms are key phytoplankton in the modern ocean that are involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological...
Research Article | Ecological and Evolutionary ScienceDistinct but Intertwined Evolutionary Histories of Multiple Salmonella enterica SubspeciesS. enterica is a major foodborne pathogen, which can be transmitted via several distinct routes from animals and environmental sources to human hosts. Multiple subspecies and serotypes of S. enterica exhibit considerable differences in virulence, host specificity, and colonization. This study...
Research Article | Ecological and Evolutionary ScienceConsistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species BoundariesThere is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is...
Research Article | Ecological and Evolutionary ScienceSpatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical ChinaIn this work, Illumina MiSeq amplicon sequencing of the ITS region was used to investigate the spatial variation and assembly mechanisms of fungal communities from different soil layers across paddy fields in subtropical China, and the results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils....
Research Article | Ecological and Evolutionary ScienceGenome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal SedimentThis study provides comprehensive metabolic insights into the Hydrothermarchaeota from comparative genomics, evolution, and community-level perspectives. Members of the Hydrothermarchaeota synergistically participate in a wide range of carbon-utilizing and element cycling processes with other microorganisms in the community. We expand the current understanding of community interactions within the hydrothermal sediment...
Research Article | Ecological and Evolutionary ScienceDiverse, Abundant, and Novel Viruses Infecting the Marine Roseobacter RCA LineageThe RCA lineage of the marine Roseobacter group represents one of the slow-growing but dominant components of marine microbial communities. Although dozens of roseophages have been characterized, no phages infecting RCA strains have been reported. In this study, we reported on the first RCA phage genomes and investigated their distribution pattern and relative abundance in comparison with other important marine phage groups....
Research Article | Ecological and Evolutionary ScienceVariability in the Response of Bacterial Community Assembly to Environmental Selection and Biotic Factors Depends on the Immigrated Bacteria, as Revealed by a Soil Microcosm ExperimentThe soil microbiota conducts important biological ecosystem functions, but the mechanism underlying community-environment interactions for soil microbiota remains unclear. By using two distinct soils for cross inoculation, we successfully simulated the assembly of the bacterial community in sterile soil. Thus, the reasons why inoculum and recipient have dominated community assembly in previous investigations are investigated in this...