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Ecological and Evolutionary Science

  • Open Access
    Quantitative Models of Phage-Antibiotic Combination Therapy
    Research Article | Ecological and Evolutionary Science
    Quantitative Models of Phage-Antibiotic Combination Therapy

    This 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...

    Rogelio A. Rodriguez-Gonzalez, Chung Yin Leung, Benjamin K. Chan, Paul E. Turner, Joshua S. Weitz
  • Open Access
    Adaptation of <span class="named-content genus-species" id="named-content-1">Lactobacillus plantarum</span> to Ampicillin Involves Mechanisms That Maintain Protein Homeostasis
    Research Article | Ecological and Evolutionary Science
    Adaptation of Lactobacillus plantarum to Ampicillin Involves Mechanisms That Maintain Protein Homeostasis

    Antibiotic 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.

    Chenxia Cao, Jicheng Wang, Yangshuo Liu, Lai-Yu Kwok, Heping Zhang, Wenyi Zhang
  • Open Access
    Horizontally Acquired Quorum-Sensing Regulators Recruited by the PhoP Regulatory Network Expand the Host Adaptation Repertoire in the Phytopathogen <em>Pectobacterium brasiliense</em>
    Research Article | Ecological and Evolutionary Science
    Horizontally Acquired Quorum-Sensing Regulators Recruited by the PhoP Regulatory Network Expand the Host Adaptation Repertoire in the Phytopathogen Pectobacterium brasiliense

    In 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).

    Daniel Bellieny-Rabelo, Ntombikayise Precious Nkomo, Divine Yufetar Shyntum, Lucy Novungayo Moleleki
  • Open Access
    Diatoms Are Selective Segregators in Global Ocean Planktonic Communities
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Diatoms Are Selective Segregators in Global Ocean Planktonic Communities

    Diatoms 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...

    Flora Vincent, Chris Bowler
  • Open Access
    Distinct but Intertwined Evolutionary Histories of Multiple <span class="named-content genus-species" id="named-content-1">Salmonella enterica</span> Subspecies
    Research Article | Ecological and Evolutionary Science
    Distinct but Intertwined Evolutionary Histories of Multiple Salmonella enterica Subspecies

    S. 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...

    Cooper J. Park, Cheryl P. Andam
  • Open Access
    Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries
    Research Article | Ecological and Evolutionary Science
    Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

    There 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...

    Matthew R. Olm, Alexander Crits-Christoph, Spencer Diamond, Adi Lavy, Paula B. Matheus Carnevali, Jillian F. Banfield
  • Open Access
    Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China
    Research Article | Ecological and Evolutionary Science
    Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China

    In 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....

    Pengfa Li, Weitao Li, Alex J. Dumbrell, Ming Liu, Guilong Li, Meng Wu, Chunyu Jiang, Zhongpei Li
  • Open Access
    Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of <em>Hydrothermarchaeota</em> in Hydrothermal Sediment
    Research Article | Ecological and Evolutionary Science
    Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment

    This 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...

    Zhichao Zhou, Yang Liu, Wei Xu, Jie Pan, Zhu-Hua Luo, Meng Li
  • Open Access
    Diverse, Abundant, and Novel Viruses Infecting the Marine <em>Roseobacter</em> RCA Lineage
    Research Article | Ecological and Evolutionary Science
    Diverse, Abundant, and Novel Viruses Infecting the Marine Roseobacter RCA Lineage

    The 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....

    Zefeng Zhang, Feng Chen, Xiao Chu, Hao Zhang, Haiwei Luo, Fang Qin, Zhiqiang Zhai, Mingyu Yang, Jing Sun, Yanlin Zhao
  • Open Access
    Variability in the Response of Bacterial Community Assembly to Environmental Selection and Biotic Factors Depends on the Immigrated Bacteria, as Revealed by a Soil Microcosm Experiment
    Research Article | Ecological and Evolutionary Science
    Variability in the Response of Bacterial Community Assembly to Environmental Selection and Biotic Factors Depends on the Immigrated Bacteria, as Revealed by a Soil Microcosm Experiment

    The 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...

    Xiaogang Wu, Yun Wang, Ying Zhu, Hao Tian, Xianchao Qin, Changzheng Cui, Liping Zhao, Pascal Simonet, Xiaojun Zhang

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