<jats:title>Abstract</jats:title> <jats:p>The principles governing microbial community assembly and the interplay between deterministic selection and stochasticity remain central debates in ecology. We investigated how chemically diverse carbon sources act as ecological filters shaping soil bacterial communities. Using replicated microcosms amended with distinct substrates (glucose, succinate, naphthalene, phenanthrene, or γ-HCH) or under starvation, we tracked community trajectories via high-frequency 16S rRNA gene sequencing (29 timepoints, triplicate) and quantitative ecological modeling. Null model analysis confirmed the carbon source as the primary deterministic filter, enforcing high reproducibility (homogeneous selection governing ~74% of assembly among replicates) and overriding stochastic effects. Crucially, abundant (&amp;gt;1%) and rare (&amp;lt;0.1%) taxa exhibited decoupled assembly mechanisms. While abundant taxa were driven largely by dispersal limitation (~59%) and variable selection, the rare biosphere displayed a temporal regime shift. Unlike the immediate response of dominant taxa, rare taxa transitioned from stochastic isolation to strong deterministic selection (surging to ~50%) only during later successional stages. This reframes the rare biosphere as a "latent responder" reservoir recruited by metabolic byproducts rather than the primary substrate. Additionally, time-resolved interaction networks revealed that under severe stress from toxicity or starvation, interactions shifted from competitive exclusion to facilitation (e.g., necromass scavenging). These patterns provide strong empirical support for the Stress Gradient Hypothesis in a microbial context. Collectively, our findings demonstrate how deterministic filtering and stress-mediated cooperation jointly structure ecosystems, providing a high-resolution temporal dataset to further interrogate these fundamental ecological principles.</jats:p>

ABSTRACT Plasmid partitioning and bacterial conjugation are critical processes ensuring plasmid maintenance and dissemination, respectively, within bacterial populations. Although traditionally regarded as distinct phenomena, these two processes are increasingly recognized as interconnected. While partitioning ensures plasmid inheritance during cell division, its potential influence on conjugative transfer remains poorly understood. A major impediment to understanding their interplay is that partition systems are often essential for plasmid stability, making it difficult to distinguish their direct effects on conjugation. In this study, we addressed this challenge using a mini-conjugative plasmid derived from thePseudomonas putidaNAH7 plasmid. This engineered plasmid, containing all conjugation-related genes, was cloned into anE. coli-compatible vector. Additionally, thepargenes from NAH7 were expressed from a separate plasmid to investigate their roles in conjugative transfer. Our results revealed that thepargene cluster plays a significant role in enhancing the conjugative transfer of the mini-conjugative plasmid. Specifically, ParB, a centromere-binding protein, functions as a transcriptional activator of conjugation-related genes with bindingparS_NAHsite. In contrast, ParR, a KorA homolog, was not found to enhance transcription directly but binds extensively to theoriTregion. This binding probably facilitates the recruitment or stabilization of the relaxosome, thereby enhancing conjugation efficiency. Together, these findings unveil a previously unappreciated role for partition proteins in stimulating bacterial conjugation, providing new insights into how plasmids coordinate vertical and horizontal dissemination, highlighting that these processes can occur simultaneously within bacterial communities. IMPORTANCE Plasmid partition systems are classified into three types. While some systems have been reported to influence conjugative transfer, this study uncovers a novel mechanism utilized by a Type I system to enhance DNA transfer. Strikingly, repeat sequences perfectly matching theparS_NAHsite—bound by ParB to activate downstream conjugative transfer genes—were identified on both plasmids and chromosomes across diverse proteobacterial taxa. Furthermore, many of these repeat sequences were localized near genes involved in conjugative transfer and partitioning, suggesting the presence of a conserved regulatory mechanism mediated by these repeats. This study provides important insights into how plasmid partition systems coordinate both vertical and horizontal dissemination. Such knowledge is essential for understanding and mitigating the spread of antibiotic resistance and other plasmid-encoded traits, and it offers a foundation for developing strategies to manage plasmid-associated genetic exchange.

<jats:title>Abstract</jats:title><jats:sec> <jats:title>Background</jats:title> <jats:p>γ-Hexachlorocyclohexane (γ-HCH), an organochlorine insecticide of anthropogenic origin, is a persistent organic pollutant (POP) that causes environmental pollution concerns worldwide. Although many γ-HCH-degrading bacterial strains are available, inoculating them directly into γ-HCH-contaminated soil is ineffective because of the low survival rate of the exogenous bacteria. Another strategy for the bioremediation of γ-HCH involves the use of transgenic plants expressing bacterial enzyme for γ-HCH degradation through phytoremediation.</jats:p> </jats:sec><jats:sec> <jats:title>Results</jats:title> <jats:p>We generated transgenic <jats:italic>Arabidopsis thaliana</jats:italic> expressing γ-HCH dehydrochlroninase LinA from bacterium <jats:italic>Sphingobium japonicum</jats:italic> strain UT26. Among the transgenic <jats:italic>Arabidopsis</jats:italic> T2 lines, we obtained one line (A5) that expressed and accumulated LinA well. The A5-derived T3 plants showed higher tolerance to γ-HCH than the non-transformant control plants, indicating that γ-HCH is toxic for <jats:italic>Arabidopsis thaliana</jats:italic> and that this effect is relieved by LinA expression. The crude extract of the A5 plants showed γ-HCH degradation activity, and metabolites of γ-HCH produced by the LinA reaction were detected in the assay solution, indicating that the A5 plants accumulated the active LinA protein. In some A5 lines, the whole plant absorbed and degraded more than 99% of γ-HCH (10 ppm) in the liquid medium within 36 h.</jats:p> </jats:sec><jats:sec> <jats:title>Conclusion</jats:title> <jats:p>The transgenic <jats:italic>Arabidopsis</jats:italic> expressing active LinA absorbed and degraded γ-HCH in the liquid medium, indicating the high potential of LinA-expressing transgenic plants for the phytoremediation of environmental γ-HCH. This study marks a crucial step toward the practical use of transgenic plants for the phytoremediation of POPs.</jats:p> </jats:sec>