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Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes.
The ISME Journal ( IF 10.8 ) Pub Date : 2020-02-04 , DOI: 10.1038/s41396-020-0596-4 Liguan Li 1 , Arnaud Dechesne 1 , Jonas Stenløkke Madsen 2 , Joseph Nesme 2 , Søren J Sørensen 2 , Barth F Smets 1
The ISME Journal ( IF 10.8 ) Pub Date : 2020-02-04 , DOI: 10.1038/s41396-020-0596-4 Liguan Li 1 , Arnaud Dechesne 1 , Jonas Stenløkke Madsen 2 , Joseph Nesme 2 , Søren J Sørensen 2 , Barth F Smets 1
Affiliation
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The current epidemic of antibiotic resistance has been facilitated by the wide and rapid horizontal dissemination of antibiotic resistance genes (ARGs) in microbial communities. Indeed, ARGs are often located on plasmids, which can efficiently shuttle genes across diverse taxa. While the existence conditions of plasmids have been extensively studied in a few model bacterial populations, their fate in complex bacterial communities is poorly understood. Here, we coupled plasmid transfer assays with serial growth experiments to investigate the persistence of the broad-host-range IncP-1 plasmid pKJK5 in microbial communities derived from a sewage treatment plant. The cultivation conditions combined different nutrient and oxygen levels, and were non-selective and non-conducive for liquid-phase conjugal transfer. Following initial transfer, the plasmid persisted in almost all conditions during a 10-day serial growth experiment (equivalent to 60 generations), with a transient transconjugant incidence up to 30%. By combining cell enumeration and sorting with amplicon sequencing, we mapped plasmid fitness effects across taxa of the microbial community. Unexpected plasmid fitness benefits were observed in multiple phylotypes of Aeromonas, Enterobacteriaceae, and Pseudomonas, which resulted in community-level plasmid persistence. We demonstrate, for the first time, that plasmid fitness effects across community members can be estimated in high-throughput without prior isolation. By gaining a fitness benefit when carrying plasmids, members within complex microbial communities might have a hitherto unrecognised potential to maintain plasmids for long-term community-wide access.
中文翻译：
质粒通过为多种系统型提供适应性优势而在微生物群落中持续存在。
在微生物群落中广泛快速地水平传播抗生素抗性基因（ARG），促进了当前的抗生素抗性流行。实际上，ARG通常位于质粒上，可以有效地将基因跨接不同的分类单元。尽管已经在一些模型细菌种群中广泛研究了质粒的存在条件，但人们对它们在复杂细菌群落中的命运却知之甚少。在这里，我们将质粒转移分析与系列生长实验相结合，以研究宽宿主范围的IncP-1质粒pKJK5在污水处理厂产生的微生物群落中的持久性。培养条件结合了不同的养分和氧气含量，对液相结合转移没有选择性和不利性。初始转移后，在连续10天的连续生长实验（相当于60代）中，质粒几乎在所有条件下均能持久存在，瞬时转导结合物的发生率高达30％。通过结合细胞计数和排序与扩增子测序，我们绘制了跨微生物群落分类单元的质粒适应性效应。在气单胞菌，肠杆菌科和假单胞菌的多种系统型中观察到了意想不到的质粒适应性益处，这导致了社区水平的质粒持久性。我们首次证明，无需事先分离即可以高通量估算整个社区成员的质粒适应性效应。通过在携带质粒时获得健身益处，复杂微生物群落中的成员可能具有迄今无法识别的潜力，可以长期维持质粒在整个社区的访问。
更新日期：2020-02-04
中文翻译：
质粒通过为多种系统型提供适应性优势而在微生物群落中持续存在。
在微生物群落中广泛快速地水平传播抗生素抗性基因（ARG），促进了当前的抗生素抗性流行。实际上，ARG通常位于质粒上，可以有效地将基因跨接不同的分类单元。尽管已经在一些模型细菌种群中广泛研究了质粒的存在条件，但人们对它们在复杂细菌群落中的命运却知之甚少。在这里，我们将质粒转移分析与系列生长实验相结合，以研究宽宿主范围的IncP-1质粒pKJK5在污水处理厂产生的微生物群落中的持久性。培养条件结合了不同的养分和氧气含量，对液相结合转移没有选择性和不利性。初始转移后，在连续10天的连续生长实验（相当于60代）中，质粒几乎在所有条件下均能持久存在，瞬时转导结合物的发生率高达30％。通过结合细胞计数和排序与扩增子测序，我们绘制了跨微生物群落分类单元的质粒适应性效应。在气单胞菌，肠杆菌科和假单胞菌的多种系统型中观察到了意想不到的质粒适应性益处，这导致了社区水平的质粒持久性。我们首次证明，无需事先分离即可以高通量估算整个社区成员的质粒适应性效应。通过在携带质粒时获得健身益处，复杂微生物群落中的成员可能具有迄今无法识别的潜力，可以长期维持质粒在整个社区的访问。
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