Polyhydroxyalkanoates (PHAs) are a family of microbially-made polyesters commercialized as biodegradable plastics. PHA production rates are predicted to increase as concerns around environmental plastic contamination and limited fossil fuel resources have increased the importance of biodegradable and bio-based plastic alternatives. Microbially-produced PHA depolymerases are the key enzymes mediating PHA biodegradation, but only a few PHA depolymerases have been well-characterized and screens employing metagenomic sequence data are lacking. Here, we used 3,078 metagenomes to analyze the distribution of PHA depolymerases in microbial communities from diverse aquatic, terrestrial and waste management systems. We significantly expand the recognized diversity of this protein family by screening 1,914 Gb of sequence data and identifying 13,869 putative PHA depolymerases in 1,295 metagenomes. Our results indicate that PHA depolymerases are unevenly distributed across environments. We predicted the highest frequency of PHA depolymerases in wastewater systems and the lowest in marine and thermal springs. In tandem, we screened 5,290 metagenome-assembled genomes to describe the phylogenetic distribution of PHA depolymerases, which is substantially broader compared to current cultured representatives. The Proteobacteria and Bacteroidota are key lineages encoding PHA depolymerases, but PHA depolymerases were predicted from members of the Bdellovibrionota, Methylomirabilota, Actinobacteriota, Firmicutes, Spirochaetota, Desulfobacterota, Myxococcota and Planctomycetota.

中文翻译：

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细菌多羟基链烷酸酯生物塑性降解基因的系统发育和全局分布

聚羟基链烷酸酯（PHA）是一类由微生物制成的聚酯，商品化为可生物降解的塑料。随着对环境塑料污染的关注和有限的化石燃料资源增加了可生物降解和生物基塑料替代品的重要性，预计PHA生产率将提高。微生物生产的PHA解聚酶是介导PHA生物降解的关键酶，但是只有少数PHA解聚酶具有良好的特性，缺乏使用宏基因组序列数据进行的筛选。在这里，我们使用了3,078个基因组，分析了来自各种水生，陆地和废物管理系统的PHA解聚酶在微生物群落中的分布。通过筛选1,914 Gb的序列数据并鉴定13个，我们大大扩展了该蛋白家族的公认多样性。1,295个基因组中有869个推定的PHA解聚酶。我们的结果表明，PHA解聚酶在整个环境中分布不均。我们预测了废水系统中PHA解聚酶的最高频率，而在海洋和温泉中则最低。同时，我们筛选了5290个由元基因组组装的基因组，以描述PHA解聚酶的系统发育分布，与当前培养的代表相比，其分布范围要广得多。Proteobacteria和Bacteroidota是编码PHA解聚酶的关键谱系，但是从Bdellovibrionota，Methylomirabilotlota，Actinobacteriota，Firmicutes，Spirochaetota，Desulfobacterota，Myxococcota和Planctomycetota的成员预测到PHA解聚酶。我们的结果表明，PHA解聚酶在整个环境中分布不均。我们预测了废水系统中PHA解聚酶的最高频率，而在海洋和温泉中则最低。同时，我们筛选了5290个由元基因组组装的基因组，以描述PHA解聚酶的系统发育分布，与当前培养的代表相比，其分布范围要广得多。Proteobacteria和Bacteroidota是编码PHA解聚酶的关键谱系，但是从Bdellovibrionota，Methylomirabilotlota，Actinobacteriota，Firmicutes，Spirochaetota，Desulfobacterota，Myxococcota和Planctomycetota的成员预测到PHA解聚酶。我们的结果表明，PHA解聚酶在整个环境中分布不均。我们预测了废水系统中PHA解聚酶的最高频率，而在海洋和温泉中则最低。同时，我们筛选了5290个由元基因组组装的基因组，以描述PHA解聚酶的系统发育分布，与当前培养的代表相比，其分布范围要广得多。Proteobacteria和Bacteroidota是编码PHA解聚酶的关键谱系，但是从Bdellovibrionota，Methylomirabilotlota，Actinobacteriota，Firmicutes，Spirochaetota，Desulfobacterota，Myxococcota和Planctomycetota的成员预测到PHA解聚酶。290个由元基因组组装的基因组，用于描述PHA解聚酶的系统发育分布，与当前培养的代表相比，其分布范围要广得多。Proteobacteria和Bacteroidota是编码PHA解聚酶的关键谱系，但是从Bdellovibrionota，Methylomirabilotlota，Actinobacteriota，Firmicutes，Spirochaetota，Desulfobacterota，Myxococcota和Planctomycetota的成员预测到PHA解聚酶。290个由元基因组组装的基因组，用于描述PHA解聚酶的系统发育分布，与当前培养的代表相比，其分布范围要广得多。Proteobacteria和Bacteroidota是编码PHA解聚酶的关键谱系，但是从Bdellovibrionota，Methylomirabilotlota，Actinobacteriota，Firmicutes，Spirochaetota，Desulfobacterota，Myxococcota和Planctomycetota的成员预测到PHA解聚酶。