Phylogenetic Distribution of Plastic-Degrading Microorganisms.
Phylogenetic Distribution of Plastic-Degrading Microorganisms.
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DOI：
10.1128/msystems.01112-20
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发表时间：
2021-01-19
期刊：
影响因子：
6.4
通讯作者：
Lear G
中科院分区：
文献类型：
--
作者：
Gambarini V;Pantos O;Kingsbury JM;Weaver L;Handley KM;Lear G
我们整理了迄今为止鉴定出的能够降解塑料的最完整的微生物数据库。这些数据使我们能够探索这些生物及其酶的系统发育分布，表明塑料降解的特征主要不是系统发育上保守的。据报道，塑料降解微生物的数量正在迅速增加，这使得在不同的微生物生命树中探索假定的塑料降解特性的保存和分布成为可能。传统的高分子量聚合物，包括聚酰胺、聚苯乙烯、聚氯乙烯和聚丙烯，被认为是降解者，它们广泛分布在生命之树的细菌和真菌分支中，尽管这些分类群中大多数降解塑料的证据似乎有限。相比之下，我们发现了合成聚合物聚乳酸（PLA）的强降解证据，并且与其降解相关的微生物物种在系统发育上保守于假心科细菌家族。我们整理了与所有类型塑料降解相关的基因和酶的数据，通过挖掘公开的微生物基因组，确定了16,170种假定的塑料降解同源物。天然聚合物聚羟基丁酸酯（PHB）的邻位化合物数量最多，为10,969个，其次是合成聚合物聚对苯二甲酸乙二醇酯（PET）和聚己内酯（PCL），分别有8,233个和6,809个邻位化合物。这些同源基因是在6000种微生物的基因组中发现的，其中大多数尚未被确定为塑料降解物。此外，所有这些物种都属于12个不同的微生物门，其中只有7门被报道为降解物。我们在交互式和可更新的系统发育树和数据库中集中了报道的塑料降解微生物的信息，以确认假定的塑料降解分类群的全球和系统发育多样性，并为微生物塑料降解能力的进化提供新的见解和未来发现的途径。重要性：我们整理了迄今为止被鉴定为能够降解塑料的最完整的微生物数据库。这些数据使我们能够探索这些生物及其酶的系统发育分布，表明塑料降解的特征主要不是系统发育上保守的。我们在12个不同门的基因组中发现了16170个假定的塑料降解同源物，这表明在其他分类群中探索这些特征具有巨大的潜力。除了使数据库可供科学界使用外，我们还创建了一个交互式的系统发育树，可以显示所有整理的信息，促进数据的可视化和探索。数据库和树都定期更新，以跟上新的科学报告。我们希望通过增加对微生物塑料降解特性的遗传多样性和进化的理解，我们的工作将为该领域做出贡献。
We have collated the most complete database of microorganisms identified as being capable of degrading plastics to date. These data allow us to explore the phylogenetic distribution of these organisms and their enzymes, showing that traits for plastic degradation are predominantly not phylogenetically conserved. The number of plastic-degrading microorganisms reported is rapidly increasing, making it possible to explore the conservation and distribution of presumed plastic-degrading traits across the diverse microbial tree of life. Putative degraders of conventional high-molecular-weight polymers, including polyamide, polystyrene, polyvinylchloride, and polypropylene, are spread widely across bacterial and fungal branches of the tree of life, although evidence for plastic degradation by a majority of these taxa appears limited. In contrast, we found strong degradation evidence for the synthetic polymer polylactic acid (PLA), and the microbial species related to its degradation are phylogenetically conserved among the bacterial family Pseudonocardiaceae. We collated data on genes and enzymes related to the degradation of all types of plastic to identify 16,170 putative plastic degradation orthologs by mining publicly available microbial genomes. The plastic with the largest number of putative orthologs, 10,969, was the natural polymer polyhydroxybutyrate (PHB), followed by the synthetic polymers polyethylene terephthalate (PET) and polycaprolactone (PCL), with 8,233 and 6,809 orthologs, respectively. These orthologous genes were discovered in the genomes of 6,000 microbial species, and most of them are as yet not identified as plastic degraders. Furthermore, all these species belong to 12 different microbial phyla, of which just 7 phyla have reported degraders to date. We have centralized information on reported plastic-degrading microorganisms within an interactive and updatable phylogenetic tree and database to confirm the global and phylogenetic diversity of putative plastic-degrading taxa and provide new insights into the evolution of microbial plastic-degrading capabilities and avenues for future discovery. IMPORTANCE We have collated the most complete database of microorganisms identified as being capable of degrading plastics to date. These data allow us to explore the phylogenetic distribution of these organisms and their enzymes, showing that traits for plastic degradation are predominantly not phylogenetically conserved. We found 16,170 putative plastic degradation orthologs in the genomes of 12 different phyla, which suggests a vast potential for the exploration of these traits in other taxa. Besides making the database available to the scientific community, we also created an interactive phylogenetic tree that can display all of the collated information, facilitating visualization and exploration of the data. Both the database and the tree are regularly updated to keep up with new scientific reports. We expect that our work will contribute to the field by increasing the understanding of the genetic diversity and evolution of microbial plastic-degrading traits.