Phylogenetic Distribution of Plastic-Degrading Microorganisms

ABSTRACT 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, i...

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Autores principales:	Victor Gambarini, Olga Pantos, Joanne M. Kingsbury, Louise Weaver, Kim M. Handley, Gavin Lear
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2021
Materias:	biodegradation phylogenetic distribution plastic Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/f55ffd224d1f4c089f0539183c1ba552
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spelling	oai:doaj.org-article:f55ffd224d1f4c089f0539183c1ba5522021-12-02T17:07:26ZPhylogenetic Distribution of Plastic-Degrading Microorganisms10.1128/mSystems.01112-202379-5077https://doaj.org/article/f55ffd224d1f4c089f0539183c1ba5522021-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.01112-20https://doaj.org/toc/2379-5077ABSTRACT 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.Victor GambariniOlga PantosJoanne M. KingsburyLouise WeaverKim M. HandleyGavin LearAmerican Society for Microbiologyarticlebiodegradationphylogenetic distributionplasticMicrobiologyQR1-502ENmSystems, Vol 6, Iss 1 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	biodegradation phylogenetic distribution plastic Microbiology QR1-502
spellingShingle	biodegradation phylogenetic distribution plastic Microbiology QR1-502 Victor Gambarini Olga Pantos Joanne M. Kingsbury Louise Weaver Kim M. Handley Gavin Lear Phylogenetic Distribution of Plastic-Degrading Microorganisms
description	ABSTRACT 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.
format	article
author	Victor Gambarini Olga Pantos Joanne M. Kingsbury Louise Weaver Kim M. Handley Gavin Lear
author_facet	Victor Gambarini Olga Pantos Joanne M. Kingsbury Louise Weaver Kim M. Handley Gavin Lear
author_sort	Victor Gambarini
title	Phylogenetic Distribution of Plastic-Degrading Microorganisms
title_short	Phylogenetic Distribution of Plastic-Degrading Microorganisms
title_full	Phylogenetic Distribution of Plastic-Degrading Microorganisms
title_fullStr	Phylogenetic Distribution of Plastic-Degrading Microorganisms
title_full_unstemmed	Phylogenetic Distribution of Plastic-Degrading Microorganisms
title_sort	phylogenetic distribution of plastic-degrading microorganisms
publisher	American Society for Microbiology
publishDate	2021
url	https://doaj.org/article/f55ffd224d1f4c089f0539183c1ba552
work_keys_str_mv	AT victorgambarini phylogeneticdistributionofplasticdegradingmicroorganisms AT olgapantos phylogeneticdistributionofplasticdegradingmicroorganisms AT joannemkingsbury phylogeneticdistributionofplasticdegradingmicroorganisms AT louiseweaver phylogeneticdistributionofplasticdegradingmicroorganisms AT kimmhandley phylogeneticdistributionofplasticdegradingmicroorganisms AT gavinlear phylogeneticdistributionofplasticdegradingmicroorganisms
_version_	1718381592710217728

Phylogenetic Distribution of Plastic-Degrading Microorganisms

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