Dataset Information

The Plastisphere - Uncovering tightly attached plastic "specific" microorganisms.

ABSTRACT: In order to understand the degradation potential of plastics in the marine environment, microorganisms that preferentially colonize and interact with plastic surfaces, as opposed to generalists potentially colonising everything, need to be identified. Accordingly, it was hypothesized that i.) plastic "specific" microorganisms are closely attached to the polymeric surface and ii.) that specificity of plastics biofilms are rather related to members of the rare biosphere. To answer these hypotheses, a three phased experiment to stepwise uncover closely attached microbes was conducted. In Phase 1, nine chemically distinct plastic films and glass were incubated in situ for 21 months in a seawater flow through system. In Phase 2, a high-pressure water jet treatment technique was used to remove the upper biofilm layers to further, in Phase 3, enrich a plastic "specific" community. To proof whether microbes colonizing different plastics are distinct from each other and from other inert hard substrates, the bacterial communities of these different substrates were analysed using 16S rRNA gene tag sequencing. Our findings indicate that tightly attached microorganisms account to the rare biosphere and suggest the presence of plastic "specific" microorganisms/assemblages which could benefit from the given plastic properties or at least grow under limited carbon resources.

SUBMITTER: Kirstein IV

PROVIDER: S-EPMC6478340 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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The Plastisphere - Uncovering tightly attached plastic "specific" microorganisms.

Kirstein Inga Vanessa IV Wichels Antje A Gullans Elisabeth E Krohne Georg G Gerdts Gunnar G

PloS one 20190423 4

In order to understand the degradation potential of plastics in the marine environment, microorganisms that preferentially colonize and interact with plastic surfaces, as opposed to generalists potentially colonising everything, need to be identified. Accordingly, it was hypothesized that i.) plastic "specific" microorganisms are closely attached to the polymeric surface and ii.) that specificity of plastics biofilms are rather related to members of the rare biosphere. To answer these hypotheses ...[more]

PMID: 31013334

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Project description: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.

Project description:Despite the increasing application of biodegradable plastic mulches (BDMs) in agriculture, the colonization and succession of the attached microbial community on BDMs during their degradation processes remain poorly characterized. Here, we buried four types of commonly used BDMs, including pure polylactic acid (PLA), pure polybutylene adipate terephthalate (PBAT), and two mixtures of PLA and PBAT (85:15 and 15:85 w/w), and one classic polyethylene (PE) mulch in soil for 5 months. Both plastic components and incubation time significantly shaped the β-diversities of microbiota on the plastic mulches (p < 0.001). Meanwhile, the microbial compositions and community structures on BDMs were significantly different from PE mulch, and when excluding PE mulch, the microbiota varied more with time than by the composition of the four BDMs. The orders Burkholderiales and Pseudonocardiales were dominant on most BDMs across different time points. The genus Ramlibacter was revealed as a common biomarker for both PLA and PBAT by random-forest model, and all biomarkers for the BDMs belonged to the dominant order Burkholderiales. In addition, degradation-related and pathogen-related functional taxa were enriched in all mulches among all 40 functional groups, while surprisingly, potential pathogens were detected at higher levels on BDMs than PE. For community assembly on all mulches, the drift and dispersal processes played more important roles than selection, and in particular, the contribution of stochastic drift increased during the degradation process of BDMs while selection decreased, while the opposite trend was observed with PE mulch. Overall, our results demonstrated some degradation species and pathogens were specifically enriched on BDMs, though stochastic processes also had important impacts on the community assembly. It suggested that, similar to conventional plastic mulch, the increased usage of BDMs could lead to potential hazards to crops and human health.

Dataset Information

The Plastisphere - Uncovering tightly attached plastic "specific" microorganisms.

Publications

The Plastisphere - Uncovering tightly attached plastic "specific" microorganisms.

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