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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.

The ubiquity of plastic debris in marine environments raises the question, what impacts do plastics have on our marine microbiota? To investigate this, we applied bacterial 16S rRNA gene and fungal ITS2 region sequencing to identify changes in microbial biofilm community compositions on marine plastic, over time. We sampled biofilm on virgin linear low-density polyethylene (LLDPE), nylon-6 (PA) and glass after 2, 6 and 12 weeks of constant immersion in Te Whakaraupō-Lyttelton Harbour, Aotearoa-New Zealand. Of the prokaryotes, Proteobacteria and Bacteroidetes were predominant in all samples and Verrucomicrobiota were most abundant in mature biofilms. Microbial communities on the three substrate types were significantly distinct from those in the surrounding seawater, regardless of age, but not between attachment substrates. Bacterial communities occurring two weeks after immersion and fungal communities at six weeks were found to vary more among substrate types than at other times; however, no significant substrate-specific communities were identified overall. Taxa closely related to previously reported plastic-biodegrading species were found in very low abundance across all substrates, including on the glass slides. Our findings suggest that microorganisms do not selectively persist on the LLDPE or PA surfaces to gain significant direct metabolic benefit, instead using these plastics primarily as an attachment surface on which they form generalist biofilm communities.

Plastic pollution is one of our most pressing environmental challenges, with billions of tons of plastic waste accumulating in our ecosystems. While recycling helps, it cannot fully address this crisis, making it crucial to find new solutions. Our study reveals how a common soil fungus, Clonostachys rosea , can break down certain plastics, specifically polycaprolactone and polyethylene terephthalate. We identified the exact genes and enzymes responsible for this ability and showed how different environmental conditions affect the fungus's plastic-degrading capabilities. Notably, we discovered that adding glucose completely stops the fungus from breaking down plastic, suggesting that careful control of growth conditions is essential for effective plastic degradation. These findings are significant because they provide a detailed blueprint for optimizing plastic biodegradation using fungi, potentially leading to more effective ways to tackle plastic pollution. This research represents a crucial step toward developing practical, environmentally friendly solutions for plastic waste management.

Drought is one of the main problems linked to climate change that is faced by agriculture, affecting various globally important crops, including sugarcane. Environmentally sustainable strategies have been sought to mitigate the effects of climate change on crops. Among them, the use of beneficial microorganisms offers a promising approach. However, it is still necessary to understand the mechanisms that regulate plant-microorganism interactions, in normal situations and under stress. In this work, the rhizosphere metagenomes of two sugarcane varieties, one resistant and the other susceptible to drought, were compared under normal conditions and under water-limiting conditions. The results showed that for the drought-resistant sugarcane variety, bacteria belonging to the order Sphingomonadales and the family Xanthomonadaceae presented increased activities in terms of mobility, colonization, and cell growth. In contrast, the rhizosphere associated with the drought-sensitive variety exhibited increases of bacteria belonging to the family Polyangiaceae, and the genus Streptomyces, with modifications in DNA metabolism and ribosome binding proteins. The results pointed to variation in the rhizosphere microbiota that was modulated by the host plant genotype, revealing potential bacterial candidates that could be recruited to assist plants during water-limiting conditions.

Background Plastic pollution is a severe threat to marine ecosystems. While some microbial enzymes can degrade certain plastics, the ability of the global ocean microbiome to break down diverse environmental plastics remains limited. We employed metatranscriptomic data from an international ocean survey to explore global and regional patterns in microbial plastic degradation potential. Results On a global oceanic scale, we found no significant correlation between levels of plastic pollution and the expression of genes encoding enzymes putatively identified as capable of plastic degradation. Even when looking at different regional scales, ocean depth layers, or plastic types, we found no strong or even moderate correlation between plastic pollution and relative abundances of transcripts for enzymes with presumed plastic biodegradation potential. Our data, however, indicate that microorganisms in the Southern Ocean show a higher potential for plastic degradation, making them more appealing candidates for bioprospecting novel plastic-degrading enzymes. Conclusion Our research contributes to understanding the complex global relationship between plastic pollution and microbial plastic degradation potential. We reveal that the transcription of putative plastic-degrading genes in the global ocean microbiome does not correlate to marine plastic pollution, highlighting the ongoing danger that plastic poses to marine environments threatened by plastic pollution.

Impacts of Marine Plastic Debris (MPD) on marine ecosystems are among the most critical environmental concerns of the past three decades. Virgin plastic is often cheaper to manufacture than recycled plastics, increasing rates of plastic released into the environment and thereby impacting ecosystem health and functioning. Along with other environmental effects, MPD can serve as a vector for marine hitchhikers, facilitating unwanted organisms’ transport and subsequent spread. Consequently, there is a growing demand for more eco-friendly replacements of conventional plastic polymers, ideally with fit-for-purpose properties and a well-understood life cycle. We enriched polybutylene succinate (PBS) with three different concentrations of oyster shell to investigate the dynamics of biofouling formation over 18 weeks at the Nelson Marina, Aotearoa/New Zealand. Our study focused on oyster shell concentration as a determinant of fouling assemblages over time. While generally considered as a waste in the aquaculture sector, we used oyster shells as a variable of interest to investigate their potential for both, environmental and economic benefits. Using bacterial 16S and eukaryotic 18S rRNA gene metabarcoding, our results revealed that following immersion in seawater, time played a more critical role than substrate type in driving biofouling community structures over the study period. In total, 33 putative non-indigenous species (NIS) and 41 bacterial families with putative plastic-degrading capability were detected on the different substrates. Our analysis of NIS recruitment revealed a lower contribution of NIS on shell-enriched substrates than unadulterated polymers samples. In contrast, the different concentrations of oyster shells did not affect the specific recruitment of bacterial degraders. Taken together, our results suggest that bio-based polymers and composites with increased potential for biodegradability, recyclability, and aptitude for the selective recruitment of marine invertebrates might offer a sustainable alternative to conventional polymers, assisting to mitigate the numerous impacts associated with MPD.

BackgroundThe gut microbiota is a key element to support host homeostasis and the development of the immune system. The relationship between the microbiota and immunity is a 2-way road, in which the microbiota contributes to the development/function of immune cells and immunity can affect the composition of microbes. In this context, natural killer T cells (NKT cells) are distinct T lymphocytes that play a role in gut immunity and are influenced by gut microbes. In our work, we investigated the involvement of invariant NKT cells (iNKT) in intestinal homeostasis.ResultsWe found that iNKT-deficient mice (iNKT-KO) had reduced levels of fecal IgA and an altered composition of the gut microbiota, with increased Bacteroidetes. The absence of iNKT cells also affected TGF-β1 levels and plasma cells, which were significantly reduced in knockout (KO) mice. In addition, when submitted to dextran sodium sulfate colitis, iNKT-KO mice had worsening of colitis when compared with wild-type (WT) mice. To further address iNKT cell contribution to intestinal homeostasis, we adoptively transferred iNKT cells to KO mice, and they were submitted to colitis. Transfer of iNKT cells improved colitis and restored fecal IgA levels and gut microbiota.ConclusionsOur results indicate that intestinal NKT cells are important modulators of intestinal homeostasis and that gut microbiota composition may be a potential target in the management of inflammatory bowel diseases.Our work demonstrates the important role of invariant natural killer T cells (iNKT cells) as modulators of gut homeostasis. Lack of iNKT cells in knockout mice results in lower levels of fecal IgA and TGF-β1, altered gut microbiota, and increased susceptibility to colitis.

Microbial degradation provides an avenue for the remediation of select plastic polymers contributing to the urgent environmental problem of global plastic pollution. We demonstrate the degradation of polycaprolactone (PCL) by Clonostachys rosea and elucidate its underlying molecular mechanisms. We constructed the genome of this fungal strain and monitored changes in gene expression when exposed to PCL. Twelve genes linked to PCL degradation were found in the genome of C. rosea, and some of them were upregulated in the presence of the plastic, including genes coding for two cutinases. We heterologously expressed the enzymes coded by both genes and confirmed their activity against PCL polymers. We also demonstrate that one of the enzymes was active against polyethylene terephthalate (PET) polymers. Glucose inhibited the expression of both genes, completely halting the plastic biodegradation process, possibly serving as a preferred and readily metabolisable carbon source compared with PCL. We confirm the presence of key metabolic pathways linked to PCL degradation in C. rosea, including fatty acid degradation, providing further evidence of the mechanisms central to plastic biodegradation.

In children with anorectal malformations (ARMs), it is essential to have a diagnostic imaging method that helps with the evaluation of the internal anatomy. In patients with a persistent cloaca, an ARM variant, in which the measurement of the urethral channel and common channel determines surgical management, there are multiple options for imaging. Magnetic resonance imaging (MRI) is an excellent method for this purpose, from which accurate measurements of channel length can be obtained. Additionally, the use of volumetric/isotropic sequences allows multiplanar reformatting. We present our experience with pelvic MRI and intracavitary non-paramagnetic contrast (MR genitography). This method uses volumetric T2-weighted images and the instillation of saline solution as a contrast agent to distinguish the common channel, length of the urethra, anatomy of the vagina, and presence and location of the rectal fistula. We believe this technique to be particularly useful for those working in settings with limited MRI resources.