Living in a bottle: Bacteria from sediment-associated Mediterranean waste and potential growth on polyethylene terephthalate

Plastic-degrading microbial communities reveal novel microorganisms, pathways, and biocatalysts for polymer degradation and bioplastic production

Plastics derived from fossil fuels are used ubiquitously owing to their exceptional physicochemical characteristics. However, the extensive and short-term use of plastics has caused environmental challenges. The biotechnological plastic conversion can help address the challenges related to plastic pollution, offering sustainable alternatives that can operate using bioeconomic concepts and promote socioeconomic benefits. In this context, using soil from a plastic-contaminated landfill, two consortia were established (ConsPlastic-A and -B) displaying versatility in developing and consuming polyethylene or polyethylene terephthalate as the carbon source of nutrition. The ConsPlastic-A and -B metagenomic sequencing, taxonomic profiling, and the reconstruction of 79 draft bacterial genomes significantly expanded the knowledge of plastic-degrading microorganisms and enzymes, disclosing novel taxonomic groups associated with polymer degradation. The microbial consortium was utilized to obtain a novel Pseudomonas putida strain (BR4), presenting a striking metabolic arsenal for aromatic compound degradation and assimilation, confirmed by genomic analyses. The BR4 displays the inherent capacity to degrade polyethylene terephthalate (PET) and produce polyhydroxybutyrate (PHB) containing hydroxyvalerate (HV) units that contribute to enhanced copolymer properties, such as increased flexibility and resistance to breakage, compared with pure PHB. Therefore, BR4 is a promising strain for developing a bioconsolidated plastic depolymerization and upcycling process. Collectively, our study provides insights that may extend beyond the artificial ecosystems established during our experiments and supports future strategies for effectively decomposing and valorizing plastic waste. Furthermore, the functional genomic analysis described herein serves as a valuable guide for elucidating the genetic potential of microbial communities and microorganisms in plastic deconstruction and upcycling.

Phototrophs as the central components of the plastisphere microbiome in coastal environments

Upon entering the marine environment, plastics are colonized by a plethora of microorganisms to form a plastisphere, influencing the fate and transport of the plastic debris and the health of marine ecosystems. The assembly of marine plastisphere is generally believed to be dominated by stochastic processes. However, it remains elusive whether microbial interaction in the assembly of plastisphere microbial communities is conserved or not. We analyzed the plastisphere microbiomes of 137 plastic debris samples from intertidal zones at different geographical locations and habitats (seagrass, coral, mangrove, beach, and open ocean) and compared them with the surrounding sediment and seawater microbiomes. Microbial community structures of the plastisphere from different locations were more similar to each other but differed substantially from the surrounding sediment and water microbiomes, implying a common mechanism of plastisphere assembly. We used different machine learning algorithms (Multinomial Logistic Regression, Support Vector Machine, Decision Trees, Random Forest, and Artificial Neural Networks) to classify plastic debris samples with high sensitivity based on the microbiome composition. Eukaryotic and prokaryotic phototrophic organisms such as green algae, diatoms, and cyanobacteria, were found to be enriched on the plastic surfaces. Network analysis revealed the central role of the phototrophic organisms in the formation and sustenance of the plastispheres. We found that phototrophs served as core members interacting strongly with heterotrophic organisms in marine plastisphere, irrespective of the sampling location, habitats, and polymer types. This would explain the stochastic assembly of the plastisphere along with conserved properties driven by the phototrophs in the surrounding environment. Our results highlight the importance of phototrophic organisms in shaping the marine plastisphere microbial communities.

Culturing the Plastisphere: comparing methods to isolate culturable bacteria colonising microplastics

Microplastics quickly become colonised by diverse microbial communities, known as the Plastisphere. There is growing concern that microplastics may support the enrichment and spread of pathogenic or antimicrobial resistant microorganisms, although research to support the unique role of microplastics in comparison to control particles remains inconclusive. Limitations to this research include the microbiological methods available for isolating adhered microbes. Culture-based methods provide some of the most established, accessible and cost-effective microbiological protocols, which could be extremely useful in helping to address some of the remaining key questions in Plastisphere research. Previous works have successfully cultured bacteria from plastics, but these have not yet been reviewed, nor compared in efficiency. In this study, we compared four common biofilm extraction methods (swabbing, sonication, vortexing, sonication followed by vortexing) to extract and culture a mixed community of bacteria from both microplastic (polyethylene, polypropylene and polystyrene) and control (wood and glass) particles. Biofilm extraction efficiency and viability of bacterial suspension was determined by comparing CFU/mL of four different groups of bacteria. This was verified against optical density and 16S rRNA qPCR. Overall, we found that all tested methods were able to remove biofilms, but to varying efficiencies. Sonicating particles with glass beads for 15 min, followed by vortexing for a further minute, generated the highest yield and therefore greatest removal efficiency of culturable, biofilm-forming bacteria.

Biofilms retard the desorption of benzo(a)pyrene from polyethylene pellets in the marine environment

Microplastics are emerging as vectors for the transport hydrophobic organic compounds (HOCs) in aquatic environments, however, their impact is poorly understood due to the lack of field studies. In this study, the pristine and benzo(a)pyrene (B[a]P) adsorbed polyethylene (PE) pellets were placed at Haihe Estuary (Tianjin, China) for 80 days to investigate desorption behavior. Combining laboratory and in situ experiments, this study firstly verified that the intra-particle diffusion was the rate-limiting step for the desorption process of B[a]P from PE microplastics under different environmental conditions. By hindering the desorption and modifying MPs surface, biofilm might play a key role in desorption process, leading to the apparent hysteresis of the field desorption process at our time scale. Potential degradation of the polymer and B[a]P by biofilms, however, would support continuing desorption. The study explored the interaction of biofilm and MPs-contaminants mixture and its implications for the environmental fate of HOCs.

Anion Exchange Membranes Based on Chemical Modification of Recycled PET Bottles

This study presents an innovative and effective solution for recycling PET bottles as raw for producing anion exchange membranes (AEMs) for electrochemical applications. This approach reduces the demand for pristine materials, a key principle of the circular economy and sustainability. PET was subjected to chemical modification by introducing cationic functional groups followed by methylation and OH- exchange process. The amination synthesis was optimized based on reaction time. The results indicate that ion exchange capacity, water uptake, and swelling ratio properties mainly depend on the degree of cationic functionalization. The optimized AEM exhibits ionic conductivity of 5.3 × 10-2 S·cm-1 and alkaline stability of 432 h in 1 M KOH at 80 °C. The membrane properties before and after the alkaline treatment were investigated using Fourier-transform infrared spectroscopy, thermogravimetric analysis, and scanning electron microscopy analysis. Computational chemistry analysis was employed to gain further insights into the membrane degradation mechanisms and pathways under alkaline conditions. This research and its findings are a step toward using recycled materials in the field of AEM technology.

Bacterial community succession and the enrichment of antibiotic resistance genes on microplastics in an oyster farm

Microplastics can be colonized by microorganisms and form plastisphere. However, knowledge of bacterial community succession and the enrichment of antibiotic resistance genes (ARGs) and pathogens on microplastics in aquaculture environments is limited. Here, we conducted a 30-day continuous exposure experiment at an oyster farm. Results showed that the alpha-diversity of communities on most microplastics continuously increased and was higher than in planktonic communities after 14 days. Microplastics could selectively enrich certain bacteria from water which can live a sessile lifestyle and promote colonization by other bacteria. The composition and function of plastisphere communities were distinct from those in the surrounding water and influenced by polymer type and exposure time. Microplastics can enrich ARGs (sul1, qnrS and blaTEM) and harbor potential pathogens (e.g., Pseudomonas aeruginosa). Therefore, microplastic pollution may pose a critical threat to aquaculture ecosystems and human health. Our study provides further insight into the ecological risks of microplastics.

Gillisia lutea sp. nov., isolated from marine aluminium residues from the Mediterranean sea

A novel Gram-reaction-negative, facultatively anaerobic, rod-shaped, non-motile, non-spore forming, orange-pigmented bacterium identified as M10.2AT, was isolated from marine residues submerged on the Malva-rosa beach (València, Spain), on the western coast of the Mediterranean Sea. This strain was catalase-positive and oxidase-negative and grew under mesophilic, neutrophilic and halophilic conditions. With respect to the 16S rRNA gene sequences, M10.2AT showed similarities with Gillisia mitskevichiae DSM 19839T and Gillisia hiemivida IC154T (97.57 and 97.50 % gene sequence similarity, respectively). The genome of M10.2AT was sequenced and has been deposited in the DDBJ/ENA/GenBank databases under the accession code JAKGTH000000000. The genomic DNA G+C content was 36.13 %. Its adscription to a novel species of the genus Gillisia was confirmed by the genomic indexes average nucleotide identity by blast (ANIb) and digital DNA-DNA hybridisation (dDDH). The major fatty acids were iso-C15 : 0, iso-C15 : 1G, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). According to the results of this polyphasic study, strain M10.2AT represents a novel species of the genus Gillisia, for which name Gillisia lutea sp. nov. (type strain M10.2AT = CECT 30308T = DSM 112385T) is proposed.

Shell disease syndromes of decapod crustaceans

The term shell disease subsumes a number of debilitating conditions affecting the outer integument (the carapace) of decapod crustaceans, such as lobsters and crabs. Herein, we seek to find commonality in the aetiology and pathology of such conditions, and those cases that result in the progressive erosion of the cuticle through to the visceral tissues by a cocktail of microbial-derived enzymes including lipases, proteases and chitinases. Aquimarina spp. are involved in shell disease in many different crustaceans across a wide geographical area, but the overall view is that the condition is polymicrobial in nature leading to dysbiosis within the microbial consortium of the damaged cuticle. The role of environment, decapod behaviour and physiology in triggering this disease is also reviewed. Finally, we provide a conceptual model for disease aetiology and suggest several avenues for future research that could improve our understanding of how such factors trigger, or exacerbate, this condition.

Contaminants from a former Croatian coal sludge dictate the structure of microbiota in the estuarine (Raša Bay) sediment and soil

Introduction

Croatian superhigh-organic-sulfur Raša coal had been mined for nearly 400 years. The release of hazardous trace elements (HTEs) and toxic organic pollutants (TOPs) into the local environment by coal mining, preparation, and combustion activities has resulted in pollution.

Methods

In this study, the diversity and composition of microbial communities in estuarine sediment and soil samples as well as community function responses to the pollutants were investigated.

Results

The results showed that PAH degradation does occur following 60 years of natural attenuation, the location is still heavily polluted by polycyclic aromatic hydrocarbons (PAHs) and HTEs. Microbial analyses have shown that high concentrations of PAHs have reduced the diversity and abundance of microbial communities. The pollution exerted an adverse, long-term impact on the microbial community structure and function in the brackish aquatic ecosystem. Microorganisms associated with the degradation of PAHs and sulfur-containing compounds have been enriched although the diversity and abundance of the microbial community have reduced. Fungi which are believed to be the main PAH degrader may play an important role initially, but the activity remains lower thereafter. It is the high concentrations of coal-derived PAHs, rather than HTEs, that have reduced the diversity and abundance of microbial communities and shaped the structure of the local microbiota.

Discussion

This study could provide a basis for the monitoring and restoration of ecosystems impacted by coal mining activities considering the expected decommission of a large number of coal plants on a global scale in the coming years due to growing global climate change concerns.

Maritalea mediterranea sp. nov., isolated from marine plastic residues

A novel Gram-reaction-negative, aerobic, motile, rod-shaped, grey bacterium, strain P4.10X^T, was isolated from plastic debris sampled from shallow waters in the Mediterranean Sea (Valencia, Spain). P4.10X^T was catalase- and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA gene sequences revealed that P4.10X^T was closely related to Maritalea myrionectae DSM 19524^T and Maritalea mobilis E6^T (98.25 and 98.03 % sequence similarity, respectively). The DNA G+C content of the genome sequence of P4.10X^T was 53.66 %. The genomic indexes average nucleotide identity by blast (ANIb) and digital DNA-DNA hybridization (dDDH) confirmed its classification as representing a novel species of the genus Maritalea. The predominant fatty acids were summed feature 8 (C_18 : 1ω7c/C_{18 : 1}ω6c) and C_18 : 1 ω7c 11-methyl. The results of this polyphasic study confirm that P4.10X^T represents a novel species of the genus Maritalea, for which the name Maritalea mediterranea sp. nov. is proposed (type strain P4.10X^T=CECT 30306^T = DSM 112386^T).

Microplastics influence the fate of antibiotics in freshwater environments: Biofilm formation and its effect on adsorption behavior

Microplastics (MPs) are substrates available for biofilms colonization in natural water environments. The biofilms formation may enhance the ability of MPs to adsorb harmful contaminants. Herein, we investigated the biofilms formation of three different MPs (PVC, PA and HDPE) in simulated natural environment, and observed the chemical structure, charge property, hydrophobicity and other properties of MPs affect microbial biomass and community composition. More importantly, potential pathogens were found in all three MPs biofilms. Furthermore, the adsorption capacities of original MPs and biological aging MPs for norfloxacin (NOR) was compared. HDPE has the largest adsorption capacity for NOR, while PA has the smallest adsorption capacity for NOR. It was concluded that the formation of biofilms enhanced the adsorption of NOR by 50.60 %, 24.17 % and 46.02 % for PVC, PA and HDPE, respectively. In addition, hydrogen-bond interaction, electrostatic interaction and hydrophobic interaction were found to dominate the adsorption of NOR by MPs. Our study contributed to improve the understanding of the interactions between aging MPs and contaminants in the natural water environments, and provided essential information for ecological risk assessment of MPs.

Bacterial colonization dynamics of different microplastic types in an anoxic salt marsh sediment and impact of adsorbed polychlorinated biphenyls on the plastisphere

Plastic debris dispersed into the environment provide a substrate for microbial colonization, constituting a new human-made ecosystem called "plastisphere", and altering the microbial species distribution in aquatic, coastal and benthic ecosystems. The study aims at exploring the interaction among microplastics (MPs) made of different polymers, a persistent organic contaminant (polychlorinated biphenyls, PCBs), and the environmental microbial communities, in an anoxic marine sediment. Plastic pellets were incubated in the field in a salt marsh anoxic sediment, to observe the stages of plastisphere formation, by quantitative PCR and 16S rRNA gene sequencing, and PCB dechlorination activity on the MPs surface. Microbes from the sediment rapidly colonized the different microplastics types, with PVC recruiting a peculiar community enriched in sulfate-reducing bacteria. The composition of the plastisphere varied along the 1-year incubation possibly in response either to warmer temperatures in spring-summer or to microhabitat's changes due to the progressive plastic surface weathering. Even if PCB contaminated MPs were able to recruit potentially dehalogenating taxa, actual dechlorination was not detectable after 1 year. This suggests that the concentration of potentially dehalorespiring bacteria in the natural environment could be too low for the onset of the dechlorination process on MP-sorbed contaminants. Our study, which is among very few available longitudinally exploring the plastisphere composition in an anoxic sediment context, is the first exploring the fate and possible biodegradation of persistent organic pollutants sorbed on MPs reaching the seafloor.

Multimodal analysis of south-eastern Black Sea sediment bacterial population diversity

This study focused on marine sediments from the Black Sea, mainly due to bacterial diversity-induced public health / biotechnology application value. Sediment samples were gathered from 14 locations at differing depths across Turkish shores on a seasonal basis over 10 months, with bacterial identifications performed through using multimodal analytical platforms. Overall, 26 differing, predominantly Gram-positive (57.5 %) bacterial species were identified for this region, including Bacillaceae (50.0 %) and Pseudomonadaceae (15.0 %). The most dominant classes were identified as Bacilli (52.5 %) and Gammaproteobacteria (40.0 %). Ten isolates (25 %) to the species level and thirty-six isolates (90 %) to the genus level were identified using VITEK® MS and Bruker Microflex® LT/SH, in comparison to 16S rRNA sequencing results. Identified species - particularly, novel reported species - can contribute to the knowledge of microbial life dwelling upon sediments of the south-eastern regions of the Black Sea.