Plastisphere microbiome: Methodology, diversity, and functionality

Broad topics of the plastisphere in various environments are reviewed, including its methodologies, diversity, functionality, and outlook. Due to their durability, malleability, low cost, plastics have become an integral material industrial consumer products [1]. Global plastic production has enormously grown from 1.5 million metric tonnes 1950 367 2020 [2]. Despite remarkable benefits convenience human lives, awareness about negative environmental impacts increased because vast amount waste. It is estimated that approximately 12,000 waste will be accumulated globally by 2050 [3]. Under action external forces, for example, solar radiation, physical abrasion, biological degradation, large pieces can break down into smaller particles, generating microplastics (diameter < 5 mm) [4-6]. Accumulating studies show ubiquitous throughout environments, marine, freshwater, atmospheric, soil ecosystems, even remotest areas planet [7-11]. Their presence persistence raised significant concerns as ingested subsequently transmitted higher trophic-level organisms through food chain, thus harm biodiversity ecosystems [12-14]. As exogenous hydrophobic substrate, microplastic surfaces provide a unique niche growth proliferation diversity microorganisms, constituting distinct ecological habitat called “plastisphere” [15-17]. Following development modern molecular methods emerging bioinformatics tools, application high-throughput DNA sequencing increasing our understanding diverse microorganisms inhabit [18, 19]. However, consensus lacking scientific community on characteristics plastisphere. For instance, previous dominantly reported microbial communities showed different compositional structures compared with living surrounding whereas several observed similar [20, 21]. The could or lower than [22, 23]. Additionally, functions may within [24, 25]. Plastisphere focused initially marine environment gradually extended freshwater indoor house [26-30]. matrices also limited definitive answers Several critical questions concerning remain unclear. Currently, whether really recruit specific unknown, few clearly illustrated processes shaping assembly microplastics. How stochastic deterministic influence unclear, knowledge gaps exist adverse effects pose ecosystem. Therefore, this review, peer-reviewed journal articles investigated were searched using Web Science (http://apps.webofknowledge.com/) keywords “microplastic(s)” (Figure S1), study designs characterization exploring consequently discussed. composition, underlying mechanisms estimated. We end considering important unanswered field future research priorities. This review provides comprehensive interpretation communities. Dr. Erik Zettler colleagues first established concept 2013 S1). High-throughput method was used characterize heterotrophs, autotrophs, predators, symbionts debris collected North Atlantic [16]. study, extensively [19]. Studies ecosystem started 2014 researchers recognized originated systems. In year, Hoellein published two papers [17, 31]. One describe bacterial assemblages colonizing sampled urbanized river Chicago, Illinois, USA. other incubated plastispheres three (river, pond, artificial stream, respectively). Community compositions significantly differ respective planktonic comparison systems, more complex, containing variable proportions mineral organic matter. Tracing solid analyte sample composed solids difficult, delayed analysis later period. 2019, Huang applied farmland sampling laboratory incubation, respectively, estimate [32, 33]. same Puglisi et al. plastic-associated biofilm constructed disposal systems (landfill sites) [34]. These found diversities, compositions, co-occurrence interactions those atmosphere most recent years. 2022, Wang via incubation [35]. summary, followed detection which originates extends finally, terrestrial habitats environments. methodology manifold. general, samples routes: sampling, situ culture, laboratory-simulated experimentation (Tables S1–S3, Figure 1). studying aquatic same, experiments dominate studies. studies, collect pick up microplastics, analyze sorting liquid details. both fresh seawater samples. Manta plankton nets commonly used, particles identified selected spot 36, 37]. sediment soil, grab samplers often used; bulk sieved, putative extracted [38-40]. transferred laboratories dry ice, stored at −80°C before analysis. certain polymer types shapes then under natural conditions. After duration, collected, surface analyzed [41-43]. simulated experiments, controlled conditions (e.g., pH, nutrients, temperature) [27, 44, 45]. simulating system coupled continuous flow device [46]. microcosm usually sterilized glass containers [28, 47]. advantages disadvantages. reveal realistic selection needs performed immediately after case biofilms change. Direct visual examination naked eyes dissecting microscopes employed, would inevitably introduce non-polymer oil residues, chitin-like materials) further analyses [48]. all particles; thus, it difficult identify differences between types. Li [29] water functions, processes, interaction networks but did not Similarly, Luo [24] film residues 55 plastic-mulching croplands subtropical China report these residues. compare results free-living materials sites, helpful species features selected. polymers, shapes, colors frequently performed. Pinnell Turner [49] evaluated conventional (polyethylene terephthalate [PET]) biodegradable (polyhydroxyalkanoate [PHA]) substrates Laguna Madre lagoon northern Gulf Mexico 28 days. They intended observe structure plastispheres. Wen [50] studied functional incubating pond Yangtze Estuary, China. color-dependent. substrates. Oberbeckmann set experiment polyethylene (PE) polystyrene (PS) pellets wooden beads along coastal-to-estuarine gradient Baltic Sea, Germany [51]. requires sufficient time growth, possible maintain constant during growing Thus, faces difficulties quantifying influences characteristics. ensure recovery cultured mesh bags Recently, employed 52-55]. Zhu [28] nylon (mesh size: 50 μm) buried them investigate operation heterogeneity contact distances differ. Even though limitations, incorporation insights variables method, simulation single multiple Yang [56] reactor incubate evaluate structure. [44] rather heavy metals, stronger limitations. major concern concentration test. principle, should maximumly simulate concentrations concentrations. declared based detected concentrations, values generally [57]. Moreover, unrealistic perform scales close experienced real environment. landfill sites aged years [58]. nearly impossible duplicate setting, e.g., temperature, redox, light intensity, indigenous microorganisms. Laboratory simulations take advantage conditions, contribute community. opinion, combination above optimal formation contributing factors. Imaging technologies, such scanning electron microscopy (SEM) combinatorial labeling spectral imaging-fluorescence hybridization (CLASI-FISH), demonstrated crowded, surface-based micro-ecosystem includes range [59-61]. Over years, next-generation (NGS) technologies gained enormous popularity Most microbiome surveys amplicon metagenomic sequencing. Polymerase chain reaction (PCR) taxonomic marker gene uncover profiles marking omnipresent 2). 16S rRNA common identifying urban rivers [62]. Ogonowski explored bacterioplankton Illumina libraries substrate-driven [63]. comparison, only handful eukaryotes [64-66]. By implementing internal transcribed spacer2 metabarcoding debris, De Tender fungal genera [67]. Although second-generation technology yielded substantial data still resolution coverage. produces short reads, forcing choose barcoding regions [68]. Hence, long-read technology, third-generation Pacific Biosystems SMRT Oxford Nanopore sequencing, been composition improved classification taxa [69, 70]. Davidov 61 level Mediterranean Sea MinION [69]. shotgun whole genomic [49, 71, 72], simultaneously capture genetic present one information across kingdoms predict functions. Jessica Bryant 2016 [73]. technical analytical breakthroughs, multiomics, metatranscriptomic, proteogenomic, metabolomic approaches, enable active members acting approaches metabolic pathways confirm predictions. huge potential analyzing plastispheres, microbes enzymes degrading plastics. Wright combined proteogenomic approach biodegradation succession (PET) [72]. Wu integrated metatranscriptomic antibiotic resistomes laboratory-incubated plastisphere, demonstrating actively expressed. Future multiomic considerably deciphering roles microbial-mediated biochemical transformations. recently topic. bacteria, archaea, fungi, eukaryotes, colonize almost current work varies 3). Alpha-, Beta-, Gamma-Proteobacteria typical enriched [66, 75-77]. mainly comprises bacteria belonging phylum Proteobacteria (Alpha- Gamma-) Bacteroidetes [42, 78-80]. majority belongs phyla (Alpha-) Actinobacteria 47, 81-83]. groups, i.e., Alpha-Proteobacteria Rhodospirillaceae), consistently [62, 81, 84-86]. numbers likely surfaces. exhibits yet conclusively demonstrated. well populate column Synechococcus Prochlorococcus species) strongly diverge able associate form [87-89]. unsurprisingly, exhibit fact, any surfaces, bottles [74], ship hulls [90], platforms [91], man-made items, animals, plants, zooplankton, micro/macro-aggregates, transparent exopolymer rocks [92]. Comparing core But until now, include comparable control materials. glass, ceramic, shells, wood formed 45, 63, 93]. No occur plastics, relative abundance groups (i.e., ceramics) substantially demonstrate predominant mode life, whereby interfaces, [94], pore spaces [95], plant roots [96]. Microplastics analogous sessile lifestyles reason abundant soil. strongest early stage colonization [63] PE, PP, PS distinctly nonplastic (cellulose beads) 2 weeks Alpha- (such Rhodobacteraceae) Gamma-proteobacteria, Flavobacteria among initial colonizers fast-growing opportunistic quickly respond changes [97]. properties hydrophilicity, roughness, electric charge, affect attachment colonizers. Previous suggest preferentially hydrophilic possibly due wettability energies [61]. why intense [43]. high roughness supply points microbes, impact [98]. importance declines. variables, salinity, nutrient content, dynamic patterns stages maturation. 15°C 25°C, Sun [27] type, induced PE PLA [99] global meta-analysis largest composition. there remains no clear conclusion how prioritized factors unknown. Leached compounds is, additives oligomers, partly [43, 61]. Significantly [82, 83, 100, 101]. A nutrient-rich recruiting copiotrophic microbes. Plastic chemicals promote inhibit growth. Overall, we conclude colonization, inner play role Interesting drive maturation theories build when life. Furthermore, assemble over essential understand species, trait abundance, members, ultimately, genes Theoretically, ecologists proposed four evolutionary namely selection, dispersal, drift, diversification, principles ecology [102]. Two theoretical lines debated examine interpret assembly: niche-based theory neutral theory, [103, 104]. obtain quantitative assembly, entire-community null model (QPEN) [105] infer phylogenetic-bin-based [106] normalized stochasticity ratio (NST) [107] Sloan [108]. suggested 26]. [20] model, NST, field-sampled process drift dispersal limitation primarily contributed assembly. indicated dominant neutral-based 27, 109]. (deterministic) dominated they goodness-of-fit observations ascribed Many communities, [100]. decrease, increase Parallelly, leach owing chemotaxis, processes. scenario spatial areas, location-specific relationships obtained, probably, selection. Simultaneously, particle relocation occurs transportation local scales. Such phenomenon uncertainty estimating More needed quantitatively determine Whether weight loss ongoing question. screened polymer-degrading [110, 111]. Delacuvellerie [110] floating sediment-associated sediments hydrocarbon-degrading Alcanivorax, Marinobacter Arenibacter implying potentially involved degradation. Multiomics evaluating degradation xenobiotic particles. allow speculation residing actually Bhagwat [112] upregulation PET hydrolysis-related enzyme metagenomics, suggesting Through approach, characterized PET-degrading degradable ability 6 depends recalcitrance substrate crystallinity) accessibility demonstrates existing highly recalcitrant PS) seldom reported. metagenomics metaproteomics polymer-unspecific appear undergoing [50]. [113] PP metaproteomic metagenomes, metabolism protein level. degrade seems closely related contain very stable backbones degrade, PET, polyurethane, polycarbonate susceptible hydrolysis catalyze Further in-depth exploration genomics warranted elemental geochemical cycles. enrichment adenylyl sulfate reductase dissimilatory sulfite sediment-interface coastal lagoon, stimulation reduction [73] plastic-attached bacteria; genes, nifH, nitrogen fixation provided substantive evidence cycling [114-116]. Su [116] denitrifying activity N2O water, overlooked source. denitrifiers hypoxic utilize nitrate/nitrite acceptors sustain [116]. Rahman [117] gene-array carbon fixation, denitrification, sulfur abundant. precisely plastisphere-induced flux, indicate change stability function Considering biomass, scale needed. pathogens around worldwide. Vibrio temperate tropical [68, 118, 119], Pseudomonas monteilii, P. mendocina, angilliseptica, syringae) [101, 120, 121]. ratios pathogens/bacteria [28]. resistance (ARGs) [26, 35, 37, 56, 122]. [122] ARGs microbiota greater Gyre, Since reservoirs refuges concern. possess complexity, hotspot horizontal transfer. findings frequency plasmid transfer bacteria. facilitate ARG propagation addition, embedded protected extracellular polymeric substances tolerant stresses discrete cells. acquisition tolerance easier presenting challenges health. reporting vectors taken caution. Biofilms considered pathogens. buoyancy, transportability co-occurring highlighted. induce risk prolonged exposure distances. To date, cannot answer question specifically ARGs. vital questions, frequent must addressed Compared unexplored. Current predictions revealed participate number ecosystems. Multiple importantly, shown predicted Multi-omic verification contamination threat Anthropocene shows sign decreasing near future. Understanding associated managing predicting risks posed pollution. systematically summarizes experimental explore continued assessment elaborate required open research. Detailed limited. Biofilm hours, however, ventured dynamics Traditional suitable tracking Microfluidic techniques structural fluid behavior microscopic therefore heterogenous microenvironment liquids. microfluidic devices optical coherence tomography valuable qualitative regarding biofilms, key influencing Diverse factors, hydrographic textures, availability, characteristics, types, charges, morphologies, There gap Biological predominately micro-eukaryotic poorly understood. All create complex neighboring cooperative behaviors enhance stress uptake. parallel, competition always pervasive space resource limitations present. variation manifold dynamic, function. lack interact each properties, Comprehensive methods, genomics, metatranscriptomics, metabolomics, help holistic view What notice unavoidably lead errors. errors stem bioinformatic analysis, causing misalignment reads mistakes genome confirmatory culture-dependent pathogenicity. Jie Linna Du overall conceptualization design. Yuanze Sun, Mochen Wu, Jingxi Zang writing discussion main content manuscript. Muke Cheng Chen figures tables authors read approved final project supported National Natural Foundation (No. 41907341) Beijing Innovation Consortium Agriculture Research System BAIC01-2023-27). declare conflict interest. manuscript does generate code data. Supplementary (figures, tables, scripts, graphical abstract, slides, videos, Chinese translated version update online DOI iMeta http://www.imeta.science/. Please note: publisher responsible functionality supporting supplied authors. Any queries (other missing content) directed corresponding author article.