A review of microscopy and comparative molecular-based methods to characterize “Plastisphere” communities

Tender, Caroline De; Schlundt, Cathleen; Devriese, Lisa; Mincer, Tracy J.; Zettler, Erik R.; Amaral‐Zettler, Linda

doi:10.1039/c7ay00260b

Cited by 77 publications

(56 citation statements)

References 68 publications

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“…B); however, the null model derived BC index comparisons did not confirm temporal differentiation (Supporting Information Table S5). These results agree with those of Pinto et al (), and while certain “core” taxa have been associated with early, intermediate, and late successional stages of biofilm development (De Tender et al ), results of the same study suggest that time does not significantly shape plastic bacterial communities. In our study, the lack of significant differentiation between plastic polymer types indicates that general biofilm processes, rather than plastic‐polymer associated characteristics (i.e., hydrophobicity, surface roughness, etc.…”

Section: Discussionsupporting

confidence: 92%

Microbial colonization of microplastics in the Caribbean Sea

Dudek

Cruz

Polidoro

et al. 2020

Limnol Oceanogr Letters

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Microplastics, plastic particles smaller than 5 mm that vary in their chemical makeup depending on the plastic type, are emerging marine pollutants that serve as a novel matrix for microbial colonization in the ocean. The communities growing on the microplastics, also termed the "plastisphere", may ultimately determine their degradation, deposition, and utilization by the food web, but the factors that shape their composition and development, such as environment, plastic type, and exposure time, are still insufficiently understood. In controlled incubation experiments carried out in a tropical bay in Panama, we show that the composition of a microplastics' bacterial biofilm is not shaped by plastic type or time exposed the environment. On the other hand, we found that the eukaryotic plastisphere was shaped by both plastic type and exposure time and found that specifically diatom communities exhibited preference for some plastic types. AbstractMicroplastics in the ocean function as an artificial microbial reef, with diverse communities of eukaryotic and bacterial microbiota colonizing its surface. It is not well understood if these communities are specific for the type of microplastic on which they develop. Here, we carried out a 6-week long incubation experiment of six common plastic polymers in Bocas del Toro, Panama. The community composition of prokaryotes based on 16S rRNA gene sequencing data, when judged under a null model analysis, shows that neither plastic polymer type nor time exposed to the environment plays a significant role in shaping biofilm communities. However, the null model analyses of eukaryotic communities based on 18S rRNA gene sequences reveal that they can be significantly influenced by plastic polymer type and time incubated. This was confirmed by scanning electron microscopy, which allowed us to distinguish plastic-specific diatom communities by the end of the incubation period.

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Section: Discussionsupporting

confidence: 92%

Microbial colonization of microplastics in the Caribbean Sea

Dudek

Cruz

Polidoro

et al. 2020

Limnol Oceanogr Letters

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“…Zettler et al . () reported that bacteria growing on polyethylene and polypropylene debris from the Sargasso Sea mainly belonged to the classes Alpha‐ and Gammaproteobacteria, similar to reports from other marine areas (Oberbeckmann et al ., , ; De Tender et al ., ). By contrast, in our study, Gammaproteobacteria and Flavobacteriia were generally rare, including the plastics‐associated biofilms, which is not surprising, because these bacteria are normally found in truly marine areas and not brackish systems, such as the Baltic Sea.…”

Section: Discussionmentioning

confidence: 97%

Evidence for selective bacterial community structuring on microplastics

Ogonowski

Motiei

Ininbergs

et al. 2018

Environmental Microbiology

272

187

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In aquatic ecosystems, microplastics are a relatively new anthropogenic substrate that can readily be colonized by biofilm-forming organisms. To examine the effects of substrate type on microbial community assembly, we exposed ambient Baltic bacterioplankton to plastic substrates commonly found in marine environments (polyethylene, polypropylene and polystyrene) as well as native (cellulose) and inert (glass beads) particles for 2 weeks under controlled conditions. The source microbial communities and those of the biofilms were analyzed by Illumina sequencing of the 16S rRNA gene libraries. All biofilm communities displayed lower diversity and evenness compared with the source community, suggesting substrate-driven selection. Moreover, the plastics-associated communities were distinctly different from those on the non-plastic substrates. Whereas plastics hosted greater than twofold higher abundance of Burkholderiales, the non-plastic substrates had a significantly higher proportion of Actinobacteria and Cytophagia. Variation in the community structure, but not the cell abundance, across the treatments was strongly linked to the substrate hydrophobicity. Thus, microplastics host distinct bacterial communities, at least during early successional stages.

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“…(b) Triplicates were sampled each week for 16S rRNA amplicon sequencing, scanning electron microscopy (SEM) and CLASI (combinatorial laser and spectral imaging) -FISH (fluorescence in situ hybridization). (c) A nested probe set of nine different probes was developed based on the most abundant taxa on plastic marine debris (PMD) identified by amplicon sequencing (Amaral-Zettler et al, 2015;De Tender et al, 2017). Each bacterial cell on PE hybridized with up to three different fluorescent probes.…”

Section: Design and Validation Of Probes And Probe Setmentioning

confidence: 99%

“…Despite the demonstrated ubiquity of biofilms on PMD in marine environments, we know very little about the composition and spatial distribution of "Plastisphere"-the thin layer of life on the surface of PMD-members or their geographical and temporal variations. Some studies use scanning electron microscopy (SEM) to visualize microbial communities (Carson, Nerheim, Carroll, & Eriksen, 2013;Masó, Fortuño, De Juan, & Demestre, 2016;Sieburth & Pratt, 1975) and others use molecular microbial profiling to determine community composition (De Tender et al, 2017;Jiang, Zhao, Zhu, & Li, 2018;Oberbeckmann, Osborn, & Duhaime, 2016). SEM provides good spatial resolution but poor taxonomic resolution, while sequencing data reveal the taxonomic composition of the community but not the spatial distribution and interaction between different taxa.…”

Section: Introductionmentioning

confidence: 99%

Spatial structure in the “Plastisphere”: Molecular resources for imaging microscopic communities on plastic marine debris

Schlundt

Welch

Knochel

et al. 2019

Molecular Ecology Resources

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Plastic marine debris (PMD) affects spatial scales of life from microbes to whales.However, understanding interactions between plastic and microbes in the "Plastisphere"-the thin layer of life on the surface of PMD-has been technologylimited. Research into microbe-microbe and microbe-substrate interactions requires knowledge of community phylogenetic composition but also tools to visualize spatial distributions of intact microbial biofilm communities. We developed a CLASI-FISH (combinatorial labelling and spectral imaging -fluorescence in situ hybridization) method using confocal microscopy to study Plastisphere communities. We created a probe set consisting of three existing phylogenetic probes (targeting all Bacteria, Alpha-, and Gammaproteobacteria) and four newly designed probes (targeting Bacteroidetes, Vibrionaceae, Rhodobacteraceae and Alteromonadaceae) labelled with a total of seven fluorophores and validated this probe set using pure cultures. Our nested probe set strategy increases confidence in taxonomic identification because targets are confirmed with two or more probes, reducing false positives. We simultaneously identified and visualized these taxa and their spatial distribution within the microbial biofilms on polyethylene samples in colonization time series experiments in coastal environments from three different biogeographical regions. Comparing the relative abundance of 16S rRNA gene amplicon sequencing data with cell-count abundance data retrieved from the microscope images of the same samples showed a good agreement in bacterial composition. Microbial communities were heterogeneous, with direct spatial relationships between bacteria, cyanobacteria and eukaryotes such as diatoms but also micro-metazoa. Our research provides a valuable resource to investigate biofilm development, succession and associations between specific microscopic taxa at micrometre scales. K E Y W O R D S biofilm, CLASI-FISH, confocal microscopy, marine plastic, succession | 621 SCHLUNDT eT aL. and Louis Kerr for help with microscopy and image analysis. AUTH O R CO NTR I B UTI O N S CS and LAA-Z conceived the project. CS, JLMW, LAA-Z, and ERZ designed the research. CS, AMK and ERZ performed research. LAA-Z and JLMW contributed reagents and analytical tools. CS, JLMW, AMK, ERZ and LAA-Z analyzed data. CS, JLMW, ERZ and LAA-Z wrote the paper. All authors read and approved the final draft of the manuscript. O RCI D

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A review of microscopy and comparative molecular-based methods to characterize “Plastisphere” communities

Abstract: A summary of molecular and visualization techniques to characterize life in the Plastisphere and compare corresponding datasets through the VAMPS website.

Cited by 77 publications

References 68 publications

Microbial colonization of microplastics in the Caribbean Sea

Microbial colonization of microplastics in the Caribbean Sea

Evidence for selective bacterial community structuring on microplastics

Spatial structure in the “Plastisphere”: Molecular resources for imaging microscopic communities on plastic marine debris

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