Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates

Biodegradable and compostable plastics are getting more attention as the environmental impacts of fossil-fuel-based plastics are revealed. Microbes can consume these plastics and biodegrade them within weeks to months under the proper conditions. The biobased polyhydroxyalkanoate (PHA) polymer family is an attractive alternative due to its physicochemical properties and biodegradability in soil, aquatic, and composting environments. Standard test methods are available for biodegradation that employ either natural inocula or defined communities, the latter being preferred for standardization and comparability. The original marine biodegradation standard test method ASTM D6691 employed such a defined consortium for testing PHA biodegradation. However, the taxonomic composition and metabolic potential of this consortium have never been confirmed using DNA sequencing technologies. To this end, we revived available members of this consortium and determined their phylogenetic placement, genomic sequence content, and metabolic potential. The revived members belonged to the Bacillaceae, Rhodobacteraceae, and Vibrionaceae families. Using a comparative genomics approach, we found all the necessary enzymes for both PHA production and utilization in most of the members. In a clearing-zone assay, three isolates also showed extracellular depolymerase activity. However, we did not find classical PHA depolymerases, but identified two potentially new extracellular depolymerases that resemble triacylglycerol lipases

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes

Ecology of the plastisphere

The plastisphere, which comprises the microbial community on plastic debris, rivals that of the built environment in spanning multiple biomes on Earth. Although human-derived debris has been entering the ocean for thousands of years, microplastics now numerically dominate marine debris and are primarily colonized by microbial and other microscopic life. The realization that this novel substrate in the marine environment can facilitate microbial dispersal and affect all aquatic ecosystems has intensified interest in the microbial ecology and evolution of this biotope. Whether a ‘core’ plastisphere community exists that is specific to plastic is currently a topic of intense investigation. This Review provides an overview of the microbial ecology of the plastisphere in the context of its diversity and function, as well as suggesting areas for further research

Microbial carrying capacity and carbon biomass of plastic marine debris

Trillions of plastic debris fragments are floating at sea, presenting a substantial surface area for microbial colonization. Numerous cultivation-independent surveys have characterized plastic-associated microbial biofilms, however, quantitative studies addressing microbial carbon biomass are lacking. Our confocal laser scanning microscopy data show that early biofilm development on polyethylene, polypropylene, polystyrene, and glass substrates displayed variable cell size, abundance, and carbon biomass, whereas these parameters stabilized in mature biofilms. Unexpectedly, plastic substrates presented lower volume proportions of photosynthetic cells after 8 weeks, compared to glass. Early biofilms displayed the highest proportions of diatoms, which could influence the vertical transport of plastic debris. In total, conservative estimates suggest 2.1 × 1021 to 3.4 × 1021 cells, corresponding to about 1% of the microbial cells in the ocean surface microlayer (1.5 × 103 to 1.1 × 104 tons of carbon biomass), inhabit plastic debris globally. As an unnatural addition to sea surface waters, the large quantity of cells and biomass carried by plastic debris has the potential to impact biodiversity, autochthonous ecological functions, and biogeochemical cycles within the ocean

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

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 technology-limited. 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

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

Plastic is currently the most abundant form of debris in the ocean. Since the early 70's, investigators have recognized the presence of life such as pennate diatoms, bryozoans and bacteria on plastic debris, sometimes referred to as the “Plastisphere”. This review provides an overview of molecular and visualization techniques used to characterize life in the Plastisphere, presents a new data portal located on the Visual Analysis of Microbial Population Structures (VAMPS) website to illustrate how one can compare plastic debris datasets collected using different high-throughput sequencing strategies, and makes recommendations on standardized operating procedures that will facilitate future comparative studies