Biodegradable plastics in Mediterranean coastal environments feature contrasting microbial succession.

Plastic pollution of the ocean is a top environmental concern. Biodegradable plastics present a potential "solution" in combating the accumulation of plastic pollution, and their production is currently increasing. While these polymers will contribute to the future plastic marine debris budget, very little is known still about the behavior of biodegradable plastics in different natural environments. In this study, we molecularly profiled entire microbial communities on laboratory confirmed biodegradable polybutylene sebacate-co-terephthalate (PBSeT) and polyhydroxybutyrate (PHB) films, and non-biodegradable conventional low-density polyethylene (LDPE) films that were incubated in situ in three different coastal environments in the Mediterranean Sea. Samples from a pelagic, benthic, and eulittoral habitat were taken at five timepoints during an incubation period of 22 months. We assessed the presence of potential biodegrading bacterial and fungal taxa and contrasted them against previously published in situ disintegration data of these polymers. Scanning electron microscopy imaging complemented our molecular data. Putative plastic degraders occurred in all environments, but there was no obvious "core" of shared plastic-specific microbes. While communities varied between polymers, the habitat predominantly selected for the underlying communities. Observed disintegration patterns did not necessarily match community patterns of putative plastic degraders.

Sargasso Sea Vibrio bacteria: Underexplored potential pathovars in a perturbed habitat.

We fully sequenced the genomes of 16 Vibrio cultivars isolated from eel larvae, plastic marine debris (PMD), the pelagic brown macroalga Sargassum, and seawater samples collected from the Caribbean and Sargasso Seas of the North Atlantic Ocean. Annotation and mapping of these 16 bacterial genome sequences to a PMD-derived Vibrio metagenome-assembled genome created for this study showcased vertebrate pathogen genes closely-related to cholera and non-cholera pathovars. Phenotype testing of cultivars confirmed rapid biofilm formation, hemolytic, and lipophospholytic activities, consistent with pathogenic potential. Our study illustrates that open ocean vibrios represent a heretofore undescribed group of microbes, some representing potential new species, possessing an amalgam of pathogenic and low nutrient acquisition genes, reflecting their pelagic habitat and the substrates and hosts they colonize.

Plastics select for distinct early colonizing microbial populations with reproducible traits across environmental gradients.

Little is known about early plastic biofilm assemblage dynamics and successional changes over time. By incubating virgin microplastics along oceanic transects and comparing adhered microbial communities with those of naturally occurring plastic litter at the same locations, we constructed gene catalogues to contrast the metabolic differences between early and mature biofilm communities. Early colonization incubations were reproducibly dominated by Alteromonadaceae and harboured significantly higher proportions of genes associated with adhesion, biofilm formation, chemotaxis, hydrocarbon degradation and motility. Comparative genomic analyses among the Alteromonadaceae metagenome assembled genomes (MAGs) highlighted the importance of the mannose-sensitive hemagglutinin (MSHA) operon, recognized as a key factor for intestinal colonization, for early colonization of hydrophobic plastic surfaces. Synteny alignments of MSHA also demonstrated positive selection for mshA alleles across all MAGs, suggesting that mshA provides a competitive advantage for surface colonization and nutrient acquisition. Large-scale genomic characteristics of early colonizers varied little, despite environmental variability. Mature plastic biofilms were composed of predominantly Rhodobacteraceae and displayed significantly higher proportions of carbohydrate hydrolysis enzymes and genes for photosynthesis and secondary metabolism. Our metagenomic analyses provide insight into early biofilm formation on plastics in the ocean and how early colonizers self-assemble, compared to mature, phylogenetically and metabolically diverse biofilms.

Large quantities of small microplastics permeate the surface ocean to abyssal depths in the South Atlantic Gyre.

Hundreds of studies have surveyed plastic debris in surface ocean gyre and convergence zones, however, comprehensive microplastics (MPs, ≤5 mm) assessments beneath these surface accumulation areas are lacking. Using in situ high-volume filtration, Manta net and MultiNet sampling, combined with micro-Fourier-transform-infrared imaging, we discovered a high abundance (up to 244.3 pieces per cubic meter [n m-3 ]) of small microplastics (SMPs, characteristically <100 µm) from the surface to near-sea floor waters of the remote South Atlantic Subtropical Gyre. Large horizontal and vertical variations in the abundances of SMP were observed, displaying inverse vertical trends in some cases. SMP abundances in pump samples were more than two orders of magnitude higher than large microplastics (LMPs, >300 µm) concurrently collected in MultiNet samples. Higher-density polymers (e.g., alkyd resins and polyamide) comprised >65% of the total pump sample count, highlighting a discrepancy between polymer compositions from previous ocean surface-based surveys, typically dominated by buoyant polymers such as polyethylene and polypropylene. Contrary to previous reports stating LMP preferentially accumulated at density gradients, SMP with presumably slower sinking rates are much less influenced by density gradients, thus resulting in a more even vertical distribution in the water column, and potentially longer residence times. Overall, our findings suggest that SMP is a critical and largely underexplored constituent of the oceanic plastic inventory. Additionally, our data support that weak current systems contribute to the formation of SMP hotspots at depth, implying a higher encounter rate for subsurface particle feeders. Our study unveils the prevalence of plastics in the entire water column, highlighting the urgency for more quantification of the deep-ocean MP, particularly the smaller size fraction, to better understand ecosystem exposure and to predict MP fate and impacts.

Climate change facilitated the early colonization of the Azores Archipelago during medieval times.

Humans have made such dramatic and permanent changes to Earth's landscapes that much of it is now substantially and irreversibly altered from its preanthropogenic state. Remote islands, until recently isolated from humans, offer insights into how these landscapes evolved in response to human-induced perturbations. However, little is known about when and how remote systems were colonized because archaeological data and historical records are scarce and incomplete. Here, we use a multiproxy approach to reconstruct the initial colonization and subsequent environmental impacts on the Azores Archipelago. Our reconstructions provide unambiguous evidence for widespread human disturbance of this archipelago starting between 700-60+50 and 850-60+60 Common Era (CE), ca. 700 y earlier than historical records suggest the onset of Portuguese settlement of the islands. Settlement proceeded in three phases, during which human pressure on the terrestrial and aquatic ecosystems grew steadily (i.e., through livestock introductions, logging, and fire), resulting in irreversible changes. Our climate models suggest that the initial colonization at the end of the early Middle Ages (500 to 900 CE) occurred in conjunction with anomalous northeasterly winds and warmer Northern Hemisphere temperatures. These climate conditions likely inhibited exploration from southern Europe and facilitated human settlers from the northeast Atlantic. These results are consistent with recent archaeological and genetic data suggesting that the Norse were most likely the earliest settlers on the islands.

Diversity and predicted inter- and intra-domain interactions in the Mediterranean Plastisphere.

This study investigated the biogeography, the presence and diversity of potentially harmful taxa harbored, and potential interactions between and within bacterial and eukaryotic domains of life on plastic debris in the Mediterranean. Using a combination of high-throughput DNA sequencing (HTS), Causal Network Analysis, and Scanning Electron Microscopy (SEM), we show regional differences and gradients in the Mediterranean microbial communities associated with marine litter, positive causal effects between microbes including between and within domains of life, and how these might impact the marine ecosystems surrounding them. Adjacent seas within the Mediterranean region showed a gradient in the microbial communities on plastic with non-overlapping endpoints (Adriatic and Ligurian Seas). The largest predicted inter-domain effects included positive effects of a novel red-algal Plastisphere member on its potential microbiome community. Freshwater and marine samples housed a diversity of fungi including some related to disease-causing microbes. Algal species related to those responsible for Harmful Blooms (HABs) were also observed on plastic pieces including members of genera not previously reported on Plastic Marine Debris (PMD).

Biofouling impacts on polyethylene density and sinking in coastal waters: A macro/micro tipping point?

Biofouling causing an increase in plastic density and sinking is one of the hypotheses to account for the unexpectedly low amount of buoyant plastic debris encountered at the ocean surface. Field surveys show that polyethylene and polypropylene, the two most abundant buoyant plastics, both occur below the surface and in sediments, and experimental studies confirm that biofouling can cause both of these plastics to sink. However, studies quantifying the actual density of fouled plastics are rare, despite the fact that density will determine the transport and eventual fate of plastic in the ocean. Here we investigated the role of microbial biofilms in sinking of polyethylene microplastic and quantified the density changes natural biofouling communities cause in the coastal waters of the North Sea. Molecular data confirmed the variety of bacteria and eukaryotes (including animals and other multicellular organisms) colonizing the plastic over time. Fouling communities increased the density of plastic and caused sinking, and the plastic remained negatively buoyant even during the winter with lower growth rates. Relative surface area alone, however, did not predict whether a plastic piece sank. Due to patchy colonization, fragmentation of sinking pieces may result in smaller pieces regaining buoyancy and returning to the surface. Our results suggest that primarily multicellular organisms cause sinking of plastic pieces with surface area to volume ratios (SA:V) below 100 (generally pieces above a couple hundred micrometers in size), and that this is a "tipping point" at which microbial biofilms become the key players causing sinking of smaller pieces with higher SA:V ratios, including most fibers that are too small for larger (multicellular) organisms to colonize.

Correction: De Vogel, F.A., et al. Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates. Microorganisms 2021, 9, 186.

The authors wish to make the following corrections to this paper [...].

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.

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.

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.

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.

Microbial Community and Potential Pathogen Shifts Along an Ornamental Fish Supply Chain.

There is broad interest in disease spread through the pet trade, but empirical research on hosts and pathogens in transit along actual trade routes is notably absent. Using next-generation DNA sequencing, and partnering with the ornamental fish industry, we tracked shifts in microbial community and potential pathogen structure associated with Sailfin Tang (Zebrasoma desjardinii) along the United States (U.S.) leg of an international supply chain. We observed striking changes in microbial diversity and composition of potential pathogens, including increased dominance of vibrios of fishes in transit. Our pilot findings suggest that high investment in fishes early in the supply chain may not matter to their long-term health depending on end destination conditions.

Seasonal Shifts in Bacterial Community Responses to Phytoplankton-Derived Dissolved Organic Matter in the Western Antarctic Peninsula.

Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August-December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur.

Comparative mitochondrial and chloroplast genomics of a genetically distinct form of Sargassum contributing to recent "Golden Tides" in the Western Atlantic.

Over the past 5 years, massive accumulations of holopelagic species of the brown macroalga Sargassum in coastal areas of the Caribbean have created "golden tides" that threaten local biodiversity and trigger economic losses associated with beach deterioration and impact on fisheries and tourism. In 2015, the first report identifying the cause of these extreme events implicated a rare form of the holopelagic species Sargassum natans (form VIII). However, since the first mention of S. natans VIII in the 1930s, based solely on morphological characters, no molecular data have confirmed this identification. We generated full-length mitogenomes and partial chloroplast genomes of all representative holopelagic Sargassum species, S. fluitans III and S. natans I alongside the putatively rare S. natans VIII, to demonstrate small but consistent differences between S. natans I and VIII (7 bp differences out of the 34,727). Our comparative analyses also revealed that both S. natans I and S. natans VIII share a very close phylogenetic relationship with S. fluitans III (94- and 96-bp differences of 34,727). We designed novel primers that amplified regions of the cox2 and cox3 marker genes with consistent polymorphic sites that enabled differentiation between the two S. natans forms (I and VIII) from each other and both from S. fluitans III in over 150 Sargassum samples including those from the 2014 golden tide event. Despite remarkable gene synteny and sequence conservation, the three Sargassum forms differ in morphology, ecology, and distribution patterns, warranting more extensive interrogation of holopelagic Sargassum genomes as a whole.

Bacterial community segmentation facilitates the prediction of ecosystem function along the coast of the western Antarctic Peninsula.

Bacterial community structure can be combined with observations of ecophysiological data to build predictive models of microbial ecosystem function. These models are useful for understanding how function might change in response to a changing environment. Here we use five spring-summer seasons of bacterial community structure and flow cytometry data from a productive coastal site along the western Antarctic Peninsula to construct models of bacterial production (BP), an ecosystem function that heterotrophic bacteria provide. Through a novel application of emergent self-organizing maps we identified eight recurrent modes in the structure of the bacterial community. A model that combined bacterial abundance, mode and the fraction of cells belonging to the high nucleic acid population (fHNA; R2=0.730, P<0.001) best described BP. Abrupt transitions between modes during the 2013-2014 spring-summer season corresponded to rapid shifts in fHNA. We conclude that parameterizing community structure data via segmentation can yield useful insights into microbial ecosystem function and ecosystem processes.

Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula.

The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.

The ecological impacts of marine debris: unraveling the demonstrated evidence from what is perceived.

Anthropogenic debris contaminates marine habitats globally, leading to several perceived ecological impacts. Here, we critically and systematically review the literature regarding impacts of debris from several scientific fields to understand the weight of evidence regarding the ecological impacts of marine debris. We quantified perceived and demonstrated impacts across several levels of biological organization that make up the ecosystem and found 366 perceived threats of debris across all levels. Two hundred and ninety-six of these perceived threats were tested, 83% of which were demonstrated. The majority (82%) of demonstrated impacts were due to plastic, relative to other materials (e.g., metals, glass) and largely (89%) at suborganismal levels (e.g., molecular, cellular, tissue). The remaining impacts, demonstrated at higher levels of organization (i.e., death to individual organisms, changes in assemblages), were largely due to plastic marine debris (> 1 mm; e.g., rope, straws, and fragments). Thus, we show evidence of ecological impacts from marine debris, but conclude that the quantity and quality of research requires improvement to allow the risk of ecological impacts of marine debris to be determined with precision. Still, our systematic review suggests that sufficient evidence exists for decision makers to begin to mitigate problematic plastic debris now, to avoid risk of irreversible harm.