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.

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.

Influence of Fishmeal-Free Diets on Microbial Communities in Atlantic Salmon (Salmo salar) Recirculation Aquaculture Systems.

UNLABELLED: Reliance on fishmeal as a primary protein source is among the chief economic and environmental concerns in aquaculture today. Fishmeal-based feeds often require harvest from wild fish stocks, placing pressure on natural ecosystems and causing price instability. Alternative diet formulations without the use of fishmeal provide a potential solution to this challenge. Although the impact of alternative diets on fish performance, intestinal inflammation, palatability, and gut microbiota has been a topic of recent interest, less is known about how alternative feeds impact the aquaculture environment as a whole. The recent focus on recirculating aquaculture systems (RAS) and the closed-containment approach to raising food fish highlights the need to maintain stable environmental and microbiological conditions within a farm environment. Microbial stability in RAS biofilters is particularly important, given its role in nutrient processing and water quality in these closed systems. If and how the impacts of alternative feeds on microbial communities in fish translate into changes to the biofilters are not known. We tested the influence of a fishmeal-free diet on the microbial communities in RAS water, biofilters, and salmon microbiomes using high-throughput 16S rRNA gene V6 hypervariable region amplicon sequencing. We grew Atlantic salmon (Salmo salar) to market size in six replicate RAS tanks, three with traditional fishmeal diets and three with alternative-protein, fishmeal-free diets. We sampled intestines and gills from market-ready adult fish, water, and biofilter medium in each corresponding RAS unit. Our results provide data on how fish diet influences the RAS environment and corroborate previous findings that diet has a clear influence on the microbiome structure of the salmon intestine, particularly within the order Lactobacillales (lactic acid bacteria). We conclude that the strong stability of taxa likely involved in water quality processing regardless of diet (e.g., Nitrospira) may further alleviate concerns regarding the use of alternative feeds in RAS operations. IMPORTANCE: The growth of the aquaculture industry has outpaced terrestrial livestock production and wild-capture fisheries for over 2 decades, currently producing nearly 50% of all seafood consumed globally. As wild-capture fisheries continue to decline, aquaculture's role in food production will grow, and it will produce an estimated 62% of all seafood consumed in 2020. A significant environmental concern of the industry is the reliance on fishmeal as a primary feed ingredient, as its production still requires harvest from wild fisheries. Our study adds to the growing body of literature on the feasibility of alternative, fishmeal-free diets. Specifically, we asked how fishmeal-free diets influence microbial communities in recirculating salmon farms. Unlike previous studies, we extended our investigation beyond the microbiome of the fish itself and asked how alterative diets influence microbial communities in water and critical biofilter habitats. We found no evidence for adverse effects of alternative diets on any microbial habitat within the farm.

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.

Marine bacteria exhibit a bipolar distribution.

The microbial cosmopolitan dispersion hypothesis often invoked to explain distribution patterns driven by high connectivity of oceanographic water masses and widespread dispersal ability has never been rigorously tested. By using a global marine bacterial dataset and iterative matrix randomization simulation, we show that marine bacteria exhibit a significantly greater dispersal limitation than predicted by our null model using the "everything is everywhere" tenet with no dispersal limitation scenario. Specifically, marine bacteria displayed bipolar distributions (i.e., species occurring exclusively at both poles and nowhere else) significantly less often than in the null model. Furthermore, we observed fewer taxa present in both hemispheres but more taxa present only in a single hemisphere than expected under the null model. Each of these trends diverged further from the null expectation as the compared habitats became more geographically distant but more environmentally similar. Our meta-analysis supported a latitudinal gradient in bacterial diversity with higher richness at lower latitudes, but decreased richness toward the poles. Bacteria in the tropics also demonstrated narrower latitudinal ranges at lower latitudes and relatively larger ranges in higher latitudes, conforming to the controversial macroecological pattern of the "Rapoport rule." Collectively, our findings suggest that bacteria follow biogeographic patterns more typical of macroscopic organisms, and that dispersal limitation, not just environmental selection, likely plays an important role. Distributions of microbes that deliver critical ecosystem services, particularly those in polar regions, may be vulnerable to the same impacts that environmental stressors, climate warming, and degradation in habitat quality are having on biodiversity in animal and plant species.

Community assembly of a euryhaline fish microbiome during salinity acclimation.

Microbiomes play a critical role in promoting a range of host functions. Microbiome function, in turn, is dependent on its community composition. Yet, how microbiome taxa are assembled from their regional species pool remains unclear. Many possible drivers have been hypothesized, including deterministic processes of competition, stochastic processes of colonization and migration, and physiological 'host-effect' habitat filters. The contribution of each to assembly in nascent or perturbed microbiomes is important for understanding host-microbe interactions and host health. In this study, we characterized the bacterial communities in a euryhaline fish and the surrounding tank water during salinity acclimation. To assess the relative influence of stochastic versus deterministic processes in fish microbiome assembly, we manipulated the bacterial species pool around each fish by changing the salinity of aquarium water. Our results show a complete and repeatable turnover of dominant bacterial taxa in the microbiomes from individuals of the same species after acclimation to the same salinity. We show that changes in fish microbiomes are not correlated with corresponding changes to abundant taxa in tank water communities and that the dominant taxa in fish microbiomes are rare in the aquatic surroundings, and vice versa. Our results suggest that bacterial taxa best able to compete within the unique host environment at a given salinity appropriate the most niche space, independent of their relative abundance in tank water communities. In this experiment, deterministic processes appear to drive fish microbiome assembly, with little evidence for stochastic colonization.

Spatial and temporal patterns of stranded intertidal marine debris: is there a picture of global change?

Floating and stranded marine debris is widespread. Increasing sea levels and altered rainfall, solar radiation, wind speed, waves, and oceanic currents associated with climatic change are likely to transfer more debris from coastal cities into marine and coastal habitats. Marine debris causes economic and ecological impacts, but understanding the scope of these requires quantitative information on spatial patterns and trends in the amounts and types of debris at a global scale. There are very few large-scale programs to measure debris, but many peer-reviewed and published scientific studies of marine debris describe local patterns. Unfortunately, methods of defining debris, sampling, and interpreting patterns in space or time vary considerably among studies, yet if data could be synthesized across studies, a global picture of the problem may be avaliable. We analyzed 104 published scientific papers on marine debris in order to determine how to evaluate this. Although many studies were well designed to answer specific questions, definitions of what constitutes marine debris, the methods used to measure, and the scale of the scope of the studies means that no general picture can emerge from this wealth of data. These problems are detailed to guide future studies and guidelines provided to enable the collection of more comparable data to better manage this growing problem.

Investigating microbial eukaryotic diversity from a global census: insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes.

Next-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. Pyrotag OTUs called at 98% sequence similarity yielded numbers of OTUs that were similar overall to those for full-length sequences when the latter were called at 97% similarity. Singleton OTUs strongly influenced estimates of species richness but not the higher-level taxonomic composition of the community. The pyrotag and full-length sequence data sets had slightly different taxonomic compositions of rhizarians, stramenopiles, cryptophytes, and haptophytes, but the two data sets had similarly high compositions of alveolates. Pyrotag-based OTUs were often derived from sequences that mapped to multiple full-length OTUs at 100% similarity. Thus, pyrotags sequenced from a single hypervariable region might not be appropriate for establishing protistan species-level OTUs. However, nonmetric multidimensional scaling plots constructed with the two data sets yielded similar clusters, indicating that beta diversity analysis results were similar for the Sanger and NGS sequences. Short pyrotag sequences can provide holistic assessments of protistan communities, although care must be taken in interpreting the results. The longer reads (>500 bp) that are now becoming available through NGS should provide powerful tools for assessing the diversity of microbial eukaryotic assemblages.

The Genomic Standards Consortium.

A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.

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.

Life in the "plastisphere": microbial communities on plastic marine debris.

Plastics are the most abundant form of marine debris, with global production rising and documented impacts in some marine environments, but the influence of plastic on open ocean ecosystems is poorly understood, particularly for microbial communities. Plastic marine debris (PMD) collected at multiple locations in the North Atlantic was analyzed with scanning electron microscopy (SEM) and next-generation sequencing to characterize the attached microbial communities. We unveiled a diverse microbial community of heterotrophs, autotrophs, predators, and symbionts, a community we refer to as the "Plastisphere". Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer. Small-subunit rRNA gene surveys identified several hydrocarbon-degrading bacteria, supporting the possibility that microbes play a role in degrading PMD. Some Plastisphere members may be opportunistic pathogens (the authors, unpublished data) such as specific members of the genus Vibrio that dominated one of our plastic samples. Plastisphere communities are distinct from surrounding surface water, implying that plastic serves as a novel ecological habitat in the open ocean. Plastic has a longer half-life than most natural floating marine substrates, and a hydrophobic surface that promotes microbial colonization and biofilm formation, differing from autochthonous substrates in the upper layers of the ocean.

A decadal view of biodiversity informatics: challenges and priorities.

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.

Spatio-temporal patterns of Synechococcus oligotypes in Moroccan lagoonal environments.

Synechococcus are unicellular cyanobacteria susceptible to environmental fluctuations and can be used as bioindicators of eutrophication in marine ecosystems. We examined their distribution in two Moroccan lagoons, Marchica on the Mediterranean coast and Oualidia on the Atlantic, in the summers of 2014 and 2015 using 16S rRNA amplicon oligotyping. Synechococcus representatives recruited a higher number of reads from the 16S rRNA in Marchica in comparison to Oualidia. We identified 31 Synechococcus oligotypes that clustered into 10 clades with different distribution patterns. The Synechococcus community was mainly represented by oligotype 1 (clade III) in Marchica. Cooccurring clades IV and I had an important relative abundance in Marchica in the summer of 2014, which is unusual, as these clades are widespread in cold waters. Moreover, Clades VII and subcluster "5.3" formed a sizeable percentage of the Synechococcus community in Marchica. Notably, we found low Synechococcus sequence counts in the Atlantic Lagoon. These results showed that the relative abundance of Synechococcus reads is not constant over space and time and that rare members of the Synechococcus community did not follow a consistent pattern. Further studies are required to decipher Synechococcus dynamics and the impact of environmental parameters on their spatial and temporal distributions.

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.

Diversity of the holopelagic Sargassum microbiome from the Great Atlantic Sargassum Belt to coastal stranding locations.

The holopelagic brown macroalgae Sargassum natans and Sargassum fluitans form essential habitats for attached and mobile fauna which contributes to a unique biodiversity in the Atlantic Ocean. However, holopelagic Sargassum natans (genotype I & VIII) and Sargassum fluitans (genotype III) have begun forming large accumulations with subsequent strandings on the western coast of Africa, the Caribbean and northern Brazil, threatening local biodiversity of coastal ecosystems and triggering economic losses. Moreover, stranded masses of holopelagic Sargassum may introduce or facilitate growth of bacteria that are not normally abundant in coastal regions where Sargassum is washing ashore. Hitherto, it is not clear how the holopelagic Sargassum microbiome varies across its growing biogeographic range and what factors drive the microbial composition. We determined the microbiome associated with holopelagic Sargassum from the Great Atlantic Sargassum Belt to coastal stranding sites in Mexico and Florida. We characterized the Sargassum microbiome via amplicon sequencing of the 16S V4 region hypervariable region of the rRNA gene. The microbial community of holopelagic Sargassum was mainly composed of photo(hetero)trophs, organic matter degraders and potentially pathogenic bacteria from the Pseudomonadaceae, Rhodobacteraceae and Vibrionaceae. Sargassum genotypes S. natans I, S. natans VIII and S. fluitans III contained similar microbial families, but relative abundances and diversity varied. LEfSE analyses further indicated biomarker genera that were indicative of Sargassum S. natans I/VIII and S. fluitans III. The holopelagic Sargassum microbiome showed biogeographic patterning with high relative abundances of Vibrio spp., but additional work is required to determine whether that represents health risks in coastal environments. Our study informs coastal management policy, where the adverse sanitary effects of stranded Sargassum might impact the health of coastal ecosystems.

Daphnia magna's Favorite Snack: Biofouled Plastics.

The influence of biofouling on zooplankton ingestion rates of plastics in freshwater environments has received limited attention. We investigated how biofouling of microplastics in wastewater effluent and in fresh surface water influences Daphnia magna's microplastic consumption. The differences in ingestion of the biofouled as compared with the virgin microplastics were higher for the surface water by a factor of seven compared with a factor of two for the effluent. The intake of biofouled microplastics by D. magna was higher compared with virgin plastics, but the reason for this preference should be further investigated. Environ Toxicol Chem 2022;41:1977-1981. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.