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Bacteriohopanepolyols (BHPs) are a diverse class of lipids produced by bacteria across a wide range of environments. In this study, we aim to further identify BHPs related to ecological niches and/or specific bacteria by characterizing the distribution of BHPs in suspended particulate matter (SPM) of the water column and in sediments in a range of lakes and coastal lagoons from the Azores Archipelago, as well as in a co-culture enriched for methanotrophs. Sediment samples from Azorean lakes with low-oxygen conditions during the summer months (i.e., Azul, Verde, Funda, and Negra) contain relatively high abundances of BHPs that are typically associated with methane-oxidizing (methanotrophic) bacteria (i.e., aminotetrol, aminopentol, and methylcarbamate-aminopentol), as well as the ethenolamine-BHPs (i.e., ethenolamine-BHpentol and ethenolamine-BHhexol) and the N-formylated aminoBHPs. Both ethenolamine-BHPs and N-formylated aminoBHPs were also detected in a methanotroph–methylotroph co-culture that was enriched from a lake. In the SPM of all water columns, bacteriohopanetetrol (BHT), BHT cyclitol ether, and aminotriol are the dominant BHPs. In SPM from Lake Funda, nucleoside BHPs (i.e., Me-adenosylhopaneHG-diMe (where HG refers to head group), N1-methylinosylhopane, 2Me-N1-inosylhopane, and Me-N1-inosylhopane) are present in low abundance or absent under oxic conditions but increase in concentration near the chemocline, suggesting potential in situ production of these nucleoside BHPs rather than an allochthonous origin. In contrast, sediments from shallow, well-mixed lakes (i.e., Empadadas, São Jorge, and Lomba) contain higher abundances of adenosylhopane and N1-methylinosylhopane, which likely originate from bacteria living in nearby soils. Based on our current results we revised the existing Rsoil index, which was previously used to infer terrestrial inputs to aquatic environments, to exclude any potential nucleosides produced in the lake water column (Rsoil-lake). In the coastal lagoons, Cubres East and Cubres West, methoxylated BHTs were detected, and higher abundances of ethenolamine-BHT were observed. This study highlights the diversity of BHPs in lakes and coastal lagoons and their potential as taxonomic markers for bacteria associated with certain ecological niches, which can be preserved in sedimentary records.

Holopelagic Sargassum has been causing massive strandings on tropical Atlantic Ocean shorelines. After stranding, the algal biomass starts to decompose, releasing nutrients, toxic gases, and potentially introduces exogenous macro and microorganisms. Describing the microbiome associated with Sargassum, and how it changes after stranding is important in identifying potential microbial introductions to coastal environments, as well as sources of potential biotechnological resources. In this study, stranding simulation experiments were done for S. fluitans III and S. natans VIII on shipboard. Samples for microbiome identification were taken at 0 hr, just after removing healthy Sargassum from the seawater, and after 24 and 48 hrs of stranding simulation under environmental conditions. The bacterial community was identified through sequencing of 16S rRNA gene V3-V4 hypervariable regions, generating a total of 2,005 Amplicon Sequence Variants (ASVs). Of those, 628 were shared between Sargassum species. The stranding simulation changed the microbial community and only 30, out of 2,005 ASVs, persisted throughout the experiment. Phototrophs were in the main functional group at 0 hr, shifting to chemoheterotrophs within the first 24 hrs of exposure of Sargassum to air conditions. The most abundant orders Microtrichales and Rhodobacterales at 0 hr, were replaced after 24 hrs of exposure by Alteromonadales and Vibrionales, the latter representing up to 91% of the relative abundance in the bacterial community. These findings suggest that after stranding, the Sargassum microbiome goes through dysbiosis, and its biomass could become a fertile ground for potentially pathogenic bacteria.

Alkenone‐derived paleotemperature reconstruction holds great promise in lake environments. However, the occurrence of multiple species of alkenone‐producing haptophyte algae in a single lake can complicate the translation of alkenone unsaturation to temperature if each species requires an individual temperature calibration. Here, we present the first systematic monitoring of two alkenone‐producing haptophytes throughout the course of a seasonal cycle in Lake George, North Dakota, using a combined approach of DNA sequencing and alkenone lipid characterization. Field sampling revealed a nonoverlapping haptophyte succession, with both an early and late season haptophyte bloom event. Culturing experiments demonstrated that the two haptophyte species responsible for these blooms had statistically similar alkenone‐temperature responses, although the culture‐based calibrations were distinct from the in situ calibration. Bloom timing of each haptophyte species corresponded to surface‐water temperatures that differed by more than 10°C, revealing that changes in bloom intensities for each species will skew the sediment‐inferred temperatures to a different stage of the growth season. These results highlight the importance of accounting for bloom timing when interpreting alkenone‐derived temperatures in sediment cores, especially in lakes that experience large seasonal fluctuations in water column temperature and salinity.

We examined the geochemistry and bacterial and archaeal community structure in the acidic (pH < 2.4) pit lake at Peña de Hierro, near the headwaters of the Río Tinto. The lake has strong vertical gradients in light, O2, pH, conductivity, and dissolved ions. Bacterial and archaeal communities between 0 and 32 m displayed low species richness and evenness. Relatives of iron cycling taxa accounted for 60-90% of the operational taxonomic units (OTUs) throughout the water column. Relatives of heterotrophic, facultative Fe(III)-reducing species made up more than a third of the bacterial and archaeal community in the photic zone. Taxa related to Fe(II) oxidizers Ferrithrix thermotolerans and Acidithix ferrooxidans were also abundant in the photic zone. Below the photic zone, relatives of the lithoautotrophic Fe(II) oxidizers Leptospirillum ferrooxidans and Ferrovum myxofaciens bloomed at different depths within or just below the oxycline. Thermoplasmatales predominated in the deep, microoxic zone of the lake. The microbial population structure of the lake appears to be influenced by the production of oxygen and organic matter by phototrophs in a narrow zone at the lake surface and by strong geochemical gradients present in the water column that create distinct niches for separate Fe(II) oxidizers.

While plastic has become omnipresent in the marine environment, knowledge of how plastic biofilm communities develop from functional metabolic and phylogenetic perspectives is nascent, although these data are central to understanding microbial ecology surrounding plastic substrates in the ocean. By incubating virgin microplastics during oceanic transects and comparing with naturally occurring plastic litter at the same locations, we constructed functional gene catalogs to contrast the metabolic differences between early and mature biofilm communities. Early colonization incubations were consistently dominated by Alteromonadaceae and harbored significantly higher proportions of genes associated with adhesion, biofilm formation, chemotaxis, defense, iron acquisition and utilization, and motility. Comparative genomic analyses with Alteromonas, Marinobacter, and Marisediminitalea metagenome assembled genomes (MAGs) spotlighted the importance of the mannose-sensitive hemagglutinin operon, adhesive genes genetically transposed from intestinal pathogens, for early colonization of hydrophobic plastic surfaces. Synteny alignments of the former operon also demonstrated apparent positive selection for mshA alleles across all MAGs. Early colonizers varied little in terms of large-scale genomic characteristics, despite the presence of latitudinal, salinity, and temperature gradients. Mature plastic biofilms, composed of predominantly Rhodobacteraceae followed by Flavobacteriaceae, that are critically important for carbon turnover in oceanic ecosystems, displayed significantly higher proportions of genes involved in oxidative phosphorylation, phosphonate metabolism, photosynthesis, secondary metabolism, and Type IV secretion. Our metagenomic analyses provide insight into early biofilm formation on virgin surfaces in the marine environment, as well as how early colonizers self-assemble, compared to mature, taxonomically, and metabolically diverse biofilms.Significance StatementLittle is known about plastic biofilm assemblage dynamics and successional changes over time. Our results demonstrate that highly reproducible and predictable types of bacteria, with similar genomic characteristics, can initially colonize plastic in the marine environment across varying environmental gradients. The key gene sets involved in foundational bacterial colonization may have broad impacts for biofilm formation on plastic surfaces used in agriculture, biomedicine, environmental science, and food science. Genomic characteristics of early colonizers may metabolically underpin the origin of the ordered succession observed in marine microbial communities and be useful for predicting microbial community membership and biogeochemical processes.

Despite the multidisciplinary and comprehensive approach taken in ref. 1, we acknowledge that there are still open questions that require further research. We emphasize that our study relies on multiple records that show the synchronous arrival of humans on multiple islands before ca. 1400 CE. Elias et al. (2) raise specific concerns about the record from Peixinho Lake, one of the five lakes included in the study, while ignoring the other multiproxy lake sediment records. The arguments presented by Elias et al. (2) do not undermine in any way the main conclusions of our paper, but still we would like to explicitly address the main criticisms with regard to the only record in question

The call for research concerning microbial interactions with marine microplastics has reached a decadal milestone, leaving scientists with not only novel insights into this field of investigation but also many unanswered questions. This chapter reflects on this decade of discovery with respect to the “Plastisphere” that refers to the thin layer of life that colonizes the outside of plastic debris, with a focus on the microscopic life that colonizes plastics in marine systems. It revisits the state of knowledge regarding the Plastisphere in the context of the Known, Unknown, and Unknowable. Early studies concentrated on bacterial members of the Plastisphere, but recently, there is greater recognition that eukaryotes are important members of this ecosystem and increasing numbers of studies are including them. Microbial consortia, as well as symbiotic, parasitic, and predator–prey relationships, undoubtedly play a role in shaping Plastisphere community structure and function.

The fate of (micro)plastic particles in the open ocean is controlled by physical and biological processes. Here, we model the effects of biofouling on the subsurface vertical distribution of spherical, virtual plastic particles with radii of 0.01–1 mm. For the physics, four vertical velocity terms are included: advection, wind-driven mixing, tidally induced mixing, and the sinking velocity of the biofouled particle. For the biology, we simulate the attachment, growth and loss of algae on particles. We track 10,000 particles for one year in three different regions with distinct biological and physical properties: the low productivity region of the North Pacific Subtropical Gyre, the high productivity region of the Equatorial Pacific and the high mixing region of the Southern Ocean. The growth of biofilm mass in the euphotic zone and loss of mass below the euphotic zone result in the oscillatory behaviour of particles, where the larger (0.1–1.0 mm) particles have much shorter average oscillation lengths ( 5000 m). Our results show that the vertical movement of particles is mainly affected by physical (wind-induced mixing) processes within the mixed layer and biological (biofilm) dynamics below the mixed layer. Furthermore, positively buoyant particles with radii of 0.01–1.0 mm can sink far below the euphotic zone and mixed layer in regions with high near-surface mixing or high biological activity. This work can easily be coupled to other models to simulate open-ocean biofouling dynamics, in order to reach a better understanding of where ocean (micro)plastic ends up.

Millimeter- and micrometer-sized plastics are well-documented in aquatic ecosystems, but little is known about sub-micrometer particles because conventional analytical techniques lack sufficient spatial resolution or the spectroscopic means to unambiguously identify individual nanometer-sized plastic particles. We combined the spatial resolution of atomic force microscopy with chemical information from infrared spectroscopy to detect, identify, and count nanoplastics down to 20 nm in diameter in samples from different depths in the South Atlantic Ocean. We present evidence for the presence of polyethylene terephthalate (PET) nanoplastics in different states of degradation at 5000 m. Using lab-based ageing of PET, we demonstrate that nanoplastics can form even without light or interaction with the plastisphere, and that macroscopic PET items are a plausible source of PET nanoplastics in the ocean.

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., This research is funded by Fundação para a Ciência e Tecnologia (DL57/2016/ ICETA/EEC2018/25) grant, DISCOVERAZORES research project (PTDC/CTA-AMB/28511/2017), the Spanish Ministry of Economy and Competitiveness research projects PaleoNAO (CGL2010-15767), RapidNAO (CGL2013-40608-R), and PaleoModes (CGL2016-75281-C2), and by the Luso-American Foundation. This work is contributing to the Institut de Ciència i Tecnologia Ambiental (ICTA) - Universitat Autonoma de Barcelona “Unit of Excellence” Maria de Maetzu (CEX2019-000940-M) grant. The International Atomic Energy Agency is grateful for the support provided to its Environment Laboratories by the Government of the Principality of Monaco.

Members of the order Isochrysidales are unique among haptophyte lineages in being the exclusive producers of alkenones, long‐chain ketones that are commonly used for paleotemperature reconstructions. Alkenone‐producing haptophytes are divided into three major groups based largely on molecular ecological data: Group I is found in freshwater lakes, Group II commonly occurs in brackish and coastal marine environments, and Group III consists of open ocean species. Each group has distinct alkenone distributions; however, only Groups II and III Isochrysidales currently have cultured representatives. The uncultured Group I Isochrysidales are distinguished geochemically by the presence of tri‐unsaturated alkenone isomers (C37:3b Me, C38:3b Et, C38:3b Me, C39:3b Et) present in water column and sediment samples, yet their genetic diversity, morphology, and environmental controls are largely unknown. Using small‐subunit (SSU) ribosomal RNA (rRNA) marker gene amplicon high‐throughput sequencing of environmental water column and sediment samples, we show that Group I is monophyletic with high phylogenetic diversity and contains a well‐supported clade separating the previously described “EV” clade from the “Greenland” clade. We infer the first partial large‐subunit (LSU) rRNA gene Group I sequence phylogeny, which uncovered additional well‐supported clades embedded within Group I. Relative to Group II, Group I revealed higher levels of genetic diversity despite conservation of alkenone signatures and a closer evolutionary relationship with Group III. In Group I, the presence of the tri‐unsaturated alkenone isomers appears to be conserved, which is not the case for Group II. This suggests differing environmental influences on Group I and II and perhaps uncovers evolutionary constraints on alkenone biosynthesis.

Isochrysidales species of the phylum Haptophyta are the exclusive producers of C37 to C42 long chain alkyl ketones, also called long chain alkenones (LCAs). While LCA distributions are known to vary with temperature and salinity, it is difficult to tease apart the direct effects of environmental parameters vs changes in the LCA-producing organisms. The Baltic Sea surface salinity gradient, which ranges from oligohaline (0.5–5 g/kg) to polyhaline (18–30 g/kg), represents a unique opportunity to study the relationships between salinity changes, species distribution and LCA biomarkers in a single ecosystem. LCA biomarkers revealed the presence of the three known Isochrysidales groups (Groups I, II and III) in Baltic Sea surface sediments, and the presence of Groups I and II were further confirmed with DNA sequencing. Group III Isochrysidales were present in the mixoeuhaline Skagerrak based on LCA signature alone. Groups I and II Isochrysidales were found for the first time in the Baltic Sea using a combination of LCAs and DNA biomarkers, solving an eighteen-year long mystery of Baltic Sea LCA-producing haptophyte identity. Group II Isochrysidales, which have a large salinity tolerance range, were spread over the Skagerrak and the complete Baltic Sea, but were characteristic for the central Baltic Sea. Oligohaline Group I Isochrysidales were representative for the northern Baltic Sea. However, evidence of Group I Isochrysidales in the central and southern Baltic Sea suggests a possible transport by surface currents since this group is typically confined to oligohaline conditions. Testing the recently developed ratio of isomeric C37 ketones (RIK37) against the Baltic Sea surface salinity gradient revealed a significant positive correlation. This may represent a salinity proxy reflecting the amount of Group I Isochrysidales relative to Group II Isochrysidales in oligohaline environments. The present study elucidates for the first time the identity and the spatial distribution of LCA producers thriving in a large and stable brackish environment.

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.

Summary Species of the floating macroalga Sargassum occur in a range of marine settings, in particular the tropical North Atlantic. Recently, inundations of Sargassum washing ashore particularly in the Caribbean, have been a socio-economic and ecological concern. Since abundance records of floating Sargassum are limited, geological sediment cores could provide clues as to the causes of the accumulations and help with predicting future growth dynamics. Open-ocean Sargassum sinks as it ages with remnants observed both on the seabed and buried in sediments. Floating Sargassum provides a habitat for many microorganisms, including N2 fixing cyanobacteria. Heterocyst glycolipids (HGs) have proven to be highly specific biomarkers for heterocystous N2 fixing cyanobacteria. HGs with hexose (C6) head groups are generally associated with free-living cyanobacteria while those with pentose (C5) head groups have been found mainly in endosymbiotic species (found within diatoms). These HGs have been used to trace the cyanobacterial occurrence and activity back in the geological record. We hypothesize that past occurrence of Sargassum can be traced in the sediment record using HGs as a quasi-biomarker for Sargassum. In this study, we looked at the HG distribution in two Sargassum species collected across the tropical North Atlantic and in associated underlying surface sediments.

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).

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.

Microplastics (MP) are defined as “any synthetic solid particle or polymeric matrix, with regular or irregular shape and with size ranging from 1 μm to 5 mm, of either primary or secondary manufacturing origin, which are insoluble in water”.

The presence of a microbial biofilm on marine plastic was described in the pages of Science Magazine over 45 years ago in one of the very first publications reporting plastic in the ocean (Carpenter and Smith, Science 175:1240–1241, 1972). After these early reports, the microbial communities associated with plastic lost attention until about 7 years ago when modern DNA sequencing began revealing the details of this “invisible” world in finer detail. The Plastisphere, or thin layer of microbial life that surrounds plastic in aquatic environments, occurs on every one of the trillions of small pieces of plastic in the ocean. This miniature ecosystem includes primary producers using sunlight and inorganic chemicals to grow, grazers feeding on these “fields” of primary producers, predators killing and eating other cells, parasites, symbionts living together with their hosts, and degraders recycling biomass and chemicals for reuse in the system. Despite the quantities of plastic documented in the ocean, the actual impact of plastic on marine ecosystems is largely unknown. The Plastisphere could play a role in the fate and impact of plastic in our environment, including increasing the productivity of open ocean environments (Bryant et al., mSystems 1:1, 2016), generating greenhouse gases (Royer et al., Plos One 13:e0200574, 2018), influencing ingestion and settling by animals (Hadfield, Ann Rev Mar Sci 3:453, 2011; Savoca et al., Sci Adv 2:e1600395, 2016), determining how long plastic takes to break down and sink (Ye and Andrady, Mar Pollut Bull 22:608–613, 1991), and transporting invasive species including potentially harmful microbes (Zettler et al. 2013. Environ Sci Technol 47:7137–7146, 2013).

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.

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.

Plastic marine debris is a global problem, but due to its widespread and patchy distribution, gathering sufficient samples for scientific research is challenging with limited ship time and human resources. Taking advantage of public interest in the impact of plastic on the marine environment, successful Citizen Science (CS) programs incorporate members of the public to provide repeated sampling for time series as well as synoptic collections over wide geographic regions. A key challenge with any CS program is to ensure standardized methods and quality control so that the samples and data can legitimately be compared and used in peer-reviewed research. This article describes several successful examples and outlines suggestions for projects cooperating with citizen scientists to provide reliable samples and accurate data, with benefits to science, citizen scientists, and society in general.

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.

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.

Three-quarters of all marine debris (MD) consists of plastic, a reflection of their worldwide use, production and waste mismanagement. Data on MD distributions can improve our ability to effectively reduce debris that escapes onto shorelines and the ocean. In this study, the Matrix Scoring Technique (Marine Strategy Framework Directive Technical Group on Marine Litter) was applied as an approach to calculate the likelihood of single debris items originating from a series of potential sources. Factors considered were: identity and function of debris, beach location, influential activities, “mix” of debris found, presence of indicator items, and quantity of MD. The standing-stock (abundance and composition) of MD was investigated in two sandy beaches (Conceição and Porto Pim) of the Azores Archipelago (NE Atlantic) for the period 2012–2018. The results of this study show promise towards the implementation of a new classification method to determine beach debris sources in remote open-ocean areas.

The Espenberg maar lakes on the Seward Peninsula, Alaska, are the largest volcanic crater lakes in the world and contain the longest known lacustrine sedimentary archives in Alaska. The lack of glacial-aged marine sedimentary archives around the Bering Land Bridge due to exposure of the shelf during sea level low-stands makes these lakes highly valuable for understanding the region’s past climate and environmental changes. Located en route to humanity’s last colonized American continents, the Seward Peninsula’s climate and environments during the last glacial period bear major anthropological significance. However, a lack of quantitative proxies has so far hampered exploration of these lakes for paleoclimate reconstructions. Here we report, for the first time, the discovery of abundant Group I alkenones and Isochrysidales in surface sediments from three maar lakes: White Fish, North Killeak and Devil Mountain, using a combination of lipid biomarker and 18S rRNA gene sequencing analyses. Our discovery adds to the expanding list of oligotrophic freshwater lakes where Group I alkenones are found, and water chemistry data contribute to the understanding of the environmental controls on Group I Isochrysidales. Our results further confirm the use of the U K37 index of Group I alkenones as a proxy for the mean temperature of the spring isotherm (MTSI) and RIK37 as a quantitative measurement for Isochrysidales group mixing. We also demonstrate the analytical challenges for analyzing alkenones in freshwater lakes and the effectiveness of eliminating coelution using silver thiolate chromatographic material (AgTCM).

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

Marine litter (ML) consists of any item of anthropogenic origin that has been lost, discarded or intentionally disposed of into the environment, being acknowledged as a worldwide environmental and ecological threat. In the last decade, there has been an attempt across different sectors to tackle, reduce and mitigate sources of litter. In this study, meso and macrodebris between 2 and 30 cm was recorded and classified in two established study areas (Porto Pim and Conceição beaches), throughout five monitoring years (2012–2018). The litter abundance, density and weighted average by abundance were evaluated in eight main categories: plastics, cloths/fabrics, glass, metals, rubber, processed lumber, other and large. Field surveys provided evidence that plastic represented 95% of all litter. ML abundance was treated as an “environmental variable” and used to determine its anomalies, temporal trends and forecasts. Results from this time-series addressed possible periodic oscillations and density peaks of litter. Reference values of ML presence were obtained and could potentially be used for developing a diagnostic tool for anthropogenic pollution in the Azores.

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.

Alkenone unsaturation indices, represented by either UK37 or UK′37, are important tools for paleoclimate studies. The UK37 index is a reflection of the average number of double bonds from di-, tri-, tetra-unsaturated alkenones, but UK′37 excludes the C37:4 in the calculation. Extensive studies indicate UK′37 provides better regressions against in situ Sea Surface Temperatures (SST) than UK37 and is the most widely used SST proxy. However, recent studies have shown that including C37:4 alkenones for lacustrine or brackish water haptophytes such as Ruttnera (Chrysotila) lamellosa and Isochrysis galbana improves temperature correlations although there are still significant deviations at the extreme high and low temperatures. In this study, we use new culture-based calibration experiments alongside published culture data and in situ water column or surface sediment data, to demonstrate that a further improved temperature calibration for alkenones is, in fact, achieved when the di-unsaturated alkenone is excluded from the computation of the unsaturation index. We propose new indices, termed UK″ [UK″37 = C37:3/(C37:3 + C37:4) or UK″38 = C38:3/(C38:3 + C38:4)], for lacustrine, brackish and estuarine waters. Our observation suggests that di-unsaturated alkenones play a less important role than tri- and tetra-unsaturated alkenones in regulating cell functions to temperature variations in lacustrine and brackish waters. We suggest using UK″ indices for paleotemperature reconstructions in the lacustrine and estuarine settings.

Microplastics (particles less than 5 mm) numerically dominate marine debris and occur from coastal waters to mid-ocean gyres, where surface circulation concentrates them. Given the prevalence of plastic marine debris (PMD) and the rise in plastic production, the impacts of plastic on marine ecosystems will likely increase. Microscopic life (the “Plastisphere”) thrives on these tiny floating “islands” of debris and can be transported long distances. Using next-generation DNA sequencing, we characterized bacterial communities from water and plastic samples from the North Pacific and North Atlantic subtropical gyres to determine whether the composition of different Plastisphere communities reflects their biogeographic origins. We found that these communities differed between ocean basins – and to a lesser extent between polymer types – and displayed latitudinal gradients in species richness. Our research reveals some of the impacts of microplastics on marine biodiversity, demonstrates that the effects and fa...

Protists (microbial eukaryotes) are diverse, major components of marine ecosystems, and are fundamental to ecosystem services. In the last 10 years, molecular studies have highlighted substantial novel diversity in marine systems including sequences with no taxonomic context. At the same time, many known protists remain without a DNA identity. Since the majority of pelagic protists are too small to identify by light microscopy, most are neither comprehensively or regularly taken into account, particularly in Long-term Ecological Research Sites. This potentially undermines the quality of research and the accuracy of predictions about biological species shifts in a changing environment. The ICES Working Group for Phytoplankton and Microbial Ecology conducted a questionnaire survey in 2013–2014 on methods and identification of protists using molecular methods plus a literature review of protist molecular diversity studies. The results revealed an increased use of high-throughput sequencing methods and a recognition that sequence data enhance the overall datasets on protist species composition. However, we found only a few long-term molecular studies and noticed a lack of integration between microscopic and molecular methods. Here, we discuss and put forward recommendations to improve and make molecular methods more accessible to Long-term Ecological Research Site investigators.

The 18S protocol detailed here is designed to amplify eukaryotes broadly with a focus on microbial eukaryotic lineages. The primers target the 18S SSU rRNA and are based on those of Amaral-Zettler et al. (2009). The constructs are designed to be used with the Illumina platform. For running these libraries on the MiSeq and HiSeq, please make sure you read the supplementary methods of Caporaso et al. (2012). You will need to make your sample more complex by adding 5-10% PhiX to your run. The outlines of the protocol are the same as the 16S protocol, but different primers, PCR conditions, and sequencing primers are used. In addition, we have designed a blocking primer that reduces the amplification of vertebrate host DNA to be used on host-associated samples, especially those that have a low eukaryotic biomass. Blocking primer strategy is based on Vestheim et al. (2008).

Prophylactic antibiotics are widespread in the aquaculture industry and are used where vaccination is impossible or overly expensive. If antibiotics impact fish as they do mice and humans, prophylactic administrations in aquaculture and ornamental fish farms may increase downstream disease susceptibility in target hosts, despite short-term pathogen control benefits. Recent research has suggested that their use exacerbates bacterial outbreaks by creating sterile, nutrient-rich environments for invading pathogens to colonize and could help to explain rising economic costs of bacterial outbreaks in aquaculture. Our findings suggest a long-term cost of prophylactic antibiotic use and demonstrate a probiotic-based solution that does not rely on full microbiome community transplantation., Prophylactic antibiotics in the aquaculture and ornamental fish industry are intended to prevent the negative impacts of disease outbreaks. Research in mice and humans suggests that antibiotics may disturb microbiome communities and decrease microbiome-mediated disease resistance, also known as “colonization resistance.” If antibiotics impact fish as they do mice and humans, prophylactic administrations on aquaculture farms may increase downstream disease susceptibility in target hosts, despite short-term pathogen control benefits. We tested the effects of antibiotics on mortality after a pathogen challenge in the Poecilia sphenops black molly and subsequently tested if probiotic inoculations could reverse any antibiotic-induced losses of disease resistance. We found that antibiotic treatment significantly increased fish mortality. We further found that our two candidate probiotic bacterial species, Phaeobacter inhibens S4Sm and Bacillus pumilus RI06-95Sm, were able to colonize black molly microbiomes and reverse the negative impacts of antibiotics. Despite the positive impact on survival, probiotic treatment did not influence overall microbiome community structure or diversity. Our results suggest that subtle manipulations of microbiome composition can have dramatic impacts on host phenotype. The results of this study have implications for how antibiotic-treated microbiomes can be restored and suggest that small-scale additions may be as effective as wholesale transplants. IMPORTANCE Prophylactic antibiotics are widespread in the aquaculture industry and are used where vaccination is impossible or overly expensive. If antibiotics impact fish as they do mice and humans, prophylactic administrations in aquaculture and ornamental fish farms may increase downstream disease susceptibility in target hosts, despite short-term pathogen control benefits. Recent research has suggested that their use exacerbates bacterial outbreaks by creating sterile, nutrient-rich environments for invading pathogens to colonize and could help to explain rising economic costs of bacterial outbreaks in aquaculture. Our findings suggest a long-term cost of prophylactic antibiotic use and demonstrate a probiotic-based solution that does not rely on full microbiome community transplantation.

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.

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.

The classic view of polar ocean foodwebs emphasizes large predators sustained by energy and material flow through short, efficient diatom−krill−predator food chains. Bacterial activity is generally low in cold polar waters compared to that at lower latitudes. This view appears to be changing, with new studies of microbial foodwebs in Arctic and Antarctic oceans. We char- acterized bacterial, archaeal, and eukaryotic community diversity and composition from 2 depths (near surface and below the euphotic zone) at 4 sites, including the inshore and offshore, and north and south corners of a sampling grid along the western coast of the Antarctic Peninsula (WAP). We detected up to 2-fold higher richness in microbial eukaryotes at surface and deep inshore northern stations as compared to southern stations, but offshore northern and southern stations revealed either no trend or higher richness at depth in the south. In contrast, bacterial and archaeal richness showed no significant differences either inshore or offshore at northern versus southern extents, but did vary with depth. Archaea were virtually absent in summer surface waters, but were present in summer deep and winter surface samples. Overall, winter bacterial and archaeal assemblages most closely resembled summer sub-euphotic zone assemblages, reflecting well-established seasonal patterns of water column turnover and stratification that result in an isolated layer of 'winter water' below the euphotic zone. Inter-domain heterotroph− phototroph interactions were evident from network analysis. The WAP is among the most rapidly warming regions on earth. Our results provide a baseline against which future change in micro- bial communities may be assessed.

We report an in-depth survey of next-generation DNA sequencing of ciliate diversity and community structure in two permanently ice-covered McMurdo Dry Valley lakes during the austral summer and autumn (November 2007 and March 2008). We tested hypotheses on the relationship between species richness and environmental conditions including environmental extremes, nutrient status, and day length. On the basis of the unique environment that exists in these high-latitude lakes, we expected that novel taxa would be present. Alpha diversity analyses showed that extreme conditions-that is, high salinity, low oxygen, and extreme changes in day length-did not impact ciliate richness; however, ciliate richness was 30% higher in samples with higher dissolved organic matter. Beta diversity analyses revealed that ciliate communities clustered by dissolved oxygen, depth, and salinity, but not by season (i.e., day length). The permutational analysis of variance test indicated that depth, dissolved oxygen, and salinity had significant influences on the ciliate community for the abundance matrices of resampled data, while lake and season were not significant. This result suggests that the vertical trends in dissolved oxygen concentration and salinity may play a critical role in structuring ciliate communities. A PCR-based strategy capitalizing on divergent eukaryotic V9 hypervariable region ribosomal RNA gene targets unveiled two new genera in these lakes. A novel taxon belonging to an unknown class most closely related to Cryptocaryon irritans was also inferred from separate gene phylogenies.

The alkenone unsaturation index (U37K or U37K′) serves as a critical tool for reconstructing temperature in marine environments. Lacustrine haptophyte algae are genetically distinct from their ubiquitous and well studied marine counterparts, and the unknown species-specific genetic imprints on long chain alkenone production by lacustrine species have hindered the widespread application of the U37K temperature proxy to lake sediment records. The haptophyte Pseudoisochrysis paradoxa produces alkenones but its U37K calibration has never been determined. It has an alkenone fingerprint abundant in tetraunsaturated alkenones, a hallmark of lacustrine environments. We present here the first calibration of the U37K index to temperature for a culture of P. paradoxa. We found that the U37K index accurately captured the alkenone response to temperature whereas the U37K′ index failed to do so, with U37K′ values below 0.08 projecting to two different temperature values. Our results add a fifth species-specific U37K calibration and provide another line of evidence that different haptophyte species require different U37K calibrations. The findings also highlight the necessary inclusion of the C37:4 alkenone when reconstructing temperatures from P. paradoxa-derived alkenone records.

Humans depend on diverse ocean ecosystems for food, jobs, and sustained well-being, yet many stressors threaten marine life. Extensive research has demonstrated that maintaining biodiversity promotes ocean health and service provision; therefore, monitoring the status and trends of marine biodiversity is important for effective ecosystem management. However, there is no systematic sustained program for evaluating ocean biodiversity. Coordinating existing monitoring and building a proactive marine biodiversity observation network will support efficient, economical resource management and conservation and should be a high priority. A synthesis of expert opinions suggests that, to be most effective, a marine biodiversity observation network should integrate biological levels, from genes to habitats; link biodiversity observations to abiotic environmental variables; site projects to incorporate environmental forcing and biogeography; and monitor adaptively to address emerging issues. We summarize examples illustrating how to leverage existing data and infrastructure to meet these goals.

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.

International audience; To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.