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Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.In this Review, Grossart and colleagues conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. They focus on currently unexplored aquatic fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.

Key Points Virus-mediated lysis of host cells results in the generation of dissolved organic carbon (DOC), dissolved organic nitrogen (DON) and dissolved organic phosphorus (DOP) via a process that is known as the 'viral shunt'. Previous quantitative estimates of the contribution of the viral shunt to biogeochemical cycles focused on host cellular constituents and overlooked the contribution of virus particles. In this Analysis article, we develop a biophysical scaling model that predicts the elemental contents and compositions of virus particles. This scaling model was validated using detailed sequence and structural contents of intact bacteriophage particles. Viruses are predicted to be enriched in phosphorus, so much so that the total phosphorus content in a burst of released viruses may approach that of the phosphorus content in an uninfected host. As a consequence, cellular debris may be depleted in phosphorus compared with the stoichiometry of hosts. Furthermore, by extrapolating the model to the ecosystem scale, marine viruses are predicted to contain an important fraction (for example, >5%) of the total DOP pool in some systems (for example, in surface waters, when virus density exceeds 3.5 × 10 10 and the DOP concentration is approximately 100 nM). Weitz and colleagues use a biophysical scaling model of intact virus particles to quantify differences in the elemental stoichiometry of marine viruses compared with their microbial hosts. They propose that, under certain circumstances, marine virus populations could make a previously unrecognised and important contribution to the reservoir and cycling of oceanic phosphorus. In marine environments, virus-mediated lysis of host cells leads to the release of cellular carbon and nutrients and is hypothesized to be a major driver of carbon recycling on a global scale. However, efforts to characterize the effects of viruses on nutrient cycles have overlooked the geochemical potential of the virus particles themselves, particularly with respect to their phosphorus content. In this Analysis article, we use a biophysical scaling model of intact virus particles that has been validated using sequence and structural information to quantify differences in the elemental stoichiometry of marine viruses compared with their microbial hosts. By extrapolating particle-scale estimates to the ecosystem scale, we propose that, under certain circumstances, marine virus populations could make an important contribution to the reservoir and cycling of oceanic phosphorus.

Global climate change includes rising temperatures and increased pCO2 concentrations in the ocean, with potential deleterious impacts on marine organisms. In this case study we conducted a four-week climate change incubation experiment, and tested the independent and combined effects of increased temperature and partial pressure of carbon dioxide (pCO2), on the microbiomes of a foundation species, the giant kelp Macrocystis pyrifera, and the surrounding water column. The water and kelp microbiome responded differently to each of the climate stressors. In the water microbiome, each condition caused an increase in a distinct microbial order, whereas the kelp microbiome exhibited a reduction in the dominant kelp-associated order, Alteromondales. The water column microbiomes were most disrupted by elevated pCO2, with a 7.3 fold increase in Rhizobiales. The kelp microbiome was most influenced by elevated temperature and elevated temperature in combination with elevated pCO2. Kelp growth was negatively associated with elevated temperature, and the kelp microbiome showed a 5.3 fold increase Flavobacteriales and a 2.2 fold increase alginate degrading enzymes and sulfated polysaccharides. In contrast, kelp growth was positively associated with the combination of high temperature and high pCO2 'future conditions', with a 12.5 fold increase in Planctomycetales and 4.8 fold increase in Rhodobacteriales. Therefore, the water and kelp microbiomes acted as distinct communities, where the kelp was stabilizing the microbiome under changing pCO2 conditions, but lost control at high temperature. Under future conditions, a new equilibrium between the kelp and the microbiome was potentially reached, where the kelp grew rapidly and the commensal microbes responded to an increase in mucus production.

Iron-oxidizing bacteria (FeOB) play an important role in the global cycling of iron, carbon, and other metals. While it has previously been assumed that bacterial evolution does not frequently involve crossing the salinity barrier, recent studies indicate that such occurrences are more common than previously thought. Our study offers strong evidence that this also happens among FeOB, with new insights into how these bacteria adapt to the new environment, including hydrothermal vents and freshwater habitats. In addition, we emphasize the importance of accurate iron-oxidizing taxa identification through sequencing, rather than relying solely on the morphology of Fe(III) oxyhydroxides and environment. On a larger scale, microorganisms within established communities need to respond to changes in salinity due to events like seawater intrusion in coastal aquifers, and thus, our findings underscore the importance of knowledge of transitions across habitat types with different salt concentrations.

Key Points The application of 'omic' approaches (for example, pyrosequencing, metagenomics, metatranscriptomics and metaproteomics) has generated unprecedented insight into Antarctic microorganisms and revealed intriguing properties about communities that can be linked to their Antarctic-specific habitats. Community composition and ecosystem function are controlled by the polar light regime, biotic and abiotic environmental factors, limnological history and seed populations, biogeography and the limits of aeolian and advective dispersal caused by physical barriers and distance between sites, and perturbation caused by ecosystem change. The polar austral summer is characterized by continuous high solar irradiance, which stimulates phototrophic growth and kinetically accelerates growth. Such communities tend to be oriented towards maximizing the effectiveness of light energy while switching to light-independent processes (for example, chemolithoautotrophy, phagotrophy and heterotrophic utilization of storage compounds) to survive the cold, dark winter. Virus–host interactions are particularly important in the Antarctic food web, in which they not only control remineralization and influence community composition but have unanticipated roles in influencing productivity cycles. Discoveries pertaining to viruses have included systems with a high diversity of novel eukaryotic viruses, phage-resistant bacteria, and archaea capable of evading, defending against and adapting to viruses. Unusual biogeochemical cycles have developed as a result of communities evolving in very specific, local environments. The indigenous communities have developed a range of traits, including a hierarchical structure, low complexity, niche adaptation, clonal dominance, mixotrophy and short-circuited nutrient cycles that enhance the use and conservation of resources. Specific taxa have a major influence on overall ecosystem function, with stability of those biomes being reliant on the key, specialized and fit members maintaining function and not being affected by ecosystem perturbation, particularly anthropocentric climate change and the introduction of alien species. Antarctica has an essential role in regulating Earth's climate and ocean ecosystem function, and Antarctica's biosphere is dominated by microorganisms. In this Review, Cavicchioli discusses the factors that shape the biogeography of Antarctic microorganisms and explores how 'omic' studies have begun to elucidate the mechanisms determining the composition and function of microbial communities in Antarctic aquatic systems. The Earth's biosphere is dominated by cold environments, and the cold biosphere is dominated by microorganisms. Microorganisms in cold Southern Ocean waters are recognized for having crucial roles in global biogeochemical cycles, including carbon sequestration, whereas microorganisms in other Antarctic aquatic biomes are not as well understood. In this Review, I consider what has been learned about Antarctic aquatic microbial ecology from 'omic' studies. I assess the factors that shape the biogeography of Antarctic microorganisms, reflect on some of the unusual biogeochemical cycles that they are associated with and discuss the important roles that viruses have in controlling ecosystem function.

Background Synthetic microplastics (≤5-mm fragments) are emerging environmental contaminants that have been found to accumulate within coastal marine sediments worldwide. The ecological impacts and fate of microplastic debris are only beginning to be revealed, with previous research into these topics having primarily focused on higher organisms and/or pelagic environments. Despite recent research into plastic-associated microorganisms in seawater, the microbial colonization of microplastics in benthic habitats has not been studied. Therefore, we employed a 14-day microcosm experiment to investigate bacterial colonization of low-density polyethylene (LDPE) microplastics within three types of coastal marine sediment from Spurn Point, Humber Estuary, U.K. Results Bacterial attachment onto LDPE within sediments was demonstrated by scanning electron microscopy and catalyzed reporter deposition fluorescence in situ hybridisation (CARD-FISH). Log-fold increases in the abundance of 16S rRNA genes from LDPE-associated bacteria occurred within 7 days with 16S rRNA gene numbers on LDPE surfaces differing significantly across sediment types, as shown by quantitative PCR. Terminal-restriction fragment length polymorphism (T-RFLP) analysis demonstrated rapid selection of LDPE-associated bacterial assemblages whose structure and composition differed significantly from those in surrounding sediments. Additionally, T-RFLP analysis revealed successional convergence of the LDPE-associated communities from the different sediments over the 14-day experiment. Sequencing of cloned 16S rRNA genes demonstrated that these communities were dominated after 14 days by the genera Arcobacter and Colwellia (totalling 84-93% of sequences). Attachment by Colwellia spp. onto LDPE within sediments was confirmed by CARD-FISH. Conclusions These results demonstrate that bacteria within coastal marine sediments can rapidly colonize LDPE microplastics, with evidence for the successional formation of plastisphere-specific bacterial assemblages. Although the taxonomic compositions of these assemblages are likely to differ between marine sediments and the water column, both Arcobacter and Colwellia spp. have previously been affiliated with the degradation of hydrocarbon contaminants within low-temperature marine environments. Since hydrocarbon-degrading bacteria have also been discovered on plastic fragments in seawater, our data suggest that recruitment of hydrocarbonoclastic bacteria on microplastics is likely to represent a shared feature between both benthic and pelagic marine habitats.

Marine dissolved organic matter (DOM) is a major carbon reservoir that acts as a critical control on the Earth’s climate. DOM dynamics are largely regulated by a complex web of chemical-microbial interactions, but the mechanisms underpinning these processes are not well understood. In a three-year time-series, we found that the identity of the microbes is more likely to change between years than the composition of the DOM molecules. The taxonomic variability suggests that metabolisms shared across taxa, encoded by genes that conduct core microbial functions, are responsible for the more stable composition of DOM. While more than three decades of marine prokaryoplankton time-series are available, a similar reference for DOM molecules was missing. This time-series provides an improved understanding of the different responses of DOM molecules and microbes to seasonal environmental changes.

Microorganisms have evolved to thrive in virtually any terrestrial and marine environment, exposing them to various mechanical cues mainly generated by fluid flow and pressure as well as surface contact. Cellular components enable bacteria to sense and respond to physical cues to optimize their function, ultimately improving bacterial fitness. Owing to newly developed biophysical techniques, we are now starting to appreciate the breadth of bacterial phenotypes influenced by mechanical inputs: adhesion, motility, biofilm formation and pathogenicity. In this Review, we discuss how microbiology and biophysics are converging to advance our understanding of the mechanobiology of microorganisms. We first review the various physical forces that bacteria experience in their natural environments and describe the structures that transmit these forces to a cell. We then discuss how forces can provide feedback to enhance adhesion and motility and how they can be transduced by dedicated cellular machinery to regulate diverse phenotypes. Finally, we provide a perspective on how mechanics influence biofilm spatial organization and homeostasis.Microbiology and biophysics are converging to advance our understanding of the mechanobiology of microorganisms. In this Review, Dufrêne and Persat discuss the physical forces that bacteria experience in their natural environments and the structures that transmit these forces to a cell. Furthermore, they explore bacterial phenotypes influenced by mechanical inputs, including adhesion, motility and biofilm formation.

Pathology has not been observed in true seals infected with Brucella pinnipedialis. A lack of intracellular survival and multiplication of B. pinnipedialis in hooded seal (Cystophora cristata) macrophages in vitro indicates a lack of chronic infection in hooded seals. Both epidemiology and bacteriological patterns in the hooded seal point to a transient infection of environmental origin, possibly through the food chain. To analyse the potential role of fish in the transmission of B. pinnipedialis, Atlantic cod (Gadus morhua) were injected intraperitoneally with 7.5 x 107 bacteria of a hooded seal field isolate. Samples of blood, liver, spleen, muscle, heart, head kidney, female gonads and feces were collected on days 1, 7, 14 and 28 post infection to assess the bacterial load, and to determine the expression of immune genes and the specific antibody response. Challenged fish showed an extended period of bacteremia through day 14 and viable bacteria were observed in all organs sampled, except muscle, until day 28. Neither gross lesions nor mortality were recorded. Anti-Brucella antibodies were detected from day 14 onwards and the expression of hepcidin, cathelicidin, interleukin (IL)-1β, IL-10, and interferon (IFN)-γ genes were significantly increased in spleen at day 1 and 28. Primary mononuclear cells isolated from head kidneys of Atlantic cod were exposed to B. pinnipedialis reference (NCTC 12890) and hooded seal (17a-1) strain. Both bacterial strains invaded mononuclear cells and survived intracellularly without any major reduction in bacterial counts for at least 48 hours. Our study shows that the B. pinnipedialis strain isolated from hooded seal survives in Atlantic cod, and suggests that Atlantic cod could play a role in the transmission of B. pinnipedialis to hooded seals in the wild.