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Gram-negative bacteria produce outer membrane vesicles (OMVs) and contain bacterial cargo including nucleic acids and proteins. The proteome of OMVs can be altered by various factors including bacterial growth stage, growth conditions, and environmental factors. However, it is currently unknown if the mechanism of OMV biogenesis can determine their proteome. In this study, we examined whether the mechanisms of OMV biogenesis influenced the production and protein composition of Pseudomonas aeruginosa OMVs. OMVs were isolated from three P. aeruginosa strains that produced OMVs either by budding alone, by explosive cell lysis, or by both budding and explosive cell lysis. We identified that the mechanism of OMV biogenesis dictated OMV quantity. Furthermore, a global proteomic analysis comparing the proteome of OMVs to their parent bacteria showed significant differences in the identification of proteins in bacteria and OMVs. Finally, we determined that the mechanism of OMV biogenesis influenced the protein composition of OMVs, as OMVs released by distinct mechanisms of biogenesis differed significantly from one another in their proteome and functional enrichment analysis. Overall, our findings reveal that the mechanism of OMV biogenesis is a main factor that determines the OMV proteome which may affect their subsequent biological functions.

Gram-positive bacteria ubiquitously produce membrane vesicles (MVs), and although they contribute to biological functions, our knowledge regarding their composition and immunogenicity remains limited. Here we examine the morphology, contents and immunostimulatory functions of MVs produced by three Staphylococcus aureus strains; a methicillin resistant clinical isolate, a methicillin sensitive clinical isolate and a laboratory-adapted strain. We observed differences in the number and morphology of MVs produced by each strain and showed that they contain microbe-associated molecular patterns (MAMPs) including protein, nucleic acids and peptidoglycan. Analysis of MV-derived RNA indicated the presence of small RNA (sRNA). Furthermore, we detected variability in the amount and composition of protein, nucleic acid and peptidoglycan cargo carried by MVs from each S. aureus strain. S. aureus MVs activated Toll-like receptor (TLR) 2, 7, 8, 9 and nucleotide-binding oligomerization domain containing protein 2 (NOD2) signalling and promoted cytokine and chemokine release by epithelial cells, thus identifying that MV-associated MAMPs including DNA, RNA and peptidoglycan are detected by pattern recognition receptors (PRRs). Moreover, S. aureus MVs induced the formation of and colocalized with autophagosomes in epithelial cells, while inhibition of lysosomal acidification using bafilomycin A1 resulted in accumulation of autophagosomal puncta that colocalized with MVs, revealing the ability of the host to degrade MVs via autophagy. This study reveals the ability of DNA, RNA and peptidoglycan associated with MVs to activate PRRs in host epithelial cells, and their intracellular degradation via autophagy. These findings advance our understanding of the immunostimulatory roles of Gram-positive bacterial MVs in mediating pathogenesis, and their intracellular fate within the host.

Aim Topographic complexity is widely accepted as a key driver of biodiversity, but at the patch‐scale, complexity–biodiversity relationships may vary spatially and temporally according to the environmental stressors complexity mitigates, and the species richness and identity of potential colonists. Using a manipulative experiment, we assessed spatial variation in patch‐scale effects of complexity on intertidal biodiversity. Location 27 sites within 14 estuaries/bays distributed globally. Time period 2015–2017. Major taxa studied Functional groups of algae, sessile and mobile invertebrates. Methods Concrete tiles of differing complexity (flat; 2.5‐cm or 5‐cm complex) were affixed at low–high intertidal elevation on coastal defence structures, and the richness and abundance of the colonizing taxa were quantified after 12 months. Results The patch‐scale effects of complexity varied spatially and among functional groups. Complexity had neutral to positive effects on total, invertebrate and algal taxa richness, and invertebrate abundances. However, effects on the abundance of algae ranged from positive to negative, depending on location and functional group. The tidal elevation at which tiles were placed accounted for some variation. The total and invertebrate richness were greater at low or mid than at high intertidal elevations. Latitude was also an important source of spatial variation, with the effects of complexity on total richness and mobile mollusc abundance greatest at lower latitudes, whilst the cover of sessile invertebrates and sessile molluscs responded most strongly to complexity at higher latitudes. Conclusions After 12 months, patch‐scale relationships between biodiversity and habitat complexity were not universally positive. Instead, the relationship varied among functional groups and according to local abiotic and biotic conditions. This result challenges the assumption that effects of complexity on biodiversity are universally positive. The va

Microbially mediated biogeochemical processes are crucial for climate regulation and may be disrupted by anthropogenic contaminants. To better manage contaminants, we need tools that make real-time causal links between stressors and altered microbial functions, and the potential consequences for ecosystem services such as climate regulation. In a manipulative field experiment, we used metatranscriptomics to investigate the impact of excess organic enrichment and metal contamination on the gene expression of nitrogen and sulfur metabolisms in coastal sediments. Our gene expression data suggest that excess organic enrichment results in (i) higher transcript levels of genes involved in the production of toxic ammonia and hydrogen sulfide and (ii) lower transcript levels associated with the degradation of a greenhouse gas (nitrous oxide). However, metal contamination did not have any significant impact on gene expression. We reveal the genetic mechanisms that may lead to altered productivity and greenhouse gas production in coastal sediments due to anthropogenic contaminants. Our data highlight the applicability of metatranscriptomics as a management tool that provides an immense breadth of information and can identify potentially impacted process measurements that need further investigation.

Viruses are ubiquitous, abundant and play an important role in all ecosystems. Here, we advance understanding of coastal sediment viruses by exploring links in the composition and abundance of sediment viromes to environmental stressors and sediment bacterial communities. We collected sediment from contaminated and reference sites in Sydney Harbour and used metagenomics to analyse viral community composition. The proportion of phages at contaminated sites was significantly greater than phages at reference sites, whereas eukaryotic viruses were relatively more abundant at reference sites. We observed shifts in viral and bacterial composition between contaminated and reference sites of a similar magnitude. Models based on sediment characteristics revealed that total organic carbon in the sediments explained most of the environmental stress-related variation in the viral dataset. Our results suggest that the presence of anthropogenic contaminants in coastal sediments could be influencing viral community composition with potential consequences for associated hosts and the environment.

Theories of species coexistence often describe a trade-off between colonising and competitive abilities. In sessile marine invertebrates, this trade-off can manifest as trends in species distributions relative to the size of isolated patches of substrate. Based on their abilities to find available substrate and competitively exclude neighbours, good colonisers tend to dominate smaller patches, whereas better competitors tend to monopolise larger patches. In theory, species with equivalent colonising and competitive abilities should display similar distributions across patch sizes. We used patch size to observe this manifestation of the competition-colonisation trade-off over 20° of latitude. The trade-off was more readily observed at lower latitudes and was proportional to the ‘ecological age’ of communities (i.e. the degree of resource acquisition and likelihood of species interactions). Results suggest that ecological age may mediate the prominence of stochastic or deterministic coexistence mechanisms and will depend on the rate of ecological processes.

The strength and importance of consumer effects are predicted to increase toward low latitudes, but this hypothesis has rarely been tested using a spatially consistent methodology. In a consumer-exclusion experiment spanning twenty degrees of latitude along the east Australian coast, the magnitude of consumer effects on sub-tidal sessile assemblage composition was not greater at low than high latitudes. Across caged and control assemblages, Shannon's diversity, Pielou's evenness, and richness of functional groups decreased with increasing latitude, but the magnitude of consumer effects on these metrics did not display consistent latitudinal gradients. Instead, latitudinal gradients in consumer effects were apparent for individual functional groups. Solitary ascidians displayed the pattern consistent with predictions of greater direct effects of predators at low than high latitude. As consumers reduced the biomass of this and other competitive dominants, groups less prone to predation (e.g., hydroids, various groups of bryozoans) were able to take advantage of freed space in the presence of consumers and show increased abundances there. This large-scale empirical study demonstrates the complexity of species interactions, and the failure of assemblage-level metrics to adequately capture consumer effects over large spatial gradients.

Historically, marine ecologists have lacked efficient tools that are capable of capturing detailed species distribution data over large areas. Emerging technologies such as high-resolution imaging and associated machine-learning image-scoring software are providing new tools to map species over large areas in the ocean. Here, we combine a novel diver propulsion vehicle (DPV) imaging system with free-to-use machine-learning software to semi-automatically generate dense and widespread abundance records of a habitat-forming algae over ~5,000 m2 of temperate reef. We employ replicable spatial techniques to test the effectiveness of traditional diver-based sampling, and better understand the distribution and spatial arrangement of one key algal species. We found that the effectiveness of a traditional survey depended on the level of spatial structuring, and generally 10–20 transects (50 × 1 m) were required to obtain reliable results. This represents 2–20 times greater replication than have been collected in previous studies. Furthermore, we demonstrate the usefulness of fine-resolution distribution modeling for understanding patterns in canopy algae cover at multiple spatial scales, and discuss applications to other marine habitats. Our analyses demonstrate that semi-automated methods of data gathering and processing provide more accurate results than traditional methods for describing habitat structure at seascape scales, and therefore represent vastly improved techniques for understanding and managing marine seascapes.

Underwater cities have long been the subject of science fiction novels and movies, but the "urban sprawl" of artificial structures being developed in marine environments has widespread ecological consequences. The practice of combining ecological principles with the planning, design, and operation of marine artificial structures is gaining in popularity, and examples of successful engineering applications are accumulating. Here we use case studies to explore marine ecological engineering in practice, and introduce a conceptual framework for designing artificial structures with multiple functions. The rate of marine urbanization will almost certainly escalate as "aquatourism" drives the development of underwater accommodations. We show that current and future marine developments could be designed to reduce negative ecological impacts while promoting ecosystem services.

Ecosystem functioning underpins the ecosystem services upon which humans rely. Critical functions, such as primary and secondary productivity, are, however, increasingly threatened by a range of anthropogenic stressors. Although the extent of the threat of contamination is large and has been increasing, pollution is one of the least-studied stressors in ecology. We did a systematic review and critical synthesis of the effects of contaminants on marine and estuarine ecosystem functioning. No other stressors besides toxic chemicals were included in this review. We identified 264 relevant studies across a range of contaminants. Toxic contaminants generally altered marine ecosystem functioning by reducing productivity and increasing respiration. Effects varied, however, according to the type of contaminant and the component(s) of the system studied (e.g. particular trophic levels, functional groups or taxonomic groups). Toxicity studies that included a measure of ecosystem function were strongly biased towards planktonic communities in contrast to studies of biodiversity, which have been dominated by work on soft-sediment communities. Toxicant studies that included measures of ecosystem function rarely included a measure of biodiversity and rarely interpreted their findings within an ecosystem function context. Studies that included multiple components of an ecosystem, that is more than one functional group of organisms, were more likely to find no effect of contamination, possibly due to ecological interactions. Studies that suffered from unclear or flawed methodology were more likely to find a significant impact of contaminants on some endpoints of ecosystem functioning than studies with appropriate designs. Synthesis and applications. Up to 70% of studies found negative impacts of contaminants on primary production. Toxic contaminants therefore have the potential to greatly affect the ecosystem services and benefits provided by these systems. Our findings will help m

Summary: We are now beginning to understand the role of intraspecific diversity on fundamental ecological phenomena. There exists a paucity of knowledge, however, regarding how intraspecific, or genetic diversity, may covary with other important factors such as propagule pressure. A combination of theoretical modelling and experimentation was used to explore the way propagule pressure and genetic richness may interact. We compare colonization rates of the Australian bivalve Saccostrea glomerata (Gould 1885). We cross propagule size and genetic richness in a factorial design in order to examine the generalities of our theoretical model. Modelling showed that diversity and propagule pressure should generally interact synergistically when positive feedbacks occur (e.g. aggregation). The strength of genotype effects depended on propagule size, or the numerical abundance of arriving individuals. When propagule size was very small (<4 individuals), however, greater genetic richness unexpectedly reduced colonization. The probability of S. glomerata colonization was 76% in genetically rich, larger propagules, almost 39 percentage points higher than in genetically poor propagules of similar size. This pattern was not observed in less dense, smaller propagules. We predict that density-dependent interactions between larvae in the water column may explain this pattern. © 2013 British Ecological Society.

In this study, 454 pyrosequencing of the 16S rRNA gene was used to investigate sediment bacterial community response to contaminant disturbance across six estuaries with differing levels of 'modification'. We observed a significant influence of metal and polycyclic aromatic hydrocarbon contaminants in shaping bacterial community composition, structure and diversity, with metals being the more influential contaminant. An abundant and pervasive 'core' set of bacteria found in every sample were largely responsible for mediating community response to contamination. These 13 core operational taxonomic units were mostly comprised of Gamma-, Delta-, Alphaproteobacteria and Acidobacteria. Sediment silt and metals together explained the most variation in bacterial community composition (19.7%). Following this strong contaminant signature, salinity and temperature represented important environmental variables predicting 10.9% of community variation. While overall network connectivity measures supported the idea of an inherently diverse soil microbiome with some degree of functional redundancy, lower values observed in contaminated sediments indicate potential structural perturbations in the community from fracturing or loss of bacterial associations. The large number of unclassified sequences obtained in this study contribute to improving our understanding of environmentally relevant strains in relation to anthropogenic contamination, which have been overlooked in laboratory studies. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Some ecosystems can undergo abrupt transformation in response to relatively small environmental change. Identifying imminent 'tipping points' is crucial for biodiversity conservation, particularly in the face of climate change. Here, we describe a tipping point mechanism likely to induce widespread regime shifts in polar ecosystems. Seasonal snow and ice-cover periodically block sunlight reaching polar ecosystems, but the effect of this on annual light depends critically on the timing of cover within the annual solar cycle. At high latitudes, sunlight is strongly seasonal, and ice-free days around the summer solstice receive orders of magnitude more light than those in winter. Early melt that brings the date of ice-loss closer to midsummer will cause an exponential increase in the amount of sunlight reaching some ecosystems per year. This is likely to drive ecological tipping points in which primary producers (plants and algae) flourish and out-compete dark-adapted communities. We demonstrate this principle on Antarctic shallow seabed ecosystems, which our data suggest are sensitive to small changes in the timing of sea-ice loss. Algae respond to light thresholds that are easily exceeded by a slight reduction in sea-ice duration. Earlier sea-ice loss is likely to cause extensive regime shifts in which endemic shallow-water invertebrate communities are replaced by algae, reducing coastal biodiversity and fundamentally changing ecosystem functioning. Modeling shows that recent changes in ice and snow cover have already transformed annual light budgets in large areas of the Arctic and Antarctic, and both aquatic and terrestrial ecosystems are likely to experience further significant change in light. The interaction between ice-loss and solar irradiance renders polar ecosystems acutely vulnerable to abrupt ecosystem change, as light-driven tipping points are readily breached by relatively slight shifts in the timing of snow and ice-loss. © 2013 John Wiley & Sons Ltd.