Ecology. Coral reef biodiversity--habitat size matters

Antimicrobial activity of coral-associated beneficial bacteria against coral disease-causing microbial pathogens

Microbial infection of immune-compromised corals influences disease severity, resulting in coral mortality. However, coral-associated beneficial bacteria are known to produce antimicrobial compounds that prevent the growth of potential pathogens and invading microbes. Hence, beneficial bacteria associated with coral Porites lutea were isolated and antimicrobial protein and bioactive secondary metabolites were extracted and tested for their antimicrobial activity against putative prokaryotic and eukaryotic coral pathogens. Bioactive secondary metabolites exhibited remarkable antagonism against various coral pathogens such as Serratia marcescens, Vibrio species, and Aspergillus sydowii. Besides, the metabolites of Cobetia marina, Cobetia amphilecti, Pseudoalteromonas neustonica, and Virgibacillus halodenitrificans manifested notable inhibition against the protozoan ciliates (Uronema marinum, Holosticha diademata, Cohnilembus verminus, and Euplotes vannus) and zooplankton that are known to be involved in the secondary pathogenesis in coral diseased lesion progression. Thus, the present study may benefit in understanding coral-associated beneficial bacteria for their antagonistic interactions with microbial pathogens, as well as their potential involvement in reducing coral disease severity.

Seq' and ARMS shall find: DNA (meta)barcoding of Autonomous Reef Monitoring Structures across the tree of life uncovers hidden cryptobiome of tropical urban coral reefs

Coral reefs are among the richest marine ecosystems on Earth, but there remains much diversity hidden within cavities of complex reef structures awaiting discovery. While the abundance of corals and other macroinvertebrates are known to influence the diversity of other reef-associated organisms, much remains unknown on the drivers of cryptobenthic diversity. A combination of standardized sampling with 12 units of the Autonomous Reef Monitoring Structure (ARMS) and high-throughput sequencing was utilized to uncover reef cryptobiome diversity across the equatorial reefs in Singapore. DNA barcoding and metabarcoding of mitochondrial cytochrome c oxidase subunit I, nuclear 18S and bacterial 16S rRNA genes revealed the taxonomic composition of the reef cryptobiome, comprising 15,356 microbial ASVs from over 50 bacterial phyla, and 971 MOTUs across 15 metazoan and 19 non-metazoan eukaryote phyla. Environmental factors across different sites were tested for relationships with ARMS diversity. Differences among reefs in diversity patterns of metazoans and other eukaryotes, but not microbial communities, were associated with biotic (coral cover) and abiotic (distance, temperature and sediment) environmental variables. In particular, ARMS deployed at reefs with higher coral cover had greater metazoan diversity and encrusting plate cover, with larger-sized non-coral invertebrates influencing spatial patterns among sites. Our study showed that DNA barcoding and metabarcoding of ARMS constitute a valuable tool for quantifying cryptobenthic diversity patterns and can provide critical information for the effective management of coral reef ecosystems.

Water column contributions to coral reef productivity: overcoming challenges of context dependence

Coral reefs are declining at an unprecedented rate. Effective management and conservation initiatives necessitate improved understanding of the drivers of production because the high rates found in these ecosystems are the foundation of the many services they provide. The water column is the nexus of coral reef ecosystem dynamics, and functions as the interface through which essentially all energy and nutrients are transferred to fuel both new and recycled production. Substantial research has described many aspects of water column dynamics, often focusing on specific components because water column dynamics are highly spatially and temporally context dependent. Although necessary, a cost of this approach is that these dynamics are often not well linked to the broader ecosystem or across systems. To help overcome the challenge of context dependence, we provide a comprehensive review of this literature, and synthesise it through the perspective of ecosystem ecology. Specifically, we provide a framework to organise the drivers of temporal and spatial variation in production dynamics, structured around five primary state factors. These state factors are used to deconstruct the environmental contexts in which three water column sub-food webs mediate 'new' and 'recycled' production. We then highlight critical pathways by which global change drivers are altering coral reefs via the water column. We end by discussing four key knowledge gaps hindering understanding of the role of the water column for mediating coral reef production, and how overcoming these could improve conservation and management strategies. Throughout, we identify areas of extensive research and those where studies remain lacking and provide a database of 84 published studies. Improved integration of water column dynamics into models of coral reef ecosystem function is imperative to achieve the understanding of ecosystem production necessary to develop effective conservation and management strategies needed to stem global coral loss.

Microbial Interactions with Dissolved Organic Matter Are Central to Coral Reef Ecosystem Function and Resilience

To thrive in nutrient-poor waters, coral reefs must retain and recycle materials efficiently. This review centers microbial processes in facilitating the persistence and stability of coral reefs, specifically the role of these processes in transforming and recycling the dissolved organic matter (DOM) that acts as an invisible currency in reef production, nutrient exchange, and organismal interactions. The defining characteristics of coral reefs, including high productivity, balanced metabolism, high biodiversity, nutrient retention, and structural complexity, are inextricably linked to microbial processing of DOM. The composition of microbes and DOM in reefs is summarized, and the spatial and temporal dynamics of biogeochemical processes carried out by microorganisms in diverse reef habitats are explored in a variety of key reef processes, including decomposition, accretion, trophictransfer, and macronutrient recycling. Finally, we examine how widespread habitat degradation of reefs is altering these important microbe-DOM interactions, creating feedbacks that reduce reef resilience to global change.

Historical Maps provide insight into a century and a half of habitat change in Fijian coasts

Meaningful conservation goals require setting baselines derived from long-term ecological records and information that is rare in many regions of the world. Historical data allow us to shift baselines back in time in order to strengthen conservation outcomes in the future.To explore how different histories of land use and development influenced coastal ecosystems in two Fijian cities (Suva and Savusavu), we compared a series of historical navigational charts. These charts recorded change in coral reef area and coastal mangrove forests, as well as expansions of hardened shorelines. We used geographic information systems (GIS) to georeference and make quantitative comparisons starting in 1,840 in Suva and 1876 in Savusavu.Our findings show that, despite increasing urbanization in the capital Suva, available coral reef habitat has not significantly changed in over 150 years, but development has hastened a nearly 50% loss of mangroves. Meanwhile, in the smaller city of Savusavu, coral habitats suffered significant loss in area and an increase in patchiness. As in Suva, shoreline hardening increased in Savusavu, but this change was not accompanied by a loss of mangroves.Nautical charts provided hitherto unavailable information on the long-term loss and alteration of coastal habitats in Fiji. Historical ecology allows scientists to combat shifting baseline syndrome and set measured standards for conservation objectives.

A genomic view of the microbiome of coral reef demosponges

Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution.

Natural and anthropogenic-induced stressors affecting the composition of fish communities on the rocky reefs of Ecuador

Natural and human-induced stressors have threatened the sustainability of the fish communities of coral-rocky reefs worldwide in the last decades. The composition of the fish communities on the reefs of Ecuador and the factors affecting spatiotemporal changes are unknown. We studied the influence of the descriptors of structural complexity, the current status of coral and human-induced variables over fish communities. A video transect method was used to assess fish communities in three zones (slope, crest, and bottom) of two reefs during two seasons (rainy and dry). The structure of fish communities was highly influenced by the zones and season; rugosity and live coral affected the fish composition on the crest and slope zones. The fractured coral and derelict fishing gear on coral produced an adverse effect on fish composition over the crest. A multifactorial process causing loss of structural complexity and affecting fish composition was identified, however, periodical assessment is required for a greater understanding of this process.

Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals

Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. To date, however, bacteria-derived antimicrobial molecules have not been identified in reef-building corals. Here, we report the isolation of an antimicrobial compound produced by Pseudovibrio sp. P12, a common and abundant coral-associated bacterium. This strain was capable of metabolizing dimethylsulfoniopropionate (DMSP), a sulfur molecule produced in high concentrations by reef-building corals and playing a role in structuring their bacterial communities. Bioassay-guided fractionation coupled with nuclear magnetic resonance (NMR) and mass spectrometry (MS), identified the antimicrobial as tropodithietic acid (TDA), a sulfur-containing compound likely derived from DMSP catabolism. TDA was produced in large quantities by Pseudovibrio sp., and prevented the growth of two previously identified coral pathogens, Vibrio coralliilyticus and V. owensii, at very low concentrations (0.5 μg/mL) in agar diffusion assays. Genome sequencing of Pseudovibrio sp. P12 identified gene homologs likely involved in the metabolism of DMSP and production of TDA. These results provide additional evidence for the integral role of DMSP in structuring coral-associated bacterial communities and underline the potential of these DMSP-metabolizing microbes to contribute to coral disease prevention.

Coral Reef Resilience through Biodiversity

Irrefutable evidence of coral reef degradation worldwide and increasing pressure from rising seawater temperatures and ocean acidification associated with climate change have led to a focus on reef resilience and a call to “manage” coral reefs for resilience. Ideally, global action to reduce emission of carbon dioxide and other greenhouse gases will be accompanied by local action. Effective management requires reduction of local stressors, identification of the characteristics of resilient reefs, and design of marine protected area networks that include potentially resilient reefs. Future research is needed on how stressors interact, on how climate change will affect corals, fish, and other reef organisms as well as overall biodiversity, and on basic ecological processes such as connectivity. Not all reef species and reefs will respond similarly to local and global stressors. Because reef-building corals and other organisms have some potential to adapt to environmental changes, coral reefs will likely persist in spite of the unprecedented combination of stressors currently affecting them. The biodiversity of coral reefs is the basis for their remarkable beauty and for the benefits they provide to society. The extraordinary complexity of these ecosystems makes it both more difficult to predict their future and more likely they will have a future.

Microbial to reef scale interactions between the reef-building coral Montastraea annularis and benthic algae

Competition between reef-building corals and benthic algae is of key importance for reef dynamics. These interactions occur on many spatial scales, ranging from chemical to regional. Using microprobes, 16S rDNA pyrosequencing and underwater surveys, we examined the interactions between the reef-building coral Montastraea annularis and four types of benthic algae. The macroalgae Dictyota bartayresiana and Halimeda opuntia, as well as a mixed consortium of turf algae, caused hypoxia on the adjacent coral tissue. Turf algae were also associated with major shifts in the bacterial communities at the interaction zones, including more pathogens and virulence genes. In contrast to turf algae, interactions with crustose coralline algae (CCA) and M. annularis did not appear to be antagonistic at any scale. These zones were not hypoxic, the microbes were not pathogen-like and the abundance of coral-CCA interactions was positively correlated with per cent coral cover. We propose a model in which fleshy algae (i.e. some species of turf and fleshy macroalgae) alter benthic competition dynamics by stimulating bacterial respiration and promoting invasion of virulent bacteria on corals. This gives fleshy algae a competitive advantage over corals when human activities, such as overfishing and eutrophication, remove controls on algal abundance. Together, these results demonstrate the intricate connections and mechanisms that structure coral reefs.

Multi-target strategies for the improved treatment of depressive states: Conceptual foundations and neuronal substrates, drug discovery and therapeutic application

Major depression is a debilitating and recurrent disorder with a substantial lifetime risk and a high social cost. Depressed patients generally display co-morbid symptoms, and depression frequently accompanies other serious disorders. Currently available drugs display limited efficacy and a pronounced delay to onset of action, and all provoke distressing side effects. Cloning of the human genome has fuelled expectations that symptomatic treatment may soon become more rapid and effective, and that depressive states may ultimately be "prevented" or "cured". In pursuing these objectives, in particular for genome-derived, non-monoaminergic targets, "specificity" of drug actions is often emphasized. That is, priority is afforded to agents that interact exclusively with a single site hypothesized as critically involved in the pathogenesis and/or control of depression. Certain highly selective drugs may prove effective, and they remain indispensable in the experimental (and clinical) evaluation of the significance of novel mechanisms. However, by analogy to other multifactorial disorders, "multi-target" agents may be better adapted to the improved treatment of depressive states. Support for this contention is garnered from a broad palette of observations, ranging from mechanisms of action of adjunctive drug combinations and electroconvulsive therapy to "network theory" analysis of the etiology and management of depressive states. The review also outlines opportunities to be exploited, and challenges to be addressed, in the discovery and characterization of drugs recognizing multiple targets. Finally, a diversity of multi-target strategies is proposed for the more efficacious and rapid control of core and co-morbid symptoms of depression, together with improved tolerance relative to currently available agents.

Methodologies for conservation assessments of the genetic biodiversity of aquatic macro-organisms

International organizations and biodiversity scientists recognize three levels of biodiversity: genetic, species, and ecosystem. However, most studies with the goal of assessing biodiversity collect data at only a single level--that of the species. Even when multiple levels of biodiversity are considered, usually only ecosystem diversity is also evaluated. Genetic diversity is virtually never considered. Yet, genetic diversity is essential for the maintenance of populations and species over ecological and evolutionary time periods. Moreover, because components of genetic diversity are independent of either species or ecosystem diversity, genetic diversity can provide a unique measure by which to assess the value of regions for conservation. Regions can be valuable for conservation of their genetic resources regardless of their levels of species or ecosystem uniqueness or diversity. In general, the same methods and statistical programs that are used to answer questions about population genetics and phylogenetics are applicable to conservation genetics. Thus, numerous genetic techniques, laboratory methods, and statistical programs are available for assessing regional levels of genetic diversity for conservation considerations. Here, we provide the rationale, techniques available, field and laboratory protocols, and statistical programs that can be used to estimate the magnitude and type of genetic diversity in regions. We also provide information on how to obtain commonly utilized statistical programs and the type of analyses that they include. The guide that we present here can be used to conduct investigations of the genetic diversity of regions under consideration for conservation of their natural resources.