Unique quantitative Symbiodiniaceae signature of coral colonies revealed through spatio-temporal survey in Moorea

One of the mechanisms of rapid adaptation or acclimatization to environmental changes in corals is through the dynamics of the composition of their associated endosymbiotic Symbiodiniaceae community. The various species of these dinoflagellates are characterized by different biological properties, some of which can confer stress tolerance to the coral host. Compelling evidence indicates that the corals' Symbiodiniaceae community can change via shuffling and/or switching but the ecological relevance and the governance of these processes remain elusive. Using a qPCR approach to follow the dynamics of Symbiodiniaceae genera in tagged colonies of three coral species over a 10-18 month period, we detected putative genus-level switching of algal symbionts, with coral species-specific rates of occurrence. However, the dynamics of the corals' Symbiodiniaceae community composition was not driven by environmental parameters. On the contrary, putative shuffling event were observed in two coral species during anomalous seawater temperatures and nutrient concentrations. Most notably, our results reveal that a suit of permanent Symbiodiniaceae genera is maintained in each colony in a specific range of quantities, giving a unique 'Symbiodiniaceae signature' to the host. This individual signature, together with sporadic symbiont switching may account for the intra-specific differences in resistance and resilience observed during environmental anomalies

A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina

<p>Abstract</p> <p>Background</p> <p>The development of new microarray technologies makes custom long oligonucleotide arrays affordable for many experimental applications, notably gene expression analyses. Reliable results depend on probe design quality and selection. Probe design strategy should cope with the limited accuracy of <it>de novo </it>gene prediction programs, and annotation up-dating. We present a novel <it>in silico </it>procedure which addresses these issues and includes experimental screening, as an empirical approach is the best strategy to identify optimal probes in the <it>in silico </it>outcome.</p> <p>Findings</p> <p>We used four criteria for <it>in silico </it>probe selection: cross-hybridization, hairpin stability, probe location relative to coding sequence end and intron position. This latter criterion is critical when exon-intron gene structure predictions for intron-rich genes are inaccurate. For each coding sequence (CDS), we selected a sub-set of four probes. These probes were included in a test microarray, which was used to evaluate the hybridization behavior of each probe. The best probe for each CDS was selected according to three experimental criteria: signal-to-noise ratio, signal reproducibility, and representative signal intensities. This procedure was applied for the development of a gene expression Agilent platform for the filamentous fungus <it>Podospora anserina </it>and the selection of a single 60-mer probe for each of the 10,556 <it>P. anserina </it>CDS.</p> <p>Conclusions</p> <p>A reliable gene expression microarray version based on the Agilent 44K platform was developed with four spot replicates of each probe to increase statistical significance of analysis.</p

Systematic Deletion of Homeobox Genes in Podospora anserina Uncovers Their Roles in Shaping the Fruiting Body

Higher fungi, which comprise ascomycetes and basidiomycetes, play major roles in the biosphere. Their evolutionary success may be due to the extended dikaryotic stage of their life cycle, which is the basis for their scientific name: the Dikarya. Dikaryosis is maintained by similar structures, the clamp in basidiomycetes and the crozier in ascomycetes. Homeodomain transcription factors are required for clamp formation in all basidiomycetes studied. We identified all the homeobox genes in the filamentous ascomycete fungus Podospora anserina and constructed deletion mutants for each of these genes and for a number of gene combinations. Croziers developed normally in these mutants, including those with up to six deleted homeogenes. However, some mutants had defects in maturation of the fruiting body, an effect that could be rescued by providing wild-type maternal hyphae. Analysis of mutants deficient in multiple homeogenes revealed interactions between the genes, suggesting that they operate as a complex network. Similar to their role in animals and plants, homeodomain transcription factors in ascomycetes are involved in shaping multicellular structures

Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium

Abstract Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine-terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions

Worldwide analysis of reef surveys sorts coral taxa by associations with recent and past heat stress

Coral reefs around the world are under threat from anomalous heat waves that are causing the widespread decline of hard corals. Different coral taxa are known to have different sensitivities to heat, although variation in susceptibilities have also been observed within the same species living in different environments. Characterizing such taxa-specific variations is key to enforcing efficient reef conservation strategies. Here, we combine worldwide-reef-survey data with remote sensed environmental variables to evaluate how local differences in taxa-specific coral cover are associated with past trends of thermal anomalies, as well as of non-heat related conditions. While the association with non-heat related environmental variation was seldom significant, we found that heat stress trends matched local differences in coral cover. Coral taxa were sorted based on the different patterns of associations with recent heat stress (measured the year before the survey) and past heat stress (measured since 1985). For branching, tabular and corymbose Acroporidae, reefs exposed to recent heat stress had lower coral cover than locally expected. Among such reefs, those previously exposed to frequent past heat stress displayed relatively higher coral cover, compared to those less frequently exposed. For massive and encrusting Poritidae, and for meandroid Favidae and Mussidae, we observed a negative association of coral cover with recent heat stress. However, unlike with Acroporidae, these associations were weaker and did not vary with past heat exposure. For Pocilloporidae, we found a positive association between coral cover and recent heat stress for reefs frequently exposed to past heat, while we found a negative association at reefs less frequently exposed to past heat. A similar pattern was observed for the branching Poritidae, although the associations were weaker and not statistically significant. Overall, these results show taxa-specific heat association patterns that might correspond to taxa-specific responses to past heat exposure, such as shifts in the assembly of coral communities, evolutionary adaptation or physiological acclimation

The Reef Environment Centralized InFormation System (RECIFS): An integrated geo-environmental database for coral reef research and conservation

Motivation Host to intricate networks of marine species, coral reefs are among the most biologically diverse ecosystems on Earth. Over the past few decades, major degradations of coral reefs have been observed worldwide, which is largely attributed to the effects of climate change and local stressors related to human activities. Now more than ever, characterizing how the environment shapes the dynamics of the reef ecosystem (e.g., shifts in species abundance, community changes, emergence of locally adapted populations) is key to uncovering the environmental drivers of reef degradation, and developing efficient conservation strategies in response. To achieve these objectives, it is pivotal that environmental data describing the processes driving such ecosystem dynamics, which occur across specific spatial and temporal scales, are easily accessible to coral reef researchers and conservation stakeholders alike. Main types of variable contained Multiple environmental variables characterizing various facets of the reef environment, including water chemistry and physics (e.g., temperature, pH, chlorophyll concentration), local anthropogenic pressures (e.g., boat traffic, distance from agricultural or urban areas) and sea currents patterns. Spatial location and grain Worldwide reef cells of 5 by 5 km. Time period and grain Last 3–4 decades, monthly and yearly resolution. Major taxa and level of measurement Environmental data important for coral reefs and associated biodiversity. Software format Interactive web application available at https://recifs.epfl.ch

OMICS Approaches to Assess Dinoflagellate Responses to Chemical Stressors

Dinoflagellates are important primary producers known to biosynthesize metabolites of interest and toxins and form Harmful Algae Blooms (HABs). Water conditions such as nutrient availability, anthropogenic contaminants or pH impact dinoflagellate toxin productions, and HABs' formation remains unclear. In this review, we present the recent contributions of OMICs approaches to the investigation of dinoflagellate responses to water chemical stressors. Transcriptomic and proteomic studies highlight whole-cell strategies to cope with nutrient deficiencies. Metabolomic studies offer a great view of toxin, lipid and sugar productions under stressors. However, the confrontation of different OMICs studies is tedious, as approaches are conducted in different species. As for other model organisms, it would be interesting to use multi-OMIC approaches to build a complete view of dinoflagellate responses to chemical stressors. Overcoming the complex genome of dinoflagellates and increasing their genomic resources is therefore essential to push further. The combination of OMICs studies will provide a much-needed global view of molecular processes, which is essential to optimize the production of dinoflagellate metabolites of interest and identify markers of HABs' formation and toxin production events

Metabarcoding reveals distinct microbiotypes in the giant clam Tridacna maxima

International audienceBackground: Giant clams and scleractinian (reef-building) corals are keystone species of coral reef ecosystems. The basis of their ecological success is a complex and fine-tuned symbiotic relationship with microbes. While the effect of environmental change on the composition of the coral microbiome has been heavily studied, we know very little about the composition and sensitivity of the microbiome associated with clams. Here, we explore the influence of increasing temperature on the microbial community (bacteria and dinoflagellates from the family Symbiodiniaceae) harbored by giant clams, maintained either in isolation or exposed to other reef species. We created artificial benthic assemblages using two coral species (Pocillopora damicornis and Acropora cytherea) and one giant clam species (Tridacna maxima) and studied the microbial community in the latter using metagenomics. Results: Our results led to three major conclusions. First, the health status of giant clams depended on the composition of the benthic species assemblages. Second, we discovered distinct microbiotypes in the studied T. maxima population, one of which was disproportionately dominated by Vibrionaceae and directly linked to clam mortality. Third, neither the increase in water temperature nor the composition of the benthic assemblage had a significant effect on the composition of the Symbiodiniaceae and bacterial communities of T. maxima