Engineering Strategies to Decode and Enhance the Genomes of Coral Symbionts

Coral Reef Population Genomics in an Age of Global Change

Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, gene flow, and hybridization have played and will continue to play an important role in the adaptation or extinction of coral reef taxa in the face of rapid environmental change, but research remains exceptionally limited compared to the urgent needs. Critical areas for future investigation include understanding evolutionary potential and the mechanisms of local adaptation, developing historical baselines, and building greater research capacity in the countries where most reef diversity is concentrated.

Harnessing synthetic biology to enhance ocean health

Ocean health is faltering, its capability for regeneration and renewal being eroded by a steady pulse of anthropomorphic impacts. Plastic waste has infiltrated all ocean biomes, climate change threatens coral reefs with extinction, and eutrophication has unleashed vast algal blooms. In the face of these challenges, synthetic biology approaches may hold untapped solutions to mitigate adverse effects, repair ecosystems, and put us on a path towards sustainable stewardship of our planet. Leveraging synthetic biology tools would enable innovative engineering approaches to augment the natural adaptive capacity of ocean biological systems to cope with the swiftness of human-induced change. Here, we present a framework for developing synthetic biology solutions for the challenges of plastic pollution, coral bleaching, and harmful algal blooms.

Network-level containment of single-species bioengineering

Ecological systems are facing major diversity losses in this century owing to Anthropogenic effects. Habitat loss, overexploitation of resources, invasion and pollution are rapidly jeopardizing the survival of whole communities. It has been recently suggested that a potential approach to flatten the curve of species extinction and prevent catastrophic shifts would involve the engineering of one selected species within one of these communities. Such possibility has started to become part of potential intervention scenarios to preserve biodiversity. Despite its potential, very little is known about the actual dynamic responses of complex ecological networks to the introduction of a synthetic strains derived from a resident species. In this paper, we address this problem by modelling the response of a community to the addition of a synthetic strain derived from a member of a stable ecosystem. We show that the community interaction matrix largely limits the spread of the engineered strain, thus suggesting that species diversity acts as an ecological firewall. The implications for future scenarios of ecosystem engineering are outlined. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.

Increased incompatibility of heterologous algal symbionts under thermal stress in the cnidarian-dinoflagellate model Aiptasia

Rising ocean temperatures are increasing the rate and intensity of coral mass bleaching events, leading to the collapse of coral reef ecosystems. To better understand the dynamics of coral-algae symbioses, it is critical to decipher the role each partner plays in the holobiont's thermotolerance. Here, we investigated the role of the symbiont by comparing transcriptional heat stress responses of anemones from two thermally distinct locations, Florida (CC7) and Hawaii (H2) as well as a heterologous host-symbiont combination composed of CC7 host anemones inoculated with the symbiont Breviolum minutum (SSB01) from H2 anemones (CC7-B01). We find that oxidative stress and apoptosis responses are strongly influenced by symbiont type, as further confirmed by caspase-3 activation assays, but that the overall response to heat stress is dictated by the compatibility of both partners. Expression of genes essential to symbiosis revealed a shift from a nitrogen- to a carbon-limited state only in the heterologous combination CC7-B01, suggesting a bioenergetic disruption of symbiosis during stress. Our results indicate that symbiosis is highly fine-tuned towards particular partner combinations and that heterologous host-symbiont combinations are metabolically less compatible under stress. These results are essential for future strategies aiming at increasing coral resilience using heterologous thermotolerant symbionts.

Ecological firewalls for synthetic biology

It has been recently suggested that engineered microbial strains could be used to protect ecosystems from undesirable tipping points and biodiversity loss. A major concern in this context is the potential unintended consequences, which are usually addressed in terms of designed genetic constructs aimed at controlling overproliferation. Here we present and discuss an alternative view grounded in the nonlinear attractor dynamics of some ecological network motifs. These ecological firewalls are designed to perform novel functionalities (such as plastic removal) while containment is achieved within the resident community. That could help provide a self-regulating biocontainment. In this way, engineered organisms have a limited spread while—when required—preventing their extinction. The basic synthetic designs and their dynamical behavior are presented, each one inspired in a given ecological class of interaction. Their possible applications are discussed and the broader connection with invasion ecology outlined.

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Population control of synthetic strains can be achieved by engineering ecological links

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We introduce ecological firewalls, inspired in four types of ecological interactions

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Our firewalls are shown to maintain diversity while performing designed functions

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Ecological firewalls will help to tackle future bioremediation strategies

Techniques to save the sea

Ocean health has declined dramatically over the past few decades, threatening the rich biodiversity and ecosystem services the ocean provides. In this feature, we look at the life science techniques that could potentially save the sea.

What is the role of zooxanthellae during coral bleaching? Review of zooxanthellae and their response to environmental stress

Coral reefs are diverse and productive but sensitive ecosystems. Due to the impact of climate change, these organisms are in danger of dying out, mainly through the process of coral bleaching, which is the process by which zooxanthellae (algal endosymbionts) are expelled from their respective coral hosts, causing the coral to lose colour and become white. Coral bleaching has been linked to increases in sea surface temperatures as well as an increase in light intensity. We reviewed the different zooxanthellae taxa and their ecological traits, as well as the information available on the protective mechanisms present in zooxanthellae cells when they experience environmental stress conditions, such as temperature fluctuations, specifically concentrating on heat shock proteins and their response to antioxidant stress. The eight clades (A–H) previously recognised were reorganised into seven existing genera. Different zooxanthellae taxa exhibit different ecological traits such as their photosynthetic stress responses to light and temperature. Zooxanthellae have the ability to regulate the number and type of heat shock proteins (Hsps) they produce during a heat response. They can also regulate the host’s respective Hsps. Antioxidant responses that can prevent coral hosts from expelling the zooxanthellae, can be found both within exposed coral tissue and the zooxanthellae cells. Despite the lower likelihood of bleaching in South African coral reefs, genetic engineering presents a useful tool to understand and adapt traits within zooxanthellae genotypes to help mitigate coral bleaching in the future.

The Molecular Language of the Cnidarian-Dinoflagellate Symbiosis

The cnidarian-dinoflagellate symbiosis is of huge importance as it underpins the success of coral reefs, yet we know very little about how the host cnidarian and its dinoflagellate endosymbionts communicate with each other to form a functionally integrated unit. Here, we review the current knowledge of interpartner molecular signaling in this symbiosis, with an emphasis on lipids, glycans, reactive species, biogenic volatiles, and noncoding RNA. We draw upon evidence of these compounds from recent omics-based studies of cnidarian-dinoflagellate symbiosis and discuss the signaling roles that they play in other, better-studied symbioses. We then consider how improved knowledge of interpartner signaling might be used to develop solutions to the coral reef crisis by, for example, engineering more thermally resistant corals.

Spatiotemporal Controllability and Environmental Risk Assessment of Genetically Engineered Gene Drive Organisms from the Perspective of European Union Genetically Modified Organism Regulation

Gene drive organisms are a recent development created by using methods of genetic engineering; they inherit genetic constructs that are passed on to future generations with a higher probability than with Mendelian inheritance. There are some specific challenges inherent to the environmental risk assessment (ERA) of genetically engineered (GE) gene drive organisms because subsequent generations of these GE organisms might show effects that were not observed or intended in the former generations. Unintended effects can emerge from interaction of the gene drive construct with the heterogeneous genetic background of natural populations and/or be triggered by changing environmental conditions. This is especially relevant in the case of gene drives with invasive characteristics and typically takes dozens of generations to render the desired effect. Under these circumstances, "next generation effects" can substantially increase the spatial and temporal complexity associated with a high level of uncertainty in ERA. To deal with these problems, we suggest the introduction of a new additional step in the ERA of GE gene drive organisms that takes 3 criteria into account: the biology of the target organisms, their naturally occurring interactions with the environment (biotic and abiotic), and their intended biological characteristics introduced by genetic engineering. These 3 criteria are merged to form an additional step in ERA, combining specific "knowns" and integrating areas of "known unknowns" and uncertainties, with the aim of assessing the spatiotemporal controllability of GE gene drive organisms. The establishment of assessing spatiotemporal controllability can be used to define so-called "cut-off criteria" in the risk analysis of GE gene drive organisms: If it is likely that GE gene drive organisms escape spatiotemporal controllability, the risk assessment cannot be sufficiently reliable because it is not conclusive. Under such circumstances, the environmental release of the GE gene drive organisms would not be compatible with the precautionary principle (PP). Integr Environ Assess Manag 2020;16:555-568. © 2020 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Bacteriophage Inspired Growth-Decoupled Recombinant Protein Production in Escherichia coli

Modulating resource allocation in bacteria to redirect metabolic building blocks to the formation of recombinant proteins rather than biomass formation remains a grand challenge in biotechnology. Here, we present a novel approach for improved recombinant protein production (RPP) using Escherichia coli (E. coli) by decoupling recombinant protein synthesis from cell growth. We show that cell division and host mRNA transcription can be successfully inhibited by coexpression of a bacteriophage-derived E. coli RNA polymerase (RNAP) inhibitor peptide and that genes overtranscribed by the orthogonal T7 RNAP can finally account to >55% of cell dry mass (CDM). This RNAP inhibitor peptide binds the E. coli RNAP and therefore prevents σ-factor 70 mediated formation of transcriptional qualified open promoter complexes. Thereby, the transcription of σ-factor 70 driven host genes is inhibited, and metabolic resources can be exclusively utilized for synthesis of the protein of interest (POI). Here, we mimic the late phase of bacteriophage infection by coexpressing a phage-derived xenogeneic regulator that reprograms the host cell and thereby are able to significantly improve RPP under industrial relevant fed-batch process conditions at bioreactor scale. We have evaluated production of several different recombinant proteins at different scales (from microscale to 20 L fed-batch scale) and have been able to improve total and soluble proteins yields up to 3.4-fold in comparison to the reference expression system E. coli BL21(DE3). This novel approach for growth-decoupled RPP has profound implications for biotechnology and bioengineering and helps to establish more cost-effective and generic manufacturing processes for biologics and biomaterials.

Endosymbiont-Mediated Adaptive Responses to Stress in Holobionts

Endosymbiosis is found in all types of ecosystems and it can be sensitive to environmental changes due to the intimate interaction between the endosymbiont and the host. Indeed, global climate change disturbs the local ambient environment and threatens endosymbiotic species, and in some cases leads to local ecosystem collapse. Recent studies have revealed that the endosymbiont can affect holobiont (endosymbiont and host together) stress tolerance as much as the host does, and manipulation of the microbial partners in holobionts may mitigate the impacts of the environmental stress. Here, we first show how the endosymbiont presence affects holobiont stress tolerance by discussing three well-studied endosymbiotic systems, which include plant-fungi, aquatic organism-algae, and insect-bacteria systems. We then review how holobionts are able to alter their stress tolerance via associated endosymbionts by changing their endosymbiont composition, by adaptation of their endosymbionts, or by acclimation of their endosymbionts. Finally, we discuss how different transmission modes (vertical or horizontal transmission) might affect the adaptability of holobionts. We propose that the endosymbiont is a good target for modifying holobiont stress tolerance, which makes it critical to more fully investigate the role of endosymbionts in the adaptive responses of holobionts to stress.

Thermal Stress and Resilience of Corals in a Climate-Changing World

Coral reef ecosystems are under the direct threat of increasing atmospheric greenhouse gases, which increase seawater temperatures in the oceans and lead to bleaching events. Global bleaching events are becoming more frequent and stronger, and understanding how corals can tolerate and survive high-temperature stress should be accorded paramount priority. Here, we review evidence of the different mechanisms that corals employ to mitigate thermal stress, which include association with thermally tolerant endosymbionts, acclimatisation, and adaptation processes. These differences highlight the physiological diversity and complexity of symbiotic organisms, such as scleractinian corals, where each species (coral host and microbial endosymbionts) responds differently to thermal stress. We conclude by offering some insights into the future of coral reefs and examining the strategies scientists are leveraging to ensure the survival of this valuable ecosystem. Without a reduction in greenhouse gas emissions and a divergence from our societal dependence on fossil fuels, natural mechanisms possessed by corals might be insufficient towards ensuring the ecological functioning of coral reef ecosystems.

Beneath the surface: community assembly and functions of the coral skeleton microbiome

Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the coral holobiont. New techniques now enable detailed studies of the endolithic habitat, and our knowledge of the skeletal microbial community and its eco-physiology is increasing rapidly, with multiple lines of evidence for the importance of the skeletal microbiota in coral health and functioning. Here, we review the roles these organisms play in the holobiont, including nutritional exchanges with the coral host and decalcification of the host skeleton. Microbial metabolism causes steep physico-chemical gradients in the skeleton, creating micro-niches that, along with dispersal limitation and priority effects, define the fine-scale microbial community assembly. Coral bleaching causes drastic changes in the skeletal microbiome, which can mitigate bleaching effects and promote coral survival during stress periods, but may also have detrimental effects. Finally, we discuss the idea that the skeleton may function as a microbial reservoir that can promote recolonization of the tissue microbiome following dysbiosis and help the coral holobiont return to homeostasis.

Conservation Genomics in a Changing Arctic

Although logistically challenging to study, the Arctic is a bellwether for global change and is becoming a model for questions pertinent to the persistence of biodiversity. Disruption of Arctic ecosystems is accelerating, with impacts ranging from mixing of biotic communities to individual behavioral responses. Understanding these changes is crucial for conservation and sustainable economic development. Genomic approaches are providing transformative insights into biotic responses to environmental change, but have seen limited application in the Arctic due to a series of limitations. To meet the promise of genome analyses, we urge rigorous development of biorepositories from high latitudes to provide essential libraries to improve the conservation, monitoring, and management of Arctic ecosystems through genomic approaches.

The past, present, and future of coral heat stress studies

The global loss and degradation of coral reefs, as a result of intensified frequency and severity of bleaching events, is a major concern. Evidence of heat stress affecting corals through loss of symbionts and consequent coral bleaching was first reported in the 1930s. However, it was not until the 1998 major global bleaching event that the urgency for heat stress studies became internationally recognized. Current efforts focus not only on examining the consequences of heat stress on corals but also on finding strategies to potentially improve thermal tolerance and aid coral reefs survival in future climate scenarios. Although initial studies were limited in comparison with modern technological tools, they provided the foundation for many of today's research methods and hypotheses. Technological advancements are providing new research prospects at a rapid pace. Understanding how coral heat stress studies have evolved is important for the critical assessment of their progress. This review summarizes the development of the field to date and assesses avenues for future research.

Harnessing synthetic biology for kelp forest conservation1

Environmental and climatic change is outpacing the ability of organisms to adapt, at an unprecedented level, resulting in range contractions and global ecosystem shifts to novel states. At the same time, scientific advances continue to accelerate, providing never-before imagined solutions to current and emerging environmental problems. Synthetic biology, the creation of novel and engineered genetic variation, is perhaps the fastest developing and transformative scientific field. Its application to solve extant and emerging environmental problems is vast, at times controversial, and technological advances have outpaced the social, ethical, and practical considerations of its use. Here, we discuss the potential direct and indirect applications of synthetic biology to kelp forest conservation. Rather than advocate or oppose its use, we identify where and when it may play a role in halting or reversing global kelp loss and discuss challenges and identify pathways of research needed to bridge the gap between technological advances and organismal biology and ecology. There is a pressing need for prompt collaboration and dialogue among synthetic biologists, ecologists, and conservationists to identify opportunities for use and ensure that extant research directions are set on trajectories to allow these currently disparate fields to converge toward practical environmental solutions.

The Active Reef Restoration Toolbox is a Vehicle for Coral Resilience and Adaptation in a Changing World

The accelerating marks of climate change on coral-reef ecosystems, combined with the recognition that traditional management measures are not efficient enough to cope with climate change tempo and human footprints, have raised a need for new approaches to reef restoration. The most widely used approach is the “coral gardening” tenet; an active reef restoration tactic based on principles, concepts, and theories used in silviculture. During the relatively short period since its inception, the gardening approach has been tested globally in a wide range of reef sites, and on about 100 coral species, utilizing hundreds of thousands of nursery-raised coral colonies. While still lacking credibility for simulating restoration scenarios under forecasted climate change impacts, and with a limited adaptation toolkit used in the gardening approach, it is still deficient. Therefore, novel restoration avenues have recently been suggested and devised, and some have already been tested, primarily in the laboratory. Here, I describe seven classes of such novel avenues and tools, which include the improved gardening methodologies, ecological engineering approaches, assisted migration/colonization, assisted genetics/evolution, assisted microbiome, coral epigenetics, and coral chimerism. These are further classified into three operation levels, each dependent on the success of the former level. Altogether, the seven approaches and the three operation levels represent a unified active reef restoration toolbox, under the umbrella of the gardening tenet, focusing on the enhancement of coral resilience and adaptation in a changing world.

Genome analysis of the rice coral Montipora capitata

Corals comprise a biomineralizing cnidarian, dinoflagellate algal symbionts, and associated microbiome of prokaryotes and viruses. Ongoing efforts to conserve coral reefs by identifying the major stress response pathways and thereby laying the foundation to select resistant genotypes rely on a robust genomic foundation. Here we generated and analyzed a high quality long-read based ~886 Mbp nuclear genome assembly and transcriptome data from the dominant rice coral, Montipora capitata from Hawai’i. Our work provides insights into the architecture of coral genomes and shows how they differ in size and gene inventory, putatively due to population size variation. We describe a recent example of foreign gene acquisition via a bacterial gene transfer agent and illustrate the major pathways of stress response that can be used to predict regulatory components of the transcriptional networks in M. capitata. These genomic resources provide insights into the adaptive potential of these sessile, long-lived species in both natural and human influenced environments and facilitate functional and population genomic studies aimed at Hawaiian reef restoration and conservation.

Synthetic Mutualism and the Intervention Dilemma

Ecosystems are complex networks of interacting individuals co-evolving with their environment. As such, changes to an interaction can influence the whole ecosystem. However, to predict the outcome of these changes, considerable understanding of processes driving the system is required. Synthetic biology provides powerful tools to aid this understanding, but these developments also allow us to change specific interactions. Of particular interest is the ecological importance of mutualism, a subset of cooperative interactions. Mutualism occurs when individuals of different species provide a reciprocal fitness benefit. We review available experimental techniques of synthetic biology focused on engineered synthetic mutualistic systems. Components of these systems have defined interactions that can be altered to model naturally occurring relationships. Integrations between experimental systems and theoretical models, each informing the use or development of the other, allow predictions to be made about the nature of complex relationships. The predictions range from stability of microbial communities in extreme environments to the collapse of ecosystems due to dangerous levels of human intervention. With such caveats, we evaluate the promise of synthetic biology from the perspective of ethics and laws regarding biological alterations, whether on Earth or beyond. Just because we are able to change something, should we?

Navigating Novelty and Risk in Resilience Management

Resilience theory is increasingly applied to the management of global change impacts. There is growing concern, however, that misapplications of resilience-based management (RBM) can sometimes lead to undesirable outcomes. We address here an inescapable conundrum in the application of resilience theory: systems will need to track environmental change, but management that aims to support adaptive capacity can introduce undesirable levels of change. We provide a framework that links concepts from novel ecosystems and resilience theory to inform management of ecosystem change. We highlight that resilience-based applications need to address risks associated with novel human impacts to improve management outcomes.

Conservation of biodiversity in the genomics era

"Conservation genomics" encompasses the idea that genome-scale data will improve the capacity of resource managers to protect species. Although genetic approaches have long been used in conservation research, it has only recently become tractable to generate genome-wide data at a scale that is useful for conservation. In this Review, we discuss how genome-scale data can inform species delineation in the face of admixture, facilitate evolution through the identification of adaptive alleles, and enhance evolutionary rescue based on genomic patterns of inbreeding. As genomic approaches become more widely adopted in conservation, we expect that they will have a positive impact on management and policy decisions.

Harnessing positive species interactions as a tool against climate-driven loss of coastal biodiversity

Habitat-forming species sustain biodiversity and ecosystem functioning in harsh environments through the amelioration of physical stress. Nonetheless, their role in shaping patterns of species distribution under future climate scenarios is generally overlooked. Focusing on coastal systems, we assess how habitat-forming species can influence the ability of stress-sensitive species to exhibit plastic responses, adapt to novel environmental conditions, or track suitable climates. Here, we argue that habitat-former populations could be managed as a nature-based solution against climate-driven loss of biodiversity. Drawing from different ecological and biological disciplines, we identify a series of actions to sustain the resilience of marine habitat-forming species to climate change, as well as their effectiveness and reliability in rescuing stress-sensitive species from increasingly adverse environmental conditions.

Advancing a New Toolkit for Conservation: From Science to Policy

Climate change and non-native wildlife diseases are exacerbating persistent challenges to biodiversity such as habitat destruction, invasive species and over-harvesting. With these increasing threats there is a pressing need to expand the conservationists' toolbox. CRISPR-Cas9 genome editing (GE) offers a precise and potentially transformative tool to confront these challenges. Researchers, regulators, conservationists and the public are all needed to engage proactively in the thoughtful and responsible development and application of these new tools.

The contribution of microbial biotechnology to mitigating coral reef degradation

The decline of coral reefs due to anthropogenic disturbances is having devastating impacts on biodiversity and ecosystem services. Here we highlight the potential and challenges of microbial manipulation strategies to enhance coral tolerance to stress and contribute to coral reef restoration and protection.