Showing papers by "Rebecca Vega Thurber published in 2019"

Minimum information about an uncultivated virus genome (MIUVIG)

Abstract: We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.

Host-associated microbiomes drive structure and function of marine ecosystems

Abstract: The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth's most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, little is known about their interactions with the vast majority of marine host species. We outline research priorities to strengthen our current knowledge of host-microbiome interactions and how they shape marine ecosystems. We argue that such advances in research will help predict responses of species, communities, and ecosystems to stressors driven by human activity and inform future management strategies.

Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov.

Abstract: Bacterial symbionts are integral to the health and homeostasis of invertebrate hosts. Notably, members of the Rickettsiales genus Wolbachia influence several aspects of the fitness and evolution of their terrestrial hosts, but few analogous partnerships have been found in marine systems. We report here the genome, phylogenetics, and biogeography of a ubiquitous and novel Rickettsiales species that primarily associates with marine organisms. We previously showed that this bacterium was found in scleractinian corals, responds to nutrient exposure, and is associated with reduced host growth and increased mortality. This bacterium, like other Rickettsiales, has a reduced genome indicative of a parasitic lifestyle. Phylogenetic analysis places this Rickettsiales within a new genus we define as "Candidatus Aquarickettsia." Using data from the Earth Microbiome Project and SRA databases, we also demonstrate that members of "Ca. Aquarickettsia" are found globally in dozens of invertebrate lineages. The coral-associated "Candidatus A. rohweri" is the first finished genome in this new clade. "Ca. A. rohweri" lacks genes to synthesize most sugars and amino acids but possesses several genes linked to pathogenicity including Tlc, an antiporter that exchanges host ATP for ADP, and a complete Type IV secretion system. Despite its inability to metabolize nitrogen, "Ca. A. rohweri" possesses the NtrY-NtrX two-component system involved in sensing and responding to extracellular nitrogen. Given these data, along with visualization of the parasite in host tissues, we hypothesize that "Ca. A. rohweri" reduces coral health by consuming host nutrients and energy, thus weakening and eventually killing host cells. Last, we hypothesize that nutrient enrichment, which is increasingly common on coral reefs, encourages unrestricted growth of "Ca. A. rohweri" in its host by providing abundant N-rich metabolites to be scavenged.

Multiple stressors interact primarily through antagonism to drive changes in the coral microbiome.

Abstract: Perturbations in natural systems generally are the combination of multiple interactions among individual stressors. However, methods to interpret the effects of interacting stressors remain challenging and are biased to identifying synergies which are prioritized in conservation. Therefore we conducted a multiple stressor experiment (no stress, single, double, triple) on the coral Pocillopora meandrina to evaluate how its microbiome changes compositionally with increasing levels of perturbation. We found that effects of nutrient enrichment, simulated predation, and increased temperature are antagonistic, rather than synergistic or additive, for a variety of microbial community diversity measures. Importantly, high temperature and scarring alone had the greatest effect on changing microbial community composition and diversity. Using differential abundance analysis, we found that the main effects of stressors increased the abundance of opportunistic taxa, and two-way interactions among stressors acted antagonistically on this increase, while three-way interactions acted synergistically. These data suggest that: (1) multiple statistical analyses should be conducted for a complete assessment of microbial community dynamics, (2) for some statistical metrics multiple stressors do not necessarily increase the disruption of microbiomes over single stressors in this coral species, and (3) the observed stressor-induced community dysbiosis is characterized by a proliferation of opportunists rather than a depletion of a proposed coral symbiont of the genus Endozoicomonas.

The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean.

Abstract: Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.

Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018)

Abstract: Interactions between the ocean and the atmosphere occur at the air-sea interface through the transfer of momentum, heat, gases and particulate matter, and through the impact of the upper-ocean biology on the composition and radiative properties of this boundary layer. The Tara Pacific expedition, launched in May 2016 aboard the schooner Tara, was a 29-month exploration with the dual goals to study the ecology of reef ecosystems along ecological gradients in the Pacific Ocean and to assess inter-island and open ocean surface plankton and neuston community structures. In addition, key atmospheric properties were measured to study links between the two boundary layer properties. A major challenge for the open ocean sampling was the lack of ship-time available for work at "stations". The time constraint led us to develop new underway sampling approaches to optimize physical, chemical, optical, and genomic methods to capture the entire community structure of the surface layers, from viruses to metazoans in their oceanographic and atmospheric physicochemical context. An international scientific consortium was put together to analyze the samples, generate data, and develop datasets in coherence with the existing Tara Oceans database. Beyond adapting the extensive Tara Oceans sampling protocols for high-resolution underway sampling, the key novelties compared to Tara Oceans' global assessment of plankton include the measurement of (i) surface plankton and neuston biogeography and functional diversity; (ii) bioactive trace metals distribution at the ocean surface and metal-dependent ecosystem structures; (iii) marine aerosols, including biological entities; (iv) geography, nature and colonization of microplastic; and (v) high-resolution underway assessment of net community production via equilibrator inlet mass spectrometry. We are committed to share the data collected during this expedition, making it an important resource important resource to address a variety of scientific questions.

Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral

Abstract: Corals are in decline worldwide due to local anthropogenic stressors, such as nutrient loading, and global stressors, such as ocean warming. Anthropogenic nutrient loading, which is often rich in nitrate, inhibits coral growth and worsens corals' response to warming while natural sources of nitrogen, such as ammonium from fish excretion, promotes coral growth. Although the effects of nutrient loading and ocean warming have been well-studied, it remains unclear how these factors may interact with biotic processes, such as corallivory, to alter coral health and the coral microbiome. This study examined how nitrate vs. ammonium enrichment altered the effects of increased seawater temperature and simulated parrotfish corallivory on the health of Pocillopora meandrina and its microbial community. We tested the effects of nitrogen source on the response to corallivory under contrasting temperatures (control: 26 °C, warming: 29 °C) in a factorial mesocosm experiment in Moorea, French Polynesia. Corals were able to maintain growth rates despite simultaneous stressors. Seawater warming suppressed wound healing rates by nearly 66%. However, both ammonium and nitrate enrichment counteracted the effect of higher temperatures on would healing rates. Elevated seawater temperature and ammonium enrichment independently increased Symbiodiniaceae densities relative to controls, yet there was no effect of nitrate enrichment on algal symbiont densities. Microbiome variability increased with the addition of nitrate or ammonium. Moreover, microbial indicator analysis showed that Desulfovibrionaceae Operational taxonomic units (OTUs) are indicators of exclusively temperature stress while Rhodobacteraceae and Saprospiraceae OTUs were indicators of high temperature, wounding, and nitrogen enrichment. Overall, our results suggest that nitrogen source may not alter the response of the coral host to simultaneous stressors, but that the associated microbial community may be distinct depending on the source of enrichment.

Variable interaction outcomes of local disturbance and El Niño-induced heat stress on coral microbiome alpha and beta diversity

Abstract: Emerging evidence indicates that individual stressors can modify the coral microbiome; however, few studies have examined the impacts of multiple stressors through natural climatic events. During periods of low and high heat stress associated with the 2015–2016 El Nino, we tracked the microbiomes of two coral species (Porites lobata and Montipora aequituberculata) across sites on Kiritimati (Christmas) Island with different levels of local disturbance (i.e. subsistence fishing, pollution, dredging). At low heat stress, local disturbance was associated with increased microbial alpha diversity (i.e. number of microbial OTUs and their relative abundance) in both species and increased beta diversity (i.e. coral to coral variation in microbial community composition) in P. lobata. High levels of thermal stress subsequently elevated microbial beta diversity in both species at the low disturbance sites up to the level experienced at the high disturbance sites under low heat stress, illustrating that each stressor can destabilize the coral microbiome. However, with high heat stress microbial alpha diversity was no longer significantly different between disturbance levels for either species. Survival of P. lobata throughout the entire El Nino event was greater at low disturbance sites than high ones (40% vs. 15%), suggesting that protection from local stressors may enhance survival of stress-tolerant corals. However, no M. aequituberculata tracked in this study survived the thermal anomaly. Whether enhanced survivorship can be directly attributed to lower microbial diversity, however, remains to be tested. Overall, we found that, rather than acting synergistically, multiple stressors either acted antagonistically to one another (alpha diversity for both coral species, beta diversity for P. lobata) or exhibited dominance (beta diversity for M. aequituberculata), suggesting that multiple stressors cause various interaction outcomes on the coral microbiome and highlighting the need for future research to evaluate these interactions and their consequences for coral resilience.

Microbiome Variation in an Intertidal Sea Anemone Across Latitudes and Symbiotic States

Abstract: Many cnidarians form symbiotic relationships with brown dinoflagellate algae in the genus Symbiodinium. Bacteria are important to this symbiosis, with diverse functions such as providing nutrients to the symbiont and pathogen protection to the cnidarian. Disrupted bacterial communities are associated with thermally stressed cnidarians, which have a higher likelihood of expelling their symbionts, an event called bleaching. To better understand the association between thermal tolerance and bacterial community structure, we studied communities associated with an exceptionally thermal tolerant cnidarian, Anthopleura elegantissima. This intertidal symbiotic sea anemone is distributed from the subtropical waters of Baja California to subarctic Alaska, and experiences daily temperature fluctuations of up to 20oC. It is also flexible in its symbioses, predominantly hosting Symbiodinium, but occasionally hosting the green algae Elliptochloris marina or existing without symbionts in an aposymbiotic state. We used 16S rRNA gene amplicon sequencing to characterize the natural variation of microbial communities associated with Anthopleura elegantissima in these three symbiotic states and across a latitudinal gradient. In this study, we identified a core microbiome, made up predominantly of taxa typically found in coastal seawater. We found that the communities associated with A. elegantissima were weakly linked to latitude. Diversity analyses revealed significantly higher species richness values for microbial communities associated with anemones hosting E. marina. Lastly the microbiome communities associated with different symbiotic states were compositionally distinct. Taken together, our results suggest that the structure of microbial communities associated with these temperate cnidarians is tightly linked to symbiotic state and weakly linked to other biogeographic phenomena.

Host-associated microbiomes and their roles in marine ecosystem functions

Abstract: The significance of mutualisms between eukaryotic hosts and microbes extends from the organismal to the ecosystem level, and mutualistic symbioses underpin the health of Earth’s most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes (microbiomes), very little is known about their interactions for the vast majority of marine host species. We outline research priorities to broaden our current knowledge of host-microbiome interactions and how they shape marine ecosystems. We argue that this research frontier will allow us to predict responses of species, communities, and ecosystems to stressors driven by human activity, and inform future management and mitigation.

Draft Genome Sequence of Phocine Herpesvirus 1 Isolated from the Brain of a Harbor Seal.

Abstract: Phocine herpesvirus 1 (PhHV-1) is a viral pathogen with high prevalence, morbidity, and mortality in harbor seals. In this study, we used a metagenomic approach to assemble the PhHV-1 genome from the brain tissue of a harbor seal. Here, we present a 119-kb draft genome of PhHV-1 comprising 76 open reading frames.