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1. Evidence for stage-based larval vulnerability and resilience to acidification in Crassostrea virginica

   https://doi.org/10.1093/mollus/eyaa022  

   Miller, A Whitman ; Reynolds, Amanda ; Minton, Mark S ; Smith, Rachel ( September 2020 , Journal of Molluscan Studies)

   null (Ed.)

   ABSTRACT Using image analysis of scanning electron micrographs (SEMs), we compared differences in growth of D-stage veligers [i.e. prodissoconch I and II (PI and PII) larvae] of eastern oysters Crassostrea virginica grown in mesohaline water under high- and low-CO2 conditions. We found SEMs to reveal no evidence of dissolution or shell structure deformity for larval shells in either of the CO2 treatments but detected prominent growth lines in the PII regions of larval shells. The number of growth lines closely approximated the duration of the experiment, suggesting that growth lines are generated daily. Mean growth line interval widths were 20% greater for larval shells cultured in low- vs high-CO2 conditions. Crassostrea virginica veliger larvae were shown to tolerate high CO2 levels and aragonite saturation states (Ωarag) < 1.0, but larval growth was slowed substantially under these conditions. Differences in growth line interval width translate into substantial changes in shell area and account for previously observed differences in total shell area between the treatments, as determined by light microscopy and image analysis. Other studies have documented high mortality and malformation of D-stage larvae in bivalves when pre-veliger life stages (i.e. eggs, gastrula and trochophores) were exposed to elevated CO2. Our experiments revealed statistical differences in rates of larval survival, settlement and subsequent early-stage spat mortality for veligers reared in high- and low-CO2 conditions. Although each of these rates was measurably affected by high CO2, the magnitude of these differences was small (range across categories = 0.7–6.3%) suggesting that the impacts may not be catastrophic, as implied by several previous studies. We believe the apparent disparity among experimental results may be best explained by differential vulnerability of pre-veliger stage larvae and veligers, whereby PI and PII larvae have greater physiological capacity to withstand environmental conditions that may be thermodynamically unfavourable to calcification (i.e. Ωarag < 1.0). 

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2. The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis

   https://doi.org/10.1002/jez.b.22915  

   Collens, Adena ; Kelley, Emma ; Katz, Laura A. ( November 2019 , Journal of Experimental Zoology Part B: Molecular and Developmental Evolution)

   John Tyler Bonner's call to re‐evaluate evolutionary theory in light of major transitions in life on Earth (e.g., from the first origins of microbial life to the evolution of sex, and the origins of multicellularity) resonate with recent discoveries on epigenetics and the concept of the hologenome. Current studies of genome evolution often mistakenly focus only on the inheritance of DNA between parent and offspring. These are in line with the widely accepted Neo‐Darwinian framework that pairs Mendelian genetics with an emphasis on natural selection as explanations for the evolution of biodiversity on Earth. Increasing evidence for widespread symbioses complicates this narrative, as is seen in Scott Gilbert's discussion of the concept of the holobiont in this series: Organisms across the tree of life coexist with substantial influence on one another through endosymbiosis, symbioses, and host‐associated microbiomes. The holobiont theory, coupled with observations from molecular studies, also requires us to understand genomes in a new way—by considering the interactions underlain by the genome of a host plus its associated microbes, a conglomerate entity referred to as the hologenome. We argue that the complex patterns of inheritance of these genomes coupled with the influence of symbionts on host gene expression make the concept of the hologenome an epigenetic phenomenon. We further argue that the aspects of the hologenome challenge of the modern evolutionary synthesis, which requires updating to remain consistent with Darwin's intent of providing natural laws that underlie the evolution of life on Earth.

    

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3. Turtle ants harbor metabolically versatile microbiomes with conserved functions across development and phylogeny

   https://doi.org/10.1093/femsec/fiac068  

   Béchade, Benoît ; Hu, Yi ; Sanders, Jon G. ; Cabuslay, Christian S. ; Łukasik, Piotr ; Williams, Bethany R. ; Fiers, Valerie J. ; Lu, Richard ; Wertz, John T. ; Russell, Jacob A. ( June 2022 , FEMS Microbiology Ecology)

   Gut bacterial symbionts can support animal nutrition by facilitating digestion and providing valuable metabolites. However, changes in symbiotic roles between immature and adult stages are not well documented, especially in ants. Here, we explored the metabolic capabilities of microbiomes sampled from herbivorous turtle ant (Cephalotes sp.) larvae and adult workers through (meta)genomic screening and in vitro metabolic assays. We reveal that larval guts harbor bacterial symbionts with impressive metabolic capabilities, including catabolism of plant and fungal recalcitrant dietary fibers and energy-generating fermentation. Additionally, several members of the specialized adult gut microbiome, sampled downstream of an anatomical barrier that dams large food particles, show a conserved potential to depolymerize many dietary fibers. Symbionts from both life stages have the genomic capacity to recycle nitrogen and synthesize amino acids and B-vitamins. With help of their gut symbionts, including several bacteria likely acquired from the environment, turtle ant larvae may aid colony digestion and contribute to colony-wide nitrogen, B-vitamin and energy budgets. In addition, the conserved nature of the digestive capacities among adult-associated symbionts suggests that nutritional ecology of turtle ant colonies has long been shaped by specialized, behaviorally-transferred gut bacteria with over 45 million years of residency.

    

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4. Shifts in the coral microbiome in response to in situ experimental deoxygenation

   https://doi.org/10.1128/aem.00577-23  

   Howard, Rachel D. ; Schul, Monica D. ; Rodriguez Bravo, Lucia M. ; Altieri, Andrew H. ; Meyer, Julie L. ( November 2023 , Applied and Environmental Microbiology)

   Biddle, Jennifer F. (Ed.)

   Global climate change impacts marine ecosystems through rising surface temperatures, ocean acidification, and deoxygenation. While the response of the coral holobiont to the first two effects has been relatively well studied, less is known about the response of the coral microbiome to deoxygenation. In this study, we investigated the response of the microbiome to hypoxia in two coral species that differ in their tolerance to hypoxia. We conductedin situoxygen manipulations on a coral reef in Bahía Almirante on the Caribbean coast of Panama, which has previously experienced documented episodes of hypoxia. Naïve coral colonies (previously unexposed to hypoxia) ofSiderastrea sidereaandAgaricia lamarckiwere transplanted to a reef and either enclosed in chambers that created hypoxic conditions or left at ambient oxygen levels. We collected samples of surface mucus and tissue after 48 hours of exposure and characterized the microbiome by sequencing 16S rRNA genes. We found that the microbiomes of the two coral species were distinct from one another and remained so after exhibiting similar shifts in microbiome composition in response to hypoxia. There was an increase in both abundance and number of taxa of anaerobic microbes after exposure to hypoxia. Some of these taxa may play beneficial roles in the coral holobiont by detoxifying the surrounding environment during hypoxic stress or may represent opportunists exploiting host stress. This work describes the first characterization of the coral microbiome under hypoxia and is an initial step toward identifying potential beneficial bacteria for corals facing this environmental stressor.

   Marine hypoxia is a threat for corals but has remained understudied in tropical regions where coral reefs are abundant. Though microbial symbioses can alleviate the effects of ecological stress, we do not yet understand the taxonomic or functional response of the coral microbiome to hypoxia. In this study, we experimentally lowered oxygen levels aroundSiderastrea sidereaandAgaricia lamarckicoloniesin situto observe changes in the coral microbiome in response to deoxygenation. Our results show that hypoxia triggers a stochastic change of the microbiome overall, with some bacterial families changing deterministically after just 48 hours of exposure. These families represent an increase in anaerobic and opportunistic taxa in the microbiomes of both coral species. Thus, marine deoxygenation destabilizes the coral microbiome and increases bacterial opportunism. This work provides novel and fundamental knowledge of the microbial response in coral during hypoxia and may provide insight into holobiont function during stress.

    

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5. Impacts of the Marine Hatchery Built Environment, Water and Feed on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola lalandi

   https://doi.org/10.3389/fmars.2021.676731  

   Minich, Jeremiah J. ; Nowak, Barbara ; Elizur, Abigail ; Knight, Rob ; Fielder, Stewart ; Allen, Eric E. ( May 2021 , Frontiers in Marine Science)

   null (Ed.)

   The fish gut microbiome is impacted by a number of biological and environmental factors including fish feed formulations. Unlike mammals, vertical microbiome transmission is largely absent in fish and thus little is known about how the gut microbiome is initially colonized during hatchery rearing nor the stability throughout growout stages. Here we investigate how various microbial-rich surfaces from the built environment “BE” and feed influence the development of the mucosal microbiome (gill, skin, and digesta) of an economically important marine fish, yellowtail kingfish, Seriola lalandi , over time. For the first experiment, we sampled gill and skin microbiomes from 36 fish reared in three tank conditions, and demonstrate that the gill is more influenced by the surrounding environment than the skin. In a second experiment, fish mucous (gill, skin, and digesta), the BE (tank side, water, inlet pipe, airstones, and air diffusers) and feed were sampled from indoor reared fish at three ages (43, 137, and 430 dph; n = 12 per age). At 430 dph, 20 additional fish were sampled from an outdoor ocean net pen. A total of 304 samples were processed for 16S rRNA gene sequencing. Gill and skin alpha diversity increased while gut diversity decreased with age. Diversity was much lower in fish from the ocean net pen compared to indoor fish. The gill and skin are most influenced by the BE early in development, with aeration equipment having more impact in later ages, while the gut “allochthonous” microbiome becomes increasingly differentiated from the environment over time. Feed had a relatively low impact on driving microbial communities. Our findings suggest that S. lalandi mucosal microbiomes are differentially influenced by the BE with a high turnover and rapid succession occurring in the gill and skin while the gut microbiome is more stable. We demonstrate how individual components of a hatchery system, especially aeration equipment, may contribute directly to microbiome development in a marine fish. In addition, results demonstrate how early life (larval) exposure to biofouling in the rearing environment may influence fish microbiome development which is important for animal health and aquaculture production. 

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