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Marine sponges have been successful in their expansion across diverse ecological niches around the globe. Pioneering work attributed this success to both a well-developed aquiferous system that allowed for efficient filter feeding on suspended organic matter and the presence of microbial symbionts that can supplement host heterotrophic feeding with photosynthate or dissolved organic carbon. We now know that sponge-microbe interactions are host-specific, highly nuanced, and provide diverse nutritional benefits to the host sponge. Despite these advances in the field, many current hypotheses pertaining to the evolution of these interactions are overly generalized; these over-simplifications limit our understanding of the evolutionary processes shaping these symbioses and how they contribute to the ecological success of sponges on modern coral reefs. To highlight the current state of knowledge in this field, we start with seminal papers and review how contemporary work using higher resolution techniques has both complemented and challenged their early hypotheses. We outline different schools of thought by discussing evidence of symbiont contribution to both host ecological divergence and convergence, nutritional specificity and plasticity, and allopatric and sympatric speciation. Based on this synthesis, we conclude that the evolutionary pressures shaping these interactions are complex, with influences from both external (nutrient limitation and competition) and internal (fitness trade-offs and evolutionary constraints) factors. We outline recent controversies pertaining to these evolutionary pressures and place our current understanding of these interactions into a broader ecological and evolutionary framework. Finally, we propose areas for future research that we believe will lead to important new developments in the field.

The pelagic Gulf of Mexico (GoM) is a complex system of dynamic physical oceanography (western boundary current, mesoscale eddies), high biological diversity, and community integration via diel vertical migration and lateral advection. Humans also heavily utilize this system, including its deep-sea components, for resource extraction, shipping, tourism, and other commercial activity. This utilization has had impacts, some with disastrous consequences. The Deepwater Horizon oil spill (DWHOS) occurred at a depth of ∼1500 m (Macondo wellhead), creating a persistent and toxic mixture of hydrocarbons and dispersant in the deep-pelagic (water column below 200 m depth) habitat. In order to assess the impacts of the DWHOS on this habitat, two large-scale research programs, described herein, were designed and executed. These programs, ONSAP and DEEPEND, aimed to quantitatively characterize the oceanic ecosystem of the northern GoM and to establish a time-series with which natural and anthropogenic changes could be detected. The approach was multi-disciplinary in nature and included in situ sampling, acoustic sensing, water column profiling and sampling, satellite remote sensing, AUV sensing, numerical modeling, genetic sequencing, and biogeochemical analyses. The synergy of these methodologies has provided new and unprecedented perspectives of an oceanic ecosystem with respect to composition, connectivity, drivers, and variability.

Oceanic diel vertical migration (DVM) constitutes the daily movement of various mesopelagic organisms migrating vertically from depth to feed in shallower waters and return to deeper water during the day. Accurate classification of taxa that participate in DVM remains non-trivial, and there can be discrepancies between methods. DEEPEND consortium (www.deependconsortium.org) scientists have been characterizing the diversity and trophic structure of pelagic communities in the northern Gulf of Mexico (nGoM). Profiling has included scientific echosounders to provide accurate and quantitative estimates of organismal density and timing as well as quantitative net sampling of micronekton. The use of environmental DNA (eDNA) can detect uncultured microbial taxa and the remnants that larger organisms leave behind in the environment. eDNA offers the potential to increase understanding of the DVM and the organisms that participate. Here we used real-time shipboard echosounder data to direct the sampling of eDNA in seawater at various time-points during the ascending and descending DVM. This approach allowed the observation of shifts in eDNA profiles concurrent with the movement of organisms in the DVM as measured by acoustic sensors. Seawater eDNA was sequenced using a high-throughput metabarcoding approach. Additionally, fine-scale acoustic data using an autonomous multifrequency echosounder was collected simultaneously with the eDNA samples and changes in organism density in the water column were compared with changes in eDNA profiles. Our results show distinct shifts in eukaryotic taxa such as copepods, cnidarians, and tunicates, over short timeframes during the DVM. These shifts in eDNA track changes in the depth of sound scattering layers (SSLs) of organisms and the density of organisms around the CTD during eDNA sampling. Dominant taxa in eDNA samples were mostly smaller organisms that may be below the size limit for acoustic detection, while taxa such as teleost fish were much less abundant in eDNA data compared to acoustic data. Overall, these data suggest that eDNA, may be a powerful new tool for understanding the dynamics and composition of the DVM, yet challenges remain to reconcile differences among sampling methodologies.

The Gulf of Mexico (GoM) is a dynamic marine ecosystem influenced by multiple natural and anthropogenic processes and inputs, such as the intrusion of warm oligotrophic water via the Loop Current, freshwater and nutrient input by the Mississippi River, and hydrocarbon inputs via natural seeps and industrial spills. Microbial plankton communities are important to pelagic food webs including in the GoM but understanding the drivers of the natural dynamics of these passively distributed microorganisms can be challenging in such a large and heterogeneous system. As part of the DEEPEND consortium, we applied high throughput 16S rRNA sequencing to investigate the spatial and temporal dynamics of pelagic microbial plankton related to several environmental conditions during two offshore cruises in 2015. Our results show dramatic community shifts across depths, especially between photic and aphotic zones. Though we only have two time points within a single year, observed temporal shifts in microbial plankton communities were restricted to the seasonally influenced epipelagic zone (0–200 m), and appear mainly driven by changes in temperature. Environmental selection in microbial plankton communities was depth-specific, with variables such as turbidity, salinity, and abundance of photosynthetic taxa strongly correlating with community structure in the epipelagic zone, while variables such as oxygen and specific nutrient concentrations were correlated with community structure at deeper depths.