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Local habitat availability can strongly affect animal communities. On coral reefs, the biodiversity of small, bottom-dwelling (‘cryptobenthic’) reef fishes and drivers of their community assembly have yet to be explored in many locations. Here, we investigate how local and regional factors shape the structure and composition of cryptobenthic reef fish communities in the Veracruz Reef System National Park (VRS) in the Gulf of Mexico (GoM). Focusing on five reefs in the VRS, we surveyed cryptobenthic reef fish communities at scales of reef outcrops (~ 3–5 m2) and isolated microhabitats, while also quantifying the benthic composition of each reef to determine microhabitat availability. We found no significant differences in species richness or abundance across park regions and reef zones, but community composition differed qualitatively across reef zones. Furthermore, we discovered strong differences in cryptobenthic reef fishes’ preferences for various microhabitats, which are likely to drive community assembly and provide evidence for species-specific vulnerabilities to reef degradation. Caves harbored the highest biodiversity and abundance of cryptobenthic fishes, while gorgonian soft corals and algae supported the fewest species and individuals. The endemic gobies Tigrigobius redimiculus and Elacatinus jarocho both showed high abundance and occurrence but displayed opposite patterns of microhabitat specialization; T. redimiculus was categorized as a microhabitat generalist, while E. jarocho was revealed as a cave-dwelling specialist species. Overall, our quantitative exploration of the cryptobenthic reef fish community in the southwest GoM provides a crucial baseline for habitat and biodiversity monitoring in the region and highlights E. jarocho as an emblematic, endemic indicator species that will be vulnerable to extinction if further reduction of habitat complexity occurs. 

Cross-ecosystem nutrient transfer can enhance coral reef functioning in an otherwise oligotrophic environment. While the influence of seabird-derived nutrients on coral reef organisms is increasingly recognized, how they are integrated into reef food webs remains unclear. Cryptobenthic reef fishes are crucial for energy transfer on coral reefs, and their fast life histories imply that they respond strongly to seabird-derived nutrients. Here, we investigate how variation in nearshore seabird nutrient subsidies affects coral reef fish communities. By comparing fish communities across locations differing in seabird nutrient inputs and using stable isotope analysis, we explore nutrient integration across depth, their influence on cryptobenthic and associated larger reef fishes and investigated the relative reliance of cryptobenthic fishes on seabird-enriched benthic and non-enriched pelagic pathways. We find that, near seabird colonies, cryptobenthic fishes’ diets can transition from pelagic to benthic dominance; cryptobenthic fish communities are larger; herbivores and all feeding groups comprising potential cryptobenthic fish predators have higher biomass. Collectively, our results stress the importance of seabirds in shaping energy pathways and suggest that, even in dynamic, ocean-swept reef systems, cryptobenthic fishes can mobilize seabird subsidies and potentially act as a nutritional bridge to higher trophic levels. 

Understanding how humans have altered coral reef food webs remains challenging due to the absence of prehistoric baselines. Here, we use fish remains preserved in fossil and archaeological deposits from Panamá and the Dominican Republic to explore how Caribbean reef fish mortality patterns have changed over millennia. By quantifying accumulation rates of shark dermal denticles (scales) and bony fish otoliths (ear stones) in reef sediments, we assess relative fish abundance, while otolith size serves as a proxy for body size at death. Comparisons of these death assemblages suggest a 75% decline in shark-derived material and a 22% reduction in the sizes of human-targeted fishes—consistent with historical exploitation. This evidence of decline in large-bodied, higher trophic level fish remains coincided with a doubling in prey fish otolith accumulation and a 17% increase in their reconstructed body sizes. These patterns in time-averaged death assemblages align with effects of release from predation, documenting an often assumed (but rarely shown) cascading effect. In contrast, otoliths of predator-sheltered cryptobenthic fishes showed no change in either accumulation or size, suggesting that ‘‘bottom–up”environmental factors were not responsible for the observed changes. Together, these data indicate that pre-exploitation predator communities strongly controlled exposed prey fishes, but this “top–down” effect diminishes rapidly toward the food chain base, especially in predator-resistant groups. Understanding trophic cascades on Caribbean reefs requires studying systems before predator depletion. 

Porous silicon (PSi) thin films on silicon substrates have been extensively investigated in the context of biosensing applications, particularly for achieving label-free optical detection of a wide range of analytes. However, mass transport challenges have made it difficult for these biosensors to achieve rapid response times and low detection limits. In this work, we introduce an approach for improving the efficiency of molecule transport in PSi by using open-ended PSi membranes atop paper substrates in a flow-through sensor scheme. The paper substrate provides structural support as well as an efficient means of draining solutions from the PSi membrane without the use of an external pump and microfluidic channels. Distinct changes in the reflectance properties of the PSi membrane are measured when molecules are captured in the membrane. A concentration dependent response of the sensor for protein detection is demonstrated. Factors influencing the interaction time of molecules in the PSi membrane and the drying time of the membrane, which directly affect the detection sensitivity and overall testing time, are discussed. The demonstrated performance of the PSi-on-paper sensor establishes the feasibility of a platform for low-cost rapid diagnostic tests with a highly sensitive, quantitative readout. 

Coronavirus genomes have evolutionary histories shaped extensively by recombination. Yet, how often recombination occurs at a cellular level, or the factors that regulate recombination rates, are poorly understood. Utilizing experimental co-infections with pairs of genetically distinct coronaviruses, we found that recombination is both frequent and rare during coinfection. Recombination occurred in every instance of co-infection yet resulted in relatively few recombinant RNAs. By integrating a discrete-time Susceptible-Infected-Removed (SIR) model, we found that rates of recombination are determined primarily by rates of cellular co-infection, rather than other possible barriers such as RNA compartmentalization. By staggering the order and timing of infection with each virus we also found that rates of co-infection are themselves heavily influenced by genetic and ecological mechanisms, including superinfection exclusion and the relative fitness of competing viruses. Our study highlights recombination as a potent yet regulated force: frequent enough to ensure a steady influx of genetic variation but also infrequent enough to maintain genomic integrity. As recombination is thought to be an important driver of host-switching and disease emergence, our study provides new insights into the factors that regulate coronavirus recombination and evolution more broadly.