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1. The role of the microbiome in human disease

   Flowers, L. (February 2023, Biomedical journal of scientific technical research)

   Since the invention of the microscope, scientists have described microbial communities on living and non-living matter. In terms of human-associated microbes, scientists have documented the beneficial effects of the microbiota for many decades. Prophylactic effects include protection from pathogens, digestion potential, and the production of essential vitamins. However, recent high-throughput methodologies and analytical advances have accelerated microbiome science and our understanding of microbial diversity in living organisms. The microbiome denotes the complex network of all the microorganisms and microbial genes located in specific biotic or abiotic environments. We now realize the enormous diversity and functionality of the microbiota in humans and the endless benefits to health and disease. Dysbiosis facilitates the manufacture of various proinflammatory mediators, biochemical imbalances, and colonization of microbes associated with disease outcomes. Additional work is necessary to determine whether changes in the human microbiome are due to anthropogenic, genetic, or environmental variations. This review will present microbiome research studies focusing on human disease. The findings documented in this article offer optimism on the profound role microorganisms play in supporting human health and how pharmaceutical interactions targeting specific microbes can decrease the incidence of human disease caused by the ecological disturbance of the normal microbiota. 

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2. Vertical Saltwater Intrusion in Coastal Aquifers Driven by Episodic Flooding: A Review

   https://doi.org/10.1029/2022WR032614  

   Cantelon, Julia A.; Guimond, Julia A.; Robinson, Clare E.; Michael, Holly A.; Kurylyk, Barret L. (November 2022, Water Resources Research)

   Abstract Low‐elevation coastal areas are increasingly vulnerable to seawater flooding as sea levels rise and the frequency and intensity of large storms increase with climate change. Seawater flooding can lead to the salinization of fresh coastal aquifers by vertical saltwater intrusion (SWI). Vertical SWI is often overlooked in coastal zone threat assessments despite the risk it poses to critical freshwater resources and salt‐intolerant ecosystems that sustain coastal populations. This review synthesizes field and modeling approaches for investigating vertical SWI and the practical and theoretical understanding of salinization and flushing processes obtained from prior studies. The synthesis explores complex vertical SWI dynamics that are influenced by density‐dependent flow and oceanic, hydrologic, geologic, climatic, and anthropogenic forcings acting on coastal aquifers across spatial and temporal scales. Key knowledge gaps, management challenges, and research opportunities are identified to help advance our understanding of the vulnerability of fresh coastal groundwater. Past modeling studies often focus on idealized aquifer systems, and thus future work could consider more diverse geologic, climatic, and topographic environments. Concurrent field and modeling programs should be sustained over time to capture interactions between physical processes, repeated salinization and flushing events, and delayed aquifer responses. Finally, this review highlights the need for improved coordination and knowledge translation across disciplines (e.g., coastal engineering, hydrogeology, oceanography, social science) to gain a more holistic understanding of vertical SWI. There also needs to be more education of communities, policy makers, and managers to motivate societal action to address coastal groundwater vulnerability in a changing climate. 

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3. Flooding Projections Due To Groundwater Emergence Caused by Sea Level Variability

   https://doi.org/10.1029/2025EF006270  

   Barnes, Austin T; Merrifield, Mark A; Bagheri, Kian; Levy, Morgan C; Davani, Hassan (July 2025, Earth's Future)

   Abstract Rising groundwater tables due to sea level rise (SLR) pose a critical but understudied threat to low‐lying coastal regions. This study uses field observations and dynamic modeling to investigate drivers of groundwater variability and to project flooding risks from emergent groundwater in Imperial Beach, California. Hourly groundwater table data from four monitoring wells (2021–2024) reveal distinct aquifer behaviors across soil types. In transmissive coastal sandy soils, groundwater levels are dominated by ocean tides, with secondary contributions from non‐tidal sea level variability and seasonal recharge. In this setting, we calibrated an empirical groundwater model to observations, and forced the model with regional SLR scenarios. We project that groundwater emergence along the low‐lying coastal road will begin by the 2060s under intermediate SLR trajectories, and escalate to near‐daily flooding by 2100. Over 20% of San Diego County's coastline shares similar transmissive sandy geology and thus similar flooding risk. Results underscore the urgency of integrating groundwater hazards into coastal resilience planning, as current adaptation strategies in Imperial Beach—focused on surface flooding—are insufficient to address infrastructure vulnerabilities from below. This study provides a transferable framework for assessing groundwater‐driven flooding in transmissive coastal aquifers, where SLR‐induced groundwater rise threatens critical infrastructure decades before permanent inundation. 

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4. Large Comparative Analyses of Primate Body Site Microbiomes Indicate that the Oral Microbiome Is Unique among All Body Sites and Conserved among Nonhuman Primates

   https://doi.org/10.1128/spectrum.01643-21  

   Asangba, Abigail E.; Mugisha, Lawrence; Rukundo, Joshua; Lewis, Rebecca J.; Halajian, Ali; Cortés-Ortiz, Liliana; Junge, Randall E.; Irwin, Mitchell T.; Karlson, Johan; Perkin, Andrew; et al (June 2022, Microbiology Spectrum)

   Kormas, Konstantinos Aristomenis (Ed.)

   ABSTRACT The study of the mammalian microbiome serves as a critical tool for understanding host-microbial diversity and coevolution and the impact of bacterial communities on host health. While studies of specific microbial systems (e.g., in the human gut) have rapidly increased, large knowledge gaps remain, hindering our understanding of the determinants and levels of variation in microbiomes across multiple body sites and host species. Here, we compare microbiome community compositions from eight distinct body sites among 17 phylogenetically diverse species of nonhuman primates (NHPs), representing the largest comparative study of microbial diversity across primate host species and body sites. Analysis of 898 samples predominantly acquired in the wild demonstrated that oral microbiomes were unique in their clustering, with distinctive divergence from all other body site microbiomes. In contrast, all other body site microbiomes clustered principally by host species and differentiated by body site within host species. These results highlight two key findings: (i) the oral microbiome is unique compared to all other body site microbiomes and conserved among diverse nonhuman primates, despite their considerable dietary and phylogenetic differences, and (ii) assessments of the determinants of host-microbial diversity are relative to the level of the comparison (i.e., intra-/inter-body site, -host species, and -individual), emphasizing the need for broader comparative microbial analyses across diverse hosts to further elucidate host-microbial dynamics, evolutionary and biological patterns of variation, and implications for human-microbial coevolution. IMPORTANCE The microbiome is critical to host health and disease, but much remains unknown about the determinants, levels, and evolution of host-microbial diversity. The relationship between hosts and their associated microbes is complex. Most studies to date have focused on the gut microbiome; however, large gaps remain in our understanding of host-microbial diversity, coevolution, and levels of variation in microbiomes across multiple body sites and host species. To better understand the patterns of variation and evolutionary context of host-microbial communities, we conducted one of the largest comparative studies to date, which indicated that the oral microbiome was distinct from the microbiomes of all other body sites and convergent across host species, suggesting conserved niche specialization within the Primates order. We also show the importance of host species differences in shaping the microbiome within specific body sites. This large, comparative study contributes valuable information on key patterns of variation among hosts and body sites, with implications for understanding host-microbial dynamics and human-microbial coevolution. 

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5. Stability of Saltwater‐Freshwater Mixing Zones in Beach Aquifers With Geologic Heterogeneity

   https://doi.org/10.1029/2023WR036056  

   Olorunsaye, Olasunkanmi; Heiss, James_W (July 2024, Water Resources Research)

   Abstract Saltwater‐freshwater mixing zones in beach aquifers support biogeochemical reactions that moderate chemical loads in fresh groundwater discharging to marine ecosystems. Existing laboratory and numerical modeling studies have demonstrated that fluid density gradients in the mixing zone can lead to free convection and the formation of density instabilities, or salt fingers, under a range of hydrologic, morphologic, and hydrogeologic conditions. However, salt fingers have rarely been observed in real‐world beach aquifers despite a growing body of field studies investigating intertidal mixing zones. In this study, we used geostatistical methods to generate randomly distributed assemblages of fine and medium sand and incorporated those geologic realizations into variable‐density variably‐saturated flow and salt transport simulations to explore the influence of geologic structure on mixing zone stability in tidally‐influenced beaches. Ensemble‐averaged model results show that geologic heterogeneity inhibits salt finger formation and promotes a stable intertidal mixing zone due to enhanced dispersion. This effect is highest for high degrees of heterogeneity and for more laterally connected geologic architecture. Compared to hydraulically equivalent homogeneous models, sediments with moderate to high heterogeneity produce mixing zones that are on average 19%–29% smaller and 3–10 times more stable due to the absence of the downward convection and seaward movement of salt fingers. The models indicate that geologic heterogeneity may explain the lack of field observations of salt fingers in real‐world intertidal mixing zones. The findings have implications for predicting the onset of free convection in beaches and for understanding intertidal pore water biogeochemistry and chemical fluxes to the ocean. 

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