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Seawater microorganisms play an important role in coral reef ecosystem functioning and can be influenced by biological, chemical, and physical features of reefs. As coral reefs continue to respond to environmental changes, the reef seawater microbiome has been proposed as a conservation tool for monitoring perturbations. However, the spatial variability of reef seawater microbial communities is not well studied, limiting our ability to make generalizable inferences across reefs. In order to better understand how microorganisms are distributed at multiple spatial scales, we examined seawater microbial communities in Florida Reef Tract and US Virgin Islands reef systems using a nested sampling design. On 3 reefs per reef system, we sampled seawater at regular spatial intervals close to the benthos. We assessed the microbial community composition of these waters using ribosomal RNA gene amplicon sequencing. Our analysis revealed that reef water microbial communities varied as a function of reef system and individual reefs, but communities did not differ within reefs and were not significantly influenced by benthic composition. For the reef system and inter-reef differences, abundant microbial taxa were found to be potentially useful indicators of environmental difference due to their high prevalence and variance. We further examined reef water microbial biogeography on a global scale using a secondary analysis of 5 studies, which revealed that microbial communities were more distinct with increasing geographic distance. These results suggest that biogeography is a distinguishing feature for reef water microbiomes, and that development of monitoring criteria may necessitate regionally specific sampling and analyses. 

Microorganisms are central to the functioning of coral reef ecosystems, but their dynamics are unstudied on most reefs. We examined the microbial ecology of shallow reefs within the Federated States of Micronesia. We surveyed 20 reefs surrounding 7 islands and atolls (Yap, Woleai, Olimarao, Kosrae, Kapingamarangi, Nukuoro, and Pohnpei), spanning 875053 km 2 . On the reefs, we found consistently higher coral coverage (mean ± SD = 36.9 ± 22.2%; max 77%) compared to macroalgae coverage (15.2 ± 15.5%; max 58%), and low abundances of fish. Reef waters had low inorganic nutrient concentrations and were dominated by Synechococcus, Prochlorococcus, and SAR11 bacteria. The richness of bacterial and archaeal communities was significantly related to interactions between island/atoll and depth. High coral coverage on reefs was linked to higher relative abundances of Flavobacteriaceae, Leisingera, Owenweeksia, Vibrio, and the OM27 clade, as well as other heterotrophic bacterial groups, consistent with communities residing in waters near corals and within coral mucus. Microbial community structure at reef depth was significantly correlated with geographic distance, suggesting that island biogeography influences reef microbial communities. Reefs at Kosrae Island, which hosted the highest coral abundance and diversity, were unique compared to other locations; seawater from Kosrae reefs had the lowest organic carbon (59.8-67.9 µM), highest organic nitrogen (4.5-5.3 µM), and harbored consistent microbial communities (>85% similar), which were dominated by heterotrophic cells. This study suggests that the reef-water microbial ecology on Micronesian reefs is influenced by the density and diversity of corals as well as other biogeographical features. 

In coral reefs and adjacent seagrass meadow and mangrove environments, short temporal scales (i.e. tidal, diurnal) may have important influences on ecosystem processes and community structure, but these scales are rarely investigated. This study examines how tidal and diurnal forcings influence pelagic microorganisms and nutrient dynamics in 3 important and adjacent coastal biomes: mangroves, coral reefs, and seagrass meadows. We sampled for microbial ( Bacteria and Archaea ) community composition, cell abundances and environmental parameters at 9 coastal sites on St. John, US Virgin Islands that spanned 4 km in distance (4 coral reefs, 2 seagrass meadows and 3 mangrove locations within 2 larger bays). Eight samplings occurred over a 48 h period, capturing day and night microbial dynamics over 2 tidal cycles. The seagrass and reef biomes exhibited relatively consistent environmental conditions and microbial community structure but were dominated by shifts in picocyanobacterial abundances that were most likely attributed to diel dynamics. In contrast, mangrove ecosystems exhibited substantial daily shifts in environmental parameters, heterotrophic cell abundances and microbial community structure that were consistent with the tidal cycle. Differential abundance analysis of mangrove-associated microorganisms revealed enrichment of pelagic oligotrophic taxa during high tide and enrichment of putative sediment-associated microbes during low tide. Our study underpins the importance of tidal and diurnal time scales in structuring coastal microbial and nutrient dynamics, with diel and tidal cycles contributing to a highly dynamic microbial environment in mangroves, and time of day likely contributing to microbial dynamics in seagrass and reef biomes. 

Drought is common in rivers, yet how this disturbance regulates metabolic activity across network scales is largely unknown. Drought often lowers gross primary production (GPP) and ecosystem respiration (ER) in small headwaters but by contrast can enhance GPP and cause algal blooms in downstream estuaries. We estimated ecosystem metabolism across a nested network of 13 reaches from headwaters to the main stem of the Connecticut River from 2015 through 2017, which encompassed a pronounced drought. During drought, GPP and ER increased, but with greater enhancement in larger rivers. Responses of GPP and ER were partially due to warmer temperatures associated with drought, particularly in the larger rivers where temperatures during summer drought were > 10°C higher than typical summer baseflow. The larger rivers also had low canopy cover, which allowed primary producers to take advantage of lower turbidity and fewer cloudy days during drought. We conclude that GPP is enhanced by higher temperature, lower turbidity, and longer water residence times that are all a function of low discharge, but ecosystem response in temperate watersheds to these drivers depends on light availability regulated by riparian canopy cover. In larger rivers, GPP increased more than ER during drought, even leading to temporary autotrophy, an otherwise rare event in the typically light‐limited heterotrophic Connecticut River main stem. With climate change, rivers and streams may become warmer and drought frequency and severity may increase. Such changes may increase autotrophy in rivers with broad implications for carbon cycling and water quality in aquatic ecosystems.