Abstract Streams process organic matter as water moves along the land‐to‐ocean continuum, making important contributions to global biogeochemical cycles. Yet, predicting stream microbial metabolism associated with biogeochemical transformations at broad spatial scales remains challenging. Using the National Ecological Observatory Network database, we investigated ecological relationships between microbial communities and environmental conditions at the subcontinental scale. We found that microbial community composition and function were best explained by site and substrate type. However, when field replicates were combined, stream physico‐chemical characteristics became strong predictors. Additionally, oxic and anoxic nitrogen‐ and methane‐related gene abundances varied with substrate type and coexisted in epipsammon samples, but not in epilithon. Overall, water quality appeared to act as a subcontinental scale environmental filter on microbial communities. However, this influence was secondary to the high spatial heterogeneity induced by small‐scale patches. Thus, nested spatial scales must be considered to fully understand benthic microbial communities' role in stream biogeochemistry.
Abstract Synechococcus inhabit both nutrient‐rich estuaries and oligotrophic waters, yet exhibit distinct niche segregation across phylogenetic clades. Previous studies indicated clade III predominated in the ultraoligotrophic Mediterranean Sea. However, the mechanisms underlying clade III's dominance over other clades in ultraoligotrophic waters remain unclear. Here, we measured bulk and clade‐specific growth rates of Synechococcus using a dilution approach during a mesocosm experiment in the Eastern Mediterranean Sea. Clade III exhibited higher growth rates than competing clades and competitive superiority for limited nutrients in mesocosms amended with ammonium and phosphate. Genomic analyses revealed clade III possessed more nitrogen/phosphorus transporters than other clades (except clade VIII and S5.2), which may contribute to their competitive advantage in ultraoligotrophic conditions. Compared to clade VIII/S5.2, clade III's lower GC content and smaller genome size are consistent with adaptation to oligotrophic systems. The unique adaptive genomic traits of clade III Synechococcus may facilitate their ecological success in ultraoligotrophic waters.
Abstract The biotic component of the marine silica cycle strongly influences global biogeochemical cycling. Active uptake of dissolved silicic acid (dSi) occurs via silicon transporters (SITs), first characterized in diatoms but widely distributed in eukaryotes. Studying SITs and SIT‐like (SIT‐L) gene transcripts provides insights into the dynamics and evolutionary history of diverse biosilicifiers. Using a 2‐yr metatranscriptomics dataset of Baltic Sea surface microbial communities, we identified SIT/SIT‐L genes associated with 11 eukaryotic classes. Although diatoms were previously assumed to drive the Baltic Sea silica cycle, silicoflagellates dominated SIT/SIT‐L expression over the sampling period. SIT/SIT‐L expression and phylogenetic analyses revealed class‐specific patterns, suggesting a complex evolutionary history in dinoflagellates and pronounced clade dynamics in diatoms. Overall, these unexpectedly complex and dynamic shifts in transcriptional investment in silicon transport revealed underappreciated microbial groups driving the Baltic Sea silica cycle.
Abstract Chlorophyll a (Chl a ) is a key indicator of phytoplankton biomass and marine primary productivity, linking ocean ecosystem change to biogeochemical cycling and climate. Understanding the environmental controls on long‐term Chl a variability is therefore essential. Here, we examine spatiotemporal variability in surface Chl a across the non‐polar global ocean (60°S–60°N) from 1998 to 2022 using Copernicus biogeochemical hindcast and ocean reanalysis datasets. Empirical orthogonal function (EOF) analysis is applied to Chl a and associated physical and biogeochemical variables, including sea surface temperature, surface sensible heat flux, mixed‐layer depth, wind speed, and nutrient concentrations. The results reveal strong regional contrasts in Chl a variability across the major ocean basins. Declining regions are associated mainly with enhanced upper‐ocean stratification and reduced nutrient resupply, whereas increasing regions are more strongly linked to enhanced nutrient availability. These findings highlight the importance of coupled physical–biogeochemical controls on global phytoplankton variability under climate forcing.
Abstract Deployment of an autonomous Zooglider in the western Mediterranean Sea revealed the presence of long phytoplankton chains attaining maximum lengths of 6.4–10.4 mm suspended in situ. Elongate chains included the diatoms Guinardia, Proboscia, two other diatom morphologies, and solitary filaments of the cyanobacterium Trichodesmium. Most elongate chains were distributed in the upper 100 m of the water column, overlapping the deep chlorophyll maximum, but some extended to depths of 400 m, suggesting occasional export into deep waters. Such elongate chains appear to be an unutilizable prey resource for most mesozooplankton grazers, including planktonic copepods and appendicularians. Elongate chains are likely to be widely distributed in the ocean, but their detection requires noninvasive measurement methods that do not disrupt the fluid environment or disturb suspended phytoplankton.
Abstract The dinoflagellate genus Gambierdiscus was detected for the first time in the Azores Archipelago, representing its northernmost record to date (> 39°N). Two strains were isolated from macroalgal substrates on Corvo and Faial Islands during the summer of 2024, coinciding with a marine heatwave in which sea‐surface temperature anomalies exceeded +2°C. Morphological and molecular analyses identified both isolates as Gambierdiscus carolinianus, extending further North the known range of this genus in the Atlantic and complementing previous records from other Macaronesian archipelagos. The Azorean isolate from Corvo clustered more closely with western Atlantic populations than with Madeira or the Canary Islands strains, suggesting long‐range connectivity potentially driven by oceanographic processes. Although no ciguatera poisoning (CP) cases have been reported in the Azores, the occurrence of Gambierdiscus highlights the need for sustained monitoring and ecological assessments to evaluate the risk of CP emergence in this remote temperate archipelago under shifting environmental conditions.
Abstract Resting stages of protists act as biological time capsules when buried in marine sediments, preserving viable cells that enable the study of ecological and evolutionary processes across timescales. Recent studies have extended the known viability in diatoms to several millennia and in dinoflagellates to over a century, while also identifying molecular and physiological mechanisms, such as selective gene activity and hormonal regulation, that sustain long‐term dormancy. These advances emphasize the role of marine seed banks in population renewal and ecosystem resilience. However, research has so far concentrated on temperate regions and has focused primarily on a few diatom and dinoflagellate taxa, leaving most other protist groups and biogeographic areas largely unexplored. In this review, we synthesize recent developments, identify critical taxonomic and geographic gaps, and emphasize the potential of resurrection ecology as a tool to investigate adaptation and evolutionary dynamics in a rapidly changing global ocean.
Abstract Reef fish have complex life cycles where pelagic larval survival and recruitment are linked to environmental and early life history traits (ELHTs). We combine light traps and otolith microstructure analysis to examine how environmental variables and ELHTs drive larval growth and settlement in the endemic Ophioblennius trinitatis. Otoliths revealed a prolonged pelagic larval duration (47–52 d), large settlement size, and lunar‐synchronized spawning and settlement. Larval growth responded to non‐linear interactions between sea surface temperature and wind regime, peaking within a narrow thermal window (26.6–27.8°C) under weak east–southeasterly winds (< 5.8 m s−1) and chlorophyll a concentrations > 0.15 mg m−3. Pre‐settlement abundance showed seasonal and interannual variability, largely driven by seasonal and year‐to‐year fluctuations, with environmental effects limited to thermo‐hydrodynamic interactions favoring coastal retention. Results show settlement in O. trinitatis is structured by intrinsic life‐history synchronization, with environmental variability modulating larval performance within narrow optimal windows, highlighting sensitivity to climate change.
Abstract Coral reef monitoring techniques are in high demand to support conservation efforts in marine ecosystems. Noninvasively measuring the spectral reflectance of corals provides rich information about their health status. However, the lack of large‐scale, high‐quality coral spectral datasets prevents the application of data‐driven spectral acquisition and analysis methods to coral reef monitoring. In this work, we present CoralSpec‐30M, a high‐resolution underwater coral spectral dataset acquired under controlled environments. The dataset contains 1286 hyperspectral images of 10 representative hard coral species, covering 1865 individual samples and 30,031,224 valid pixels. Each image is a 512 × 512 reflectance cube spanning 400 to 800 nm at 2.9 nm spectral intervals (136 bands). Coral samples are captured under paired white/blue illumination. The dataset also includes coral masks, manually labeled pixel‐wise semantic annotations, and machine‐learning–generated class masks. This dataset supports the development of data‐driven approaches for coral reef monitoring and related coral research.
Abstract Cyanobacterial harmful algal blooms (cyanoHABs) are often associated with warm water temperatures and low wind speeds, but quantifying thresholds in meteorological conditions is challenging. Using 4208 cyanoHAB reports from 405 lakes in New York State (USA), we calculated anomalies in daily wind speed and air temperature for each report and the 5 d preceding it. On the day of a cyanoHAB, lakes had lower than average wind speeds and higher than average air temperatures. Notably, the magnitude of these anomalies was influenced by the trophic state of each lake, with nutrient‐limited lakes having larger anomalies on the day of a cyanoHAB. Additionally, the absence of either anomaly type reduced the likelihood of a cyanoHAB, particularly in nutrient‐poor lakes. These results enhance our understanding of the proximate drivers and thresholds regulating cyanoHABs across varying trophic states, suggesting that large‐scale changes in climate may substantially impact future cyanoHAB development.
Abstract Global warming alters the physiology of ectotherm consumers, potentially making their diets more herbivorous. However, the relevance and generality of these changes remain poorly understood in a multispecies context. To address this critical knowledge gap, we experimentally tested the temperature‐dependent feeding preference of the invasive mysid Limnomysis benedeni on different combinations of autotrophic (phytoplankton) and heterotrophic (zooplankton) prey species varying in body size. Warming increased the ratio of autotrophic‐to‐heterotrophic prey consumption across all treatments, driven by reduced heterotrophic prey consumption and, where larger zooplankton (Brachionus calyciflorus and Daphnia magna) were present, an additional increase in phytoplankton ingestion. Total carbon ingestion did not increase consistently with warming, indicating diet reallocation instead of increased overall feeding intensity at higher temperatures. These findings suggest that warming can change the trophic role of invasive consumers, potentially modulating their effects on community dynamics, and provide a basis for future research in more realistic ecological settings.
Abstract Macrophytes are foundation species whose use as nature‐based solution (NbS) in aquatic ecosystems can help reduce climate change impacts while mitigating biodiversity loss. The discrepancy in research and application of macrophytes as NbS across inland and marine coastal ecosystems is an opportunity to expand the concept and learn from different approaches. We report on an initiative uniting marine and freshwater scientists that compared knowledge on macrophytes as NbS across realms, identified advances and gaps in their use, and synthesized challenges and opportunities for application. We conducted a bibliometric analysis and an expert participatory exercise around recent review papers. We reveal that most NbS papers on macrophytes are marine‐focused, with distinct topics emphasized across realms, highlighting complementarity of expertise and potential extension to inland waters. We provide recommendations to encourage researchers and stakeholders to embrace the value of macrophytes across a broad range of contexts for a more sustainable future.
Abstract Although collectively reservoirs constitute a globally significant source of anthropogenic methane (CH4), there are still few investigations of reservoir CH4 fluxes and their controls that span multiple seasons, years, and reservoir types. Here we present results from a 2‐yr study of diffusive and ebullitive CH4 fluxes in four contrasting reservoirs in the Pacific Northwest United States. Using floating chambers outfitted with CH4 sensors (n = 105), supported by gas chromatography and environmental monitoring, we identified chlorophyll a, water temperature, season, reservoir type (run‐of‐river vs. storage), and hydrostatic pressure fluctuations as significant predictors of CH4 flux. These findings indicate that water‐level fluctuations and chlorophyll a are associated with increased ebullitive flux in reservoir forebays, reinforce previous work demonstrating that neglecting ebullition can substantially underestimate total CH4 emissions, and highlight that strong seasonal variability necessitates full annual sampling to accurately constrain emission estimates.
Abstract The contribution of sinking fecal pellets to the biological carbon pump depends on pellet properties, producer abundance, and the depth and timing of pellet production, which can be modulated by diel vertical migration. We examined diel variability in zooplankton fecal pellet flux in the subarctic Northeast Pacific using two image‐based tools: the Underwater Vision Profiler (UVP5) and upward‐facing cameras (GelCam) on a surface‐tethered sediment trap array. We classified three morphologically distinct fecal pellet types across both platforms: long fecal pellets from crustaceans, tabular pellets from salps, and ellipsoid pellets from appendicularians. This enabled complementary estimates of pellet abundance, modeled carbon content, and flux. Daily composites revealed distinct diel patterns in three zooplankton groups and their associated pellet flux. A simple model linking vertical migration with pellet production, sinking, and attenuation reproduced the observed temporal variability. Together, these results highlight how diel behavior and physiology impact vertical carbon transport.
Abstract Small estuaries link uplands and nearshore marine environments but are understudied in many regions. We quantified spatial and temporal variability in CH4, CO2, nutrients, and organic matter in a small, deep, bar‐built tropical estuary in Fajardo, Puerto Rico. The estuary was typically impounded and strongly stratified at all three sampling locations. Across 5 sampling dates, the pycnocline was sharp, with salinity of 0 in the upper meter and up to 17 ppt at 3–5 m. Methane concentrations at the surface were extraordinarily high for a mangrove‐fringed tropical estuary, averaging from 26 to 59 μM at three stations. Surface methane flux was 17.1 mM/m2/day. Methane concentrations were high throughout the water column, declined temporarily following estuarine flushing that increased salinity, and were correlated with CO2 (r2 = 0.48, p < 0.01). Small bar‐built estuaries are common in Puerto Rico and other high‐wave energy environments and should be included in assessments of greenhouse gas emissions.
Abstract Drainage canals are potential hotspots of methane (CH4) emissions from degraded peatlands in Southeast Asia. Estimates of CH4 emissions from these canals remain scarce, and both the temporal variability and pathways of CH4 emissions are uncertain. Here, we present a year‐round study of CH4 emissions from canals draining peatlands in Southeast Asia. We quantified diffusive and ebullitive fluxes and tracked canal CH4 dynamics by measuring δ13C‐CH4. Diffusion was the primary pathway of CH4 fluxes throughout the year, accounting for > 80% of net CH4 emissions. Periods of low rainfall limited CH4 oxidation and enhanced diffusive CH4 emissions, particularly in canals blocked to rewet the adjacent peat soils. By synthesizing data from past studies, we find an apparent decrease in canal CH4 emissions with time following peatland drainage. Our results highlight the importance of considering seasonal to decadal variation in efforts to include drainage canals in the global CH4 budget.
Accurately quantifying air-sea CO2 exchange remains a central challenge for the measurement, reporting, and verification (MRV) of marine carbon dioxide removal. I apply direct eddy covariance measurements of CO2 fluxes at a macroalgae-dominated coast to compile the first gas transfer velocity (k(660)) parameterization for such a habitat. k(660) exhibited a quadratic dependence on wind speed of the form: k(660) = 0.183 x U-10(2 )+ 2:17. Random forest analysis showed that wind speed and wind-wave interaction control k(660) at high wind speed, and a suite of drivers enhance k(660) under calm conditions, generating a non-zero intercept with significant impacts for CO2 flux modelling. A simulated macroalgal marine carbon dioxide removal intervention demonstrated the sensitivity of removals to k(660) uncertainty, via its effect on CO2 equilibration timescale, with variation across k(660) models causing shifts comparable to those by operational emissions. Finally, a new framework embedding site-specific equilibration dynamics into marine carbon dioxide removal accounting is presented, offering an understandable and defensible tool for measurement, reporting, and verification.
Abstract Oxic methane (CH4) production (OMP) occurs in diverse oxygenated surface waters worldwide. However, phytoplankton‐driven OMP in natural marine environments remains poorly documented. During a research cruise in the highly productive southern East China Sea, we measured OMP by incubating phytoplankton‐rich surface waters and found that CH4 production was positively correlated with chlorophyll a concentration and primary production, and that natural phytoplankton communities predominated by diatoms led to higher CH4 production. Oxic methane production ranged between 0.9 and 2.1 mg CH4 g Chl a−1 h−1, indicating that 0.02–0.06% of the photosynthetically fixed CO2 could be released as CH4. Measurements of the phytoplankton‐free filtrate demonstrated a negligible contribution to OMP by heterotrophs, substantiating that phytoplankton are contributing to the CH4 oversaturation in the coastal oxic layer of this region. Moreover, high OMP in the photic zone partially counterbalances photosynthetic CO2 sequestration by phytoplankton and should be accounted for in assessing fluxes of greenhouse gases.
Abstract Traditional views suggest that overall phytoplankton biomass in the tropical Pacific should be proportional to La Niña intensity because of enhanced nutrient supplies from equatorial upwelling associated with La Niña intensity. Here, composite analysis of satellite‐derived chlorophyll a (Chl a, a proxy for biomass) data across five multiyear La Niña (M‐LN) events (1997–2023) showed a double increase in the tropical Pacific average Chl a in the 2nd/3rd years [La Niña(2)] of M‐LN compared to the 1st year [La Niña(1)], despite declining La Niña intensities. This unexpected rise is attributed to a ∼ 1‐yr lagged response of the off‐equatorial phytoplankton to La Niña/El Niño. The lagged response of off‐equatorial Chl a to La Niña(1) superimposed with the immediate response of equatorial Chl a to La Niña(2) amplifies overall Chl a levels during La Niña(2). Simulations from Earth System Models support this mechanism. Our findings imply that increased M‐LN events may mitigate warming‐induced biomass decline in the tropical Pacific.
