Application of a Fast Isoprene Sensor (FIS) for measuring isoprene production from marine samples

Research into isoprene production from marine sources traditionally relies on gas chromatography techniques which are labor intensive, provide a slow sample turnover, and require significant method training. An alternative method is the use of a Fast Isoprene Sensor (FIS), a chemiluminescence‐based approach that provides real time isoprene analysis, but is relatively simple to run and also portable. Until now, the FIS has been used in terrestrial but not aquatic isoprene studies. Due to the added difficulties with marine compared with terrestrial sampling, particularly potential interference from dimethyl sulfide (DMS), we have developed a new protocol that allows accurate and reliable data to be obtained from FIS analysis. The detection limit of our modified system to standard gas was 0.02 nM (0.5 ppbv), while minimum isoprene production detected by the FIS was 0.59 nmol h−1 (for Thalassiosira weissflogii). We also compared our FIS‐based approach with GC analysis of isoprene emission from marine samples of micro‐ and macro‐algae, and demonstrated a strong similarity (r2 = 0.910, slope = 1.003). The ability to use FIS analysis with marine samples will significantly broaden the scope of isoprene research in marine environments, permitting remote field work, and allow previously unanswered questions to be addressed.</jats:p

Light-driven dynamics between calcification and production in functionally diverse coral reef calcifiers

Coral reef metabolism underpins ecosystem function and is defined by the processes of photosynthesis, respiration, calcification, and calcium carbonate dissolution. However, the relationships between these physiological processes at the organismal level and their interactions with light remain unclear. We examined metabolic rates across a range of photosynthesising calcifiers in the Caribbean: the scleractinian corals Acropora cervicornis, Orbicella faveolata, Porites astreoides, and Siderastrea siderea, and crustose coralline algae (CCA) under varying natural light conditions. Net photosynthesis and calcification showed a parabolic response to light across all species, with differences among massive corals, branching corals, and CCA that reflect their relative functional roles on the reef. At night, all organisms were net respiring, and most were net calcifying, although some incubations demonstrated instances of net calcium carbonate (CaCO3) dissolution. Peak metabolic rates at light-saturation (maximum photosynthesis and calcification) and average dark rates (respiration and dark calcification) were positively correlated across species. Interspecies relationships among photosynthesis, respiration, and calcification indicate that calcification rates are linked to energy production at the organismal level in calcifying reef organisms. The species-specific ratios of net calcification to photosynthesis varied with light over a diurnal cycle. The dynamic nature of calcification/photosynthesis ratios over a diurnal cycle questions the use of this metric as an indicator for reef function and health at the ecosystem scale unless temporal variability is accounted for, and a new metric is proposed. The complex light-driven dynamics of metabolic processes in coral reef organisms indicate that a more comprehensive understanding of reef metabolism is needed for predicting the future impacts of global change

SCUBA noise alters community structure and cooperation at Pederson’s cleaner shrimp cleaning stations

Recreational SCUBA diving is widespread and increasing on coral reefs worldwide. Standard open-circuit SCUBA equipment is inherently noisy and, by seeking out areas of high biodiversity, divers inadvertently expose reef communities to an intrusive source of anthropogenic noise. Currently, little is known about SCUBA noise as an acoustic stressor, and there is a general lack of empirical evidence on community-level impacts of anthropogenic noise on coral reefs. Here, we conducted a playback experiment on Caribbean reefs to investigate impacts of SCUBA noise on fish communities and interspecific cooperation at ecologically important cleaning stations of the Pederson’s cleaner shrimp Ancylomenes pedersoni. When exposed to SCUBA-noise playback, the total occurrence of fishes at the cleaning stations decreased by 7%, and the community and cleaning clientele compositions were significantly altered, with 27% and 25% of monitored species being affected, respectively. Compared with ambient-sound playback, SCUBA-noise playback resulted in clients having to wait 29% longer for cleaning initiation and receiving 43% less cleaning; however, cheating, signalling, posing and time spent cleaning were not affected by SCUBA-noise playback. Our study is the first to demonstrate experimentally that SCUBA noise can have at least some negative impacts on reef organisms, confirming it as an ecologically relevant pollutant. Moreover, by establishing acoustic disturbance as a likely mechanism for known impacts of diver presence on reef animals, we also identify a potential avenue for mitigation in these valuable ecosystems.</p

Deeper Caribbean reef fish communities show greater taxonomic and functional change in dominance structure over a nine-year period

Fish communities at greater depths on a reef are thought to be less affected by disturbances that more strongly impact shallower areas. As a result, these deeper communities might be expected to show less change in their diversity and composition over time compared to those in shallow water. To test this hypothesis, we analysed changes in reef fish composition at 5-15 m and 25-40 m on reefs around Utila, Honduras, across two time periods: 2014-2015 and 2022-2023. We estimated taxonomic and functional α- and β- diversity using coverage-based standardisation and Hill-Chao numbers at orders q = 0 (species richness) and q = 2 (inverse Simpson index). Results showed that the α-diversity of fish communities was more consistent at 25-40 m than at shallower depths between the two time periods. However, β-diversity of dominant species and traits (q = 2) increased at greater depths, indicating that deeper fish communities became more distinct from one another in both structure and function, as well as more different from shallower communities at the same sites. Changes in diversity also varied between sites, highlighting the role of sitespecific conditions in shaping and maintaining fish communities across depths. Overall, the findings are not consistent with the expectation that greater depth reduces temporal community variability, and they raise questions about whether depth alone can serve as a refuge for reef fish

Light-driven dynamics between calcification and production in functionally diverse coral reef calcifiers

Coral reef metabolism underpins ecosystem function and is defined by the processes of photosynthesis, respiration, calcification, and calcium carbonate dissolution. However, the relationships between these physiological processes at the organismal level and their interactions with light remain unclear. We examined metabolic rates across a range of photosynthesising calcifiers in the Caribbean: the scleractinian corals Acropora cervicornis, Orbicella faveolata, Porites astreoides, and Siderastrea siderea, and crustose coralline algae (CCA) under varying natural light conditions. Net photosynthesis and calcification showed a parabolic response to light across all species, with differences among massive corals, branching corals, and CCA that reflect their relative functional roles on the reef. At night, all organisms were net respiring, and most were net calcifying, although some incubations demonstrated instances of net calcium carbonate (CaCO3) dissolution. Peak metabolic rates at light-saturation (maximum photosynthesis and calcification) and average dark rates (respiration and dark calcification) were positively correlated across species. Interspecies relationships among photosynthesis, respiration, and calcification indicate that calcification rates are linked to energy production at the organismal level in calcifying reef organisms. The species-specific ratios of net calcification to photosynthesis varied with light over a diurnal cycle. The dynamic nature of calcification/photosynthesis ratios over a diurnal cycle questions the use of this metric as an indicator for reef function and health at the ecosystem scale unless temporal variability is accounted for, and a new metric is proposed. The complex light-driven dynamics of metabolic processes in coral reef organisms indicate that a more comprehensive understanding of reef metabolism is needed for predicting the future impacts of global change

Site-level variation in field of view is associated with altered anti-predator responses in farming damselfish

The three-dimensional (3D) structure of habitats influences how prey detect and respond to predators, but the specific roles of different aspects of structural complexity remain poorly understood, particularly in coral reef ecosystems. We used 3D models of 3 Caribbean reef sites to quantify 3 structural metrics at site level: field of view (the extent of observable area), refuge density (density of holes), and rugosity (reef surface roughness). We then observed the anti-predator behavior of damselfish, parrotfish, and wrasses at each site. Territorial damselfish showed species-specific responses to habitat structure, especially in relation to field of view. Stegastes adustus, for example, exhibited shorter flight initiation distances (FIDs) at the site with the highest field of view, consistent with expectations from optimal escape theory. In contrast, wrasse and parrotfish species showed little variation in behavior across sites, though larger individuals tended to have longer FIDs and flight distances. Refuge density was similar across sites, likely reflecting long-term regional loss of fine-scale complexity in the Caribbean. While rugosity is widely used as a proxy for reef complexity, our results suggest that field of view may be more strongly associated with differences in anti-predator behavior, particularly in damselfish. These findings highlight the need to assess multiple dimensions of habitat structure, as even closely related species may exhibit distinct behavioral adaptations to their 3D environment

Unifying Coral Reef States Through Space and Time Reveals a Changing Ecosystem

Aim Ecological state shifts that alter the structure and function of entire ecosystems are a concerning consequence of human impact. Yet, when, where and why discrete ecological states emerge remains difficult to predict and monitor, especially in high‐diversity systems. We sought to quantify state shifts and their drivers through space and time in the most ecologically complex marine ecosystem: tropical coral reefs. Location Worldwide. Time Period 1987–2019. Major Taxa Studied Coral reef communities. Methods Using a global dataset of 3375 coral reef surveys, along with 13 time series datasets ranging between 1987 and 2019, we applied a novel double‐dichotomy approach to classify coral reefs into four simplified and discrete states based on the relative contributions of corals versus algae to benthic cover and small‐bodied versus large‐bodied fishes to fish standing stock. We then examined state shifts considering a range of spatial predictors and tested whether states have shifted directionally over time, and the nature of the most common transitions. Results We show that geographic, environmental and anthropogenic context fundamentally shapes coral reef states at the local scale, which explains disparities among case studies, and stakes out critical baseline expectations for regional management efforts. We also reveal clear multi‐decadal state shifts on coral reefs: over time, systems dominated by reef‐building corals and small‐bodied, planktivorous fishes tend to have been replaced with reefs characterised by algae and larger‐bodied fishes. Main Conclusions Our results suggest a previously unrecognised transition from systems that harness external subsidies through small‐bodied consumers associated with structurally complex live corals, to herbivore‐dominated systems with stronger bottom‐up dynamics. Overall, the partitioning of complex reef ecosystems into a small suite of discrete ecological states suggests that spatial context‐dependency, shifting baselines and changes in reef functioning are crucial considerations for coral reef management in the 21st century

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world\u27s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km² resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e., offset) between in-situ soil temperature measurements, based on time series from over 1200 1-km² pixels (summarized from 8500 unique temperature sensors) across all the world’s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in-situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

BioTIME 2.0 : expanding and improving a database of biodiversity time series

Funding: H2020 European Research Council (Grant Number(s): GA 101044975, GA 101098020).Motivation: Here, we make available a second version of the BioTIME database, which compiles records of abundance estimates for species in sample events of ecological assemblages through time. The updated version expands version 1.0 of the database by doubling the number of studies and includes substantial additional curation to the taxonomic accuracy of the records, as well as the metadata. Moreover, we now provide an R package (BioTIMEr) to facilitate use of the database. Main Types of Variables: Included The database is composed of one main data table containing the abundance records and 11 metadata tables. The data are organised in a hierarchy of scales where 11,989,233 records are nested in 1,603,067 sample events, from 553,253 sampling locations, which are nested in 708 studies. A study is defined as a sampling methodology applied to an assemblage for a minimum of 2 years. Spatial Location and Grain: Sampling locations in BioTIME are distributed across the planet, including marine, terrestrial and freshwater realms. Spatial grain size and extent vary across studies depending on sampling methodology. We recommend gridding of sampling locations into areas of consistent size. Time Period and Grain: The earliest time series in BioTIME start in 1874, and the most recent records are from 2023. Temporal grain and duration vary across studies. We recommend doing sample-level rarefaction to ensure consistent sampling effort through time before calculating any diversity metric. Major Taxa and Level of Measurement: The database includes any eukaryotic taxa, with a combined total of 56,400 taxa. Software Format: csv and. SQL.Peer reviewe