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Biodiversity is changing at an accelerating rate at both local and regional scales. Beta diversity, which quantifies species turnover between these two scales, is emerging as a key driver of ecosystem function that can inform spatial conservation. Yet measuring biodiversity remains a major challenge, especially in aquatic ecosystems. Decoding environmental DNA (eDNA) left behind by organisms offers the possibility of detecting species sans direct observation, a Rosetta Stone for biodiversity. While eDNA has proven useful to illuminate diversity in aquatic ecosystems, its utility for measuring beta diversity over spatial scales small enough to be relevant to conservation purposes is poorly known. Here we tested how eDNA performs relative to underwater visual census (UVC) to evaluate beta diversity of marine communities. We paired UVC with 12S eDNA metabarcoding and used a spatially structured hierarchical sampling design to assess key spatial metrics of fish communities on temperate rocky reefs in southern California. eDNA provided a more-detailed picture of the main sources of spatial variation in both taxonomic richness and community turnover, which primarily arose due to strong species filtering within and among rocky reefs. As expected, eDNA detected more taxa at the regional scale (69 vs. 38) which accumulated quickly with space and plateaued at only ~ 11 samples. Conversely, the discovery rate of new taxa was slower with no sign of saturation for UVC. Based on historical records in the region (2000–2018) we found that 6.9 times more UVC samples would be required to detect 50 taxa compared to eDNA. Our results show that eDNA metabarcoding can outperform diver counts to capture the spatial patterns in biodiversity at fine scales with less field effort and more power than traditional methods, supporting the notion that eDNA is a critical scientific tool for detecting biodiversity changes in aquatic ecosystems.

 

Global loss of biodiversity and its associated ecosystem services is occurring at an alarming rate and is predicted to accelerate in the future. Metacommunity theory provides a framework to investigate multi-scale processes that drive change in biodiversity across space and time. Short-term ecological studies across space have progressed our understanding of biodiversity through a metacommunity lens, however, such snapshots in time have been limited in their ability to explain which processes, at which scales, generate observed spatial patterns. Temporal dynamics of metacommunities have been understudied, and large gaps in theory and empirical data have hindered progress in our understanding of underlying metacommunity processes that give rise to biodiversity patterns. Fortunately, we are at an important point in the history of ecology, where long-term studies with cross-scale spatial replication provide a means to gain a deeper understanding of the multiscale processes driving biodiversity patterns in time and space to inform metacommunity theory. The maturation of coordinated research and observation networks, such as the United States Long Term Ecological Research (LTER) program, provides an opportunity to advance explanation and prediction of biodiversity change with observational and experimental data at spatial and temporal scales greater than any single research group could accomplish. Synthesis of LTER network community datasets illustrates that long-term studies with spatial replication present an under-utilized resource for advancing spatio-temporal metacommunity research. We identify challenges towards synthesizing these data and present recommendations for addressing these challenges. We conclude with insights about how future monitoring efforts by coordinated research and observation networks could further the development of metacommunity theory and its applications aimed at improving conservation efforts. 

Sea urchins are key grazers in coastal seas, where they can survive a variety of conditions and diets, enhancing their ecological impact on kelp forests and other ecosystems. Using 16S rRNA gene sequencing, we characterized bacterial communities associated with guts of the two dominant sea urchin species in southern California, the red urchinMesocentrotus franciscanus, and the purple urchinStrongylocentrotus purpuratus. Our results show that the two urchin species have distinct gut microbiomes that vary with habitat. The taxonomic composition of their microbiomes suggests that they may facilitate digestion of food and be a source of nutrition themselves. These results highlight the role of microbiomes within macroorganisms as an extended ecological trait, and suggest that microbes may be crucial to resource use and partitioning in co‐occurring species.

 

The relationship between biodiversity and stability, or its inverse, temporal variability, is multidimensional and complex. Temporal variability in aggregate properties, like total biomass or abundance, is typically lower in communities with higher species diversity (i.e., the diversity–stability relationship [DSR]). At broader spatial extents, regional‐scale aggregate variability is also lower with higher regional diversity (in plant systems) and with lower spatial synchrony. However, focusing exclusively on aggregate properties of communities may overlook potentially destabilizing compositional shifts. It is not yet clear how diversity is related to different components of variability across spatial scales, nor whether regional DSRs emerge across a broad range of organisms and ecosystem types. To test these questions, we compiled a large collection of long‐term metacommunity data spanning a wide range of taxonomic groups (e.g., birds, fish, plants, invertebrates) and ecosystem types (e.g., deserts, forests, oceans). We applied a newly developed quantitative framework for jointly analyzing aggregate and compositional variability across scales. We quantified DSRs for composition and aggregate variability in local communities and metacommunities. At the local scale, more diverse communities were less variable, but this effect was stronger for aggregate than compositional properties. We found no stabilizing effect of γ‐diversity on metacommunity variability, but β‐diversity played a strong role in reducing compositional spatial synchrony, which reduced regional variability. Spatial synchrony differed among taxa, suggesting differences in stabilization by spatial processes. However, metacommunity variability was more strongly driven by local variability than by spatial synchrony. Across a broader range of taxa, our results suggest that high γ‐diversity does not consistently stabilize aggregate properties at regional scales without sufficient spatial β‐diversity to reduce spatial synchrony.

 

Data from five sites of the International Long Term Ecological Research (ILTER) network in the North-Eastern Pacific, Western Arctic Ocean, Northern Baltic Sea, South-Eastern North Sea and in the Western Mediterranean Sea were analyzed by dynamic factor analysis (DFA) to trace common multi-year trends in abundance and composition of phytoplankton, benthic fauna and temperate reef fish. Multiannual trends were related to climate and environmental variables to study interactions. Two common trends in biological responses were detected, with temperature and climate indices as explanatory variables in four of the five LTER sites considered. Only one trend was observed at the fifth site, the Northern Baltic Sea, where no explanatory variables were identified. Our findings revealed quasi-synchronous biological shifts in the different marine ecosystems coincident with the 2000 climatic regime shift and provided evidence on a possible further biological shift around 2010. The observed biological modifications were coupled with abrupt or continuous increase in sea water and air temperature confirming the key-role of temperature in structuring marine communities. 

Foundation species structure communities, promote biodiversity, and stabilize ecosystem processes by creating locally stable environmental conditions. Despite their critical importance, the role of foundation species in stabilizing natural communities has seldom been quantified. In theory, the stability of a foundation species should promote community stability by enhancing species richness, altering the population fluctuations of individual species, or both. Here we tested the hypothesis that the stability of a marine foundation species, the giant kelpMacrocystis pyrifera, increased the stability of the aggregate biomass of a phylogenetically diverse assemblage of understory algae and sessile invertebrates that compete for space beneath the giant kelp canopy. To achieve this goal, we analyzed an 18‐yr time series of the biomass of giant kelp and its associated benthic community collected from 32 plots distributed among nine shallow reefs in the Santa Barbara Channel, USA. We showed that the stability of understory algae and sessile invertebrates was positively and indirectly related to the stability of giant kelp, which primarily resulted from giant kelp's direct positive association with species richness. The stability of all community types was positively related to species richness via increased species stability and species asynchrony. The stabilizing effects of richness were three to four times stronger when algae and invertebrates were considered separately rather than in combination. Our finding that diversity–stability relationships were stronger in communities consisting of species with similar resource requirements suggests that competition for shared resources rather than differential responses to environmental conditions played a more important role in stabilizing the community. Increasing threats to structure‐forming foundation species worldwide necessitates a detailed understanding of how they influence their associated community. This study is among the first to show that dampened temporal fluctuations in the biomass of a foundation species is an important determinant of the stability of the complex communities it supports.