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1. Geographic Variation in Salt Marsh Structure and Function for Nekton: a Guide to Finding Commonality Across Multiple Scales

   https://doi.org/10.1007/s12237-020-00894-y  

   Ziegler, Shelby L. ; Baker, Ronald ; Crosby, Sarah C. ; Colombano, Denise D. ; Barbeau, Myriam A. ; Cebrian, Just ; Connolly, Rod M. ; Deegan, Linda A. ; Gilby, Ben L. ; Mallick, Debbrota ; et al ( January 2021 , Estuaries and Coasts)

   Coastal salt marshes are distributed widely across the globe and are considered essential habitat for many fish and crustacean species. Yet, the literature on fishery support by salt marshes has largely been based on a few geographically distinct model systems, and as a result, inadequately captures the hierarchical nature of salt marsh pattern, process, and variation across space and time. A better understanding of geographic variation and drivers of commonalities and differences across salt marsh systems is essential to informing future management practices. Here, we address the key drivers of geographic variation in salt marshes: hydroperiod, seascape configuration, geomorphology, climatic region, sediment supply and riverine input, salinity, vegetation composition, and human activities. Future efforts to manage, conserve, and restore these habitats will require consideration of how environmental drivers within marshes affect the overall structure and subsequent function for fisheries species. We propose a future research agenda that provides both the consistent collection and reporting of sources of variation in small-scale studies and collaborative networks running parallel studies across large scales and geographically distinct locations to provide analogous information for data poor locations. These comparisons are needed to identify and prioritize restoration or conservation efforts, identify sources of variation among regions,more »and best manage fisheries and food resources across the globe. Introduction Understanding the drivers of geographic variation in the condition and composition of habitats is crucial to our capacity to generalize management plans across space and time and to clarify and perhaps challenge assumptions of functional equivalence among sites. Broadly defined wetland types such as salt marshes are often assumed to provide similar functions throughout their global range, such as providing nursery habitat for fishery species. However, a growing body of evidence suggests substantial geographic variation in the functioning of salt marsh and other coastal ecosystems (Bradley et al. 2020; Whalen et al. 2020). Variation in ecological patterns and processes within habitat types can alter community structure and dynamics. Local-scale patterns and processes (e.g., patch [10s of meters], local [100s of meters]) can be influenced by processes that occur at larger spatial scales (e.g., regional [kms], global), thereby causing geographic differences in the function and ecosystem service delivery of a given habitat type. Salt marshes (which include vegetated platform, interconnected tidal creeks, fringing mudflats, ponds, and pools) are widely distributed (Fig. 1) and function as valuable nursery habitats by providing key resources for many estuarine species that transition to marine or aquatic habitats as adults (Beck et al. 2001; Minello et al. 2003; Sheaves et al. 2015). However, factors that underlie variability in the delivery of ecological functions are still inadequately understood. Previous studies have explored geographic variation in the function of salt marshes for fish and mobile crustaceans (“nekton”; e.g., Minello et al. 2012, Baker et al. 2013). However, field studies that compare multiple sites across a geographical gradient are typically limited in duration and scale. In addition, the explanatory variables (e.g., elevation, flooding duration, plant structure) collected by smaller scale studies are often inconsistent and therefore limit generalizations across sites.« less
2. Predictable Changes in Eelgrass Microbiomes with Increasing Wasting Disease Prevalence across 23° Latitude in the Northeastern Pacific

   https://doi.org/10.1128/msystems.00224-22  

   Beatty, Deanna S. ; Aoki, Lillian R. ; Rappazzo, Brendan ; Bergman, Chelsea ; Domke, Lia K. ; Duffy, J. Emmett ; Dubois, Katie ; Eckert, Ginny L. ; Gomes, Carla ; Graham, Olivia J. ; et al ( August 2022 , mSystems)

   Raina, Jean-Baptiste (Ed.)

   ABSTRACT Predicting outcomes of marine disease outbreaks presents a challenge in the face of both global and local stressors. Host-associated microbiomes may play important roles in disease dynamics but remain understudied in marine ecosystems. Host–pathogen–microbiome interactions can vary across host ranges, gradients of disease, and temperature; studying these relationships may aid our ability to forecast disease dynamics. Eelgrass, Zostera marina , is impacted by outbreaks of wasting disease caused by the opportunistic pathogen Labyrinthula zosterae . We investigated how Z. marina phyllosphere microbial communities vary with rising wasting disease lesion prevalence and severity relative to plant and meadow characteristics like shoot density, longest leaf length, and temperature across 23° latitude in the Northeastern Pacific. We detected effects of geography (11%) and smaller, but distinct, effects of temperature (30-day max sea surface temperature, 4%) and disease (lesion prevalence, 3%) on microbiome composition. Declines in alpha diversity on asymptomatic tissue occurred with rising wasting disease prevalence within meadows. However, no change in microbiome variability (dispersion) was detected between asymptomatic and symptomatic tissues. Further, we identified members of Cellvibrionaceae, Colwelliaceae, and Granulosicoccaceae on asymptomatic tissue that are predictive of wasting disease prevalence across the geographic range (3,100 kilometers). Functional roles of Colwelliaceae andmore »Granulosicoccaceae are not known. Cellvibrionaceae, degraders of plant cellulose, were also enriched in lesions and adjacent green tissue relative to nonlesioned leaves. Cellvibrionaceae may play important roles in disease progression by degrading host tissues or overwhelming plant immune responses. Thus, inclusion of microbiomes in wasting disease studies may improve our ability to understand variable rates of infection, disease progression, and plant survival. IMPORTANCE The roles of marine microbiomes in disease remain poorly understood due, in part, to the challenging nature of sampling at appropriate spatiotemporal scales and across natural gradients of disease throughout host ranges. This is especially true for marine vascular plants like eelgrass ( Zostera marina ) that are vital for ecosystem function and biodiversity but are susceptible to rapid decline and die-off from pathogens like eukaryotic slime-mold Labyrinthula zosterae (wasting disease). We link bacterial members of phyllosphere tissues to the prevalence of wasting disease across the broadest geographic range to date for a marine plant microbiome-disease study (3,100 km). We identify Cellvibrionaceae, plant cell wall degraders, enriched (up to 61% relative abundance) within lesion tissue, which suggests this group may be playing important roles in disease progression. These findings suggest inclusion of microbiomes in marine disease studies will improve our ability to predict ecological outcomes of infection across variable landscapes spanning thousands of kilometers.« less
3. Climatic, physical, and biogeochemical changes drive rapid oxygen loss and recovery in a marine ecosystem

   https://doi.org/10.1038/s41598-019-52430-z  

   Wilson, Jesse ; Ucharm, Gerda ; Beman, J. Michael ( November 2019 , Scientific Reports)

   Dissolved oxygen (DO) concentrations shape the biogeochemistry and ecological structure of aquatic ecosystems; as a result, understanding how and why DO varies in space and time is of fundamental importance. Using high-resolution,in situDO time-series collected over the course of a year in a novel marine ecosystem (Jellyfish Lake, Palau), we show that DO declined throughout the marine lake and subsequently recovered in the upper water column. These shifts were accompanied by variations in water temperature and were correlated to changes in wind, precipitation, and especially sea surface height that occurred during the 2015–2016 El Niño-Southern Oscillation event. Multiple approaches used to calculate rates of community respiration, net community production, and gross primary production from DO changes showed that DO consumption and production did not accelerate nor collapse; instead, their variance increased during lake deoxygenation and recovery, and then stabilized. Spatial and temporal variations in rates were significantly related to climatic variability and changes in DO, and causality testing indicated that these relationships were both correlative and causative. Our data indicate that climatic, physical, and biogeochemical properties and processes collectively regulated DO, producing linked feedbacks that drove DO decline and recovery.
4. Temperature and mass scaling affect cutaneous and pulmonary respiratory performance in a diving frog

   https://doi.org/10.1111/1749-4877.12551  

   MCWHINNIE, Ryan B. ; SCKRABULIS, Jason P. ; RAFFEL, Thomas R. ( January 2021 , Integrative Zoology)

   Global climate change is altering patterns of temperature variation, with unpredictable consequences for species and ecosystems. The Metabolic Theory of Ecology (MTE) provides a powerful framework for predicting climate change impacts on ectotherm metabolic performance. MTE postulates that physiological and ecological processes are limited by organism metabolic rates, which scale predictably with body mass and temperature. The purpose of this study was to determine if different metabolic proxies generate different empirical estimates of key MTE model parameters for the aquatic frog Xenopus laevis when allowed to exhibit normal diving behavior. We used a novel methodological approach in combining a flow-through respirometry setup with the open-source Arduino platform to measure mass and temperature effects on 4 different proxies for whole-body metabolism (total O2 consumption, cutaneous O2 consumption, pulmonary O2 consumption, and ventilation frequency), following thermal acclimation to one of 3 temperatures (8°C, 17°C, or 26°C). Different metabolic proxies generated different mass-scaling exponents (b) and activation energy (EA) estimates, highlighting the importance of metabolic proxy selection when parameterizing MTE-derived models. Animals acclimated to 17°C had higher O2 consumption across all temperatures, but thermal acclimation did not influence estimates of key MTE parameters EA and b. Cutaneous respiration generated lower MTE parameters thanmore »pulmonary respiration, consistent with temperature and mass constraints on dissolved oxygen availability, SA:V ratios, and diffusion distances across skin. Our results show that the choice of metabolic proxy can have a big impact on empirical estimates for key MTE model parameters.« less
5. Generalized Linear Models outperform commonly used canonical analysis in estimating spatial structure of presence/absence data

   https://doi.org/10.7717/peerj.9777  

   Carlos-Júnior, Lélis A. ; Creed, Joel C. ; Marrs, Rob ; Lewis, Rob J. ; Moulton, Timothy P. ; Feijó-Lima, Rafael ; Spencer, Matthew ( January 2020 , PeerJ)

   Background Ecological communities tend to be spatially structured due to environmental gradients and/or spatially contagious processes such as growth, dispersion and species interactions. Data transformation followed by usage of algorithms such as Redundancy Analysis (RDA) is a fairly common approach in studies searching for spatial structure in ecological communities, despite recent suggestions advocating the use of Generalized Linear Models (GLMs). Here, we compared the performance of GLMs and RDA in describing spatial structure in ecological community composition data. We simulated realistic presence/absence data typical of many β -diversity studies. For model selection we used standard methods commonly used in most studies involving RDA and GLMs. Methods We simulated communities with known spatial structure, based on three real spatial community presence/absence datasets (one terrestrial, one marine and one freshwater). We used spatial eigenvectors as explanatory variables. We varied the number of non-zero coefficients of the spatial variables, and the spatial scales with which these coefficients were associated and then compared the performance of GLMs and RDA frameworks to correctly retrieve the spatial patterns contained in the simulated communities. We used two different methods for model selection, Forward Selection (FW) for RDA and the Akaike Information Criterion (AIC) for GLMs. The performancemore »of each method was assessed by scoring overall accuracy as the proportion of variables whose inclusion/exclusion status was correct, and by distinguishing which kind of error was observed for each method. We also assessed whether errors in variable selection could affect the interpretation of spatial structure. Results Overall GLM with AIC-based model selection (GLM/AIC) performed better than RDA/FW in selecting spatial explanatory variables, although under some simulations the methods performed similarly. In general, RDA/FW performed unpredictably, often retaining too many explanatory variables and selecting variables associated with incorrect spatial scales. The spatial scale of the pattern had a negligible effect on GLM/AIC performance but consistently affected RDA’s error rates under almost all scenarios. Conclusion We encourage the use of GLM/AIC for studies searching for spatial drivers of species presence/absence patterns, since this framework outperformed RDA/FW in situations most likely to be found in natural communities. It is likely that such recommendations might extend to other types of explanatory variables.« less