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1. Seasonal and interannual variation in high-latitude estuarine fish community structure along a glacial to non-glacial watershed gradient in Southeast Alaska

   https://doi.org/10.1007/s10641-022-01241-9  

   Beaudreau, Anne H. ; Bergstrom, Carolyn A. ; Whitney, Emily J. ; Duncan, Douglas H. ; Lundstrom, Nina C. ( March 2022 , Environmental Biology of Fishes)

   Along the Gulf ofAlaska, rapid glacier retreat has driven changes in transport of freshwater, sediments, and nutrients to estuary habitats. Over the coming decades, deglaciation will lead to a temporary increase, followed by a long-term decline of glacial influence on estuaries. Therefore, quantifying the current variability in estuarine fish community structure in regions predicted to be most affected by glacier loss is necessary to anticipate future impacts. We analyzed fish community data collected monthly (April through September) over 7 years (2013–2019) from glacially influenced estuaries along the southeastern Gulf of Alaska. River delta sites within estuaries were sampled along a natural gradient of glacial to non-glacial watersheds to characterize variation in fish communities exposed to varying degrees of glacial influence. Differences in seasonal patterns of taxa richness and abundance between the most and least glacially influenced sites suggest that hydrological drivers influence the structure of delta fish communities. The most glacially influenced sites had lower richness but higher abundance overall compared to those with least glacial influence; however, differences among sites were small compared to differences across months. Two dominant species—Pacific staghorn sculpin and starry flounder—contributed most to spatial and temporal variation in community composition; however, given only small interannual differences in richness and abundance over the period of the study, we conclude that year-to-year variation at these sites is relatively low at present. Our study provides an important benchmark against which to compare shifts in fish communities as watersheds and downstream estuaries continue to transform in the coming decades.

    

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2. Hydroclimate Drives Seasonal Riverine Export Across a Gradient of Glacierized High‐Latitude Coastal Catchments

   https://doi.org/10.1029/2022WR033305  

   Jenckes, J. ; Munk, L. A. ; Ibarra, D. E. ; Boutt, D. F. ; Fellman, J. ; Hood, E. ( April 2023 , Water Resources Research)

   Glacierized coastal catchments of the Gulf of Alaska (GoA) are undergoing rapid hydrologic fluctuations in response to climate change. These catchments deliver dissolved and suspended inorganic and organic matter to nearshore marine environments, however, these glacierized coastal catchments are relatively understudied and little is known about total solute and particulate fluxes to the ocean. We present hydrologic, physical, and geochemical data collected during April–October 2019–2021 from 10 streams along gradients of glacial fed to non‐glacial (i.e., precipitation) fed, in one Southcentral and one Southeast Alaska region. Hydrologic data reveal that glaciers drive the seasonal runoff patterns. The ẟ¹⁸O signature and specific conductance show distinctive seasonal variations in stream water sources between the study regions apparently due to the large amounts of rain in Southeast Alaska. Total dissolved solids concentrations and yields were elevated in the Southcentral region, due to lithologic influence on dissolved loads, however, the hydroclimate is the primary driver of the timing of dissolved and suspended yields. We show the yields of dissolved organic carbon is higher and that the δ¹³C_POCis enriched in the Southeast streams illustrating contrasts in organic carbon export across the GoA. Finally, we illustrate how future yields of solutes and sediments to the GoA may change as watersheds evolve from glacial influenced to precipitation dominated. This integrated analysis provides insights into how watershed characteristics beyond glacier coverage control properties of freshwater inputs to the GoA and the importance of expanding study regions to multiple hydroclimate regimes.

    

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3. Northeast Pacific eelgrass fish communities characterized by environmental DNA represent local diversity and show habitat specificity

   https://doi.org/10.1002/edn3.431  

   Beatty, Deanna S. ; Deen, Emma ; Gross, Collin ; Stachowicz, John J. ( July 2023 , Environmental DNA)

   Fish biodiversity is an important indicator of ecosystem health and a priority for the National Park Service in Drakes Estero, a shallow estuary within Point Reyes National Seashore, Marin County, California. However, fish diversity has yet to be described following the removal of oyster aquaculture infrastructure within Drakes Estero from 2016 to 2017. We used environmental DNA (eDNA) to characterize fish biodiversity within Drakes Estero. We amplified fish eDNA with MiFish primers and classified sequences with a 12S rRNA reference database. We identified 110 unique operational taxonomic units (OTUs, at 97% similarity) within the estuary from 40 samples across 4 sites. From these 110 OTUs, we identified 9 species and 13 taxonomic groups at the genus, family, order, or class level within the estuary. Species‐level assignments are limited by a lack of representative sequences targeted by the MiFish primers for 42% of eelgrass fishes in our region that we identified from a literature review in the Northeast Pacific (NEP) from Elkhorn Slough to Humboldt Bay. Despite this limitation, we identified some common Drakes Estero fishes with our eDNA surveys, including the three‐spined stickleback (Gasterosteus aculeatus), Pacific staghorn sculpin (Leptocottus armatus), surfperches (Embiotocidae), gobies (Gobiidae), and a hound shark (Triakidae). We also compared fish biodiversity within the estuary with that from nearby Limantour Beach, a coastal site. Limantour beach differed in community composition from Drakes Estero and was characterized by high relative abundances of anchovy (Engraulissp.) and herring (Clupeasp.). Thus, we can distinguish estuarine and non‐estuarine sites (<10 km away) with eDNA surveys. Further, eDNA surveys accounted for greater fish diversity than seine surveys conducted at one site within the estuary. Environmental DNA surveys will likely be a useful tool to monitor fish biodiversity across eelgrass estuaries in the Northeast Pacific, especially as reference databases become better populated with regional species.

    

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4. 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)

   null (Ed.)

   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, 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. 

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5. Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus

   https://doi.org/10.1128/mSphere.00401-20  

   Minich, Jeremiah J. ; Petrus, Semar ; Michael, Julius D. ; Michael, Todd P. ; Knight, Rob ; Allen, Eric E. ; McMahon, Katherine ( June 2020 , mSphere)

   ABSTRACT Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries by increasing stress and disease. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, gastrointestinal tract [GI], and pyloric ceca) from 229 Pacific chub mackerel, Scomber japonicus , collected across 38 time points spanning 1 year from the Scripps Institution of Oceanography Pier (La Jolla, CA). Mucosal sites had unique microbial communities significantly different from the surrounding seawater and sediment communities with over 10 times more total diversity than seawater. The external surfaces of skin and gill were more similar to seawater, while digesta was more similar to sediment. Alpha and beta diversity of the skin and gill was explained by environmental and biological factors, specifically, sea surface temperature, chlorophyll a , and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by regional migration of chub mackerel subpopulations by nanopore sequencing a 14,769-bp region of the 16,568-bp mitochondria across all temporal fish specimens. A cosmopolitan pathogen, Photobacterium damselae , was prevalent across multiple body sites all year but highest in the skin, GI, and digesta between June and September, when the ocean is warmest. The longitudinal fish microbiome study evaluates the extent to which the environment and host biology drives mucosal microbial ecology and establishes a baseline for long-term surveys linking environment stressors to mucosal health of wild marine fish. IMPORTANCE Pacific chub mackerel, Scomber japonicus , are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may change. In this study, we performed a holistic analysis of all mucosal sites on the fish over a 1-year time series to explore seasonal variation and to understand the environmental drivers of the microbiome. Understanding seasonality in the fish microbiome is also applicable to aquaculture production for producers to better understand and predict when disease outbreaks may occur based on changing environmental conditions in the ocean. 

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