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Rhodoliths are important foundation species of the benthic photic zone but are poorly known and rarely studied in Alaska. A bed of Lithothamnion soriferum rhodoliths was discovered in 2008 in Kinzarof Lagoon, Alaska, a shallow-water embayment dominated by eelgrass (Zostera marina). Rhodolith spatial extent and biomass were estimated to assess trends and environmental factors that may influence rhodolith distribution and abundance during four years spread over a 12-year period (2008–2010, and 2019). Presence and biomass of rhodoliths were negatively associated with percent eelgrass cover. Biomass of rhodoliths also decreased with increased water temperature. Rhodoliths occurred in two primary areas of the lagoon, a 182 ha core area in a shallow water (mean tide depth of −0.03 m MLLW) tidal channel with low eelgrass density, and a 22 ha outlying area at shallower water depths (>0.2 m MLLW) with moderate to high eelgrass cover. There was no apparent trend in rhodolith biomass over the study period despite wide variation in mean annual estimates. This study establishes a baseline for continued investigations and monitoring of this important benthic resource in Alaska.

Migratory waterfowl vector plant seeds and other tissues, but little attention has focused on the potential of avian vectoring of plant pathogens. Extensive meadows of eelgrass (Zostera marina) in southwest Alaska support hundreds of thousands of waterfowl during fall migration and may be susceptible to plant pathogens. We recovered DNA of organisms pathogenic to eelgrass from environmental samples and in the cloacal contents of eight of nine waterfowl species that annually migrate along the Pacific coast of North America and Asia. Coupled with a signal of asymmetrical gene flow of eelgrass running counter to that expected from oceanic and coastal currents between Large Marine Ecosystems, this evidence suggests waterfowl are vectors of eelgrass pathogens., Migratory waterfowl vector plant seeds and other tissues, but little attention has focused on the potential of avian vectoring of species pathogenic on plants. When coupled with a signal of asymmetrical gene flow of eelgrass running counter to that expected from oceanic and coastal currents between Large Marine Ecosystems, our data support a model implicating waterfowl as vectors of plant pathogens. If waterfowl are vectoring eelgrass pathogens during their annual migratory cycles care must be taken when selecting seagrass restoration sites.

Many marine organisms show significant levels of genetic heterogeneity on local spatial scales despite exhibiting limited genetic structure at large geographic scales which can be produced through a variety of mechanisms. The Arctic cod (Boreogadus saida) is a circumpolar species and is a vital species in Arctic food webs. To examine population genetic structure of Arctic cod at macro- and micro-geographic scales, we characterized variation at mitochondrial DNA (mtDNA) and microsatellite loci among Arctic cod located in the Chukchi and Beaufort seas in Alaska. We found two distinct mtDNA haplotype clusters, although there was no underlying geographic pattern (FST = −0.001). Congruent with this finding, microsatellite loci suggested a panmictic population (FST = 0.001) across northern Alaskan marine waters at a large spatial scale. However, we found slight but significant micro-geographic partitioning of genetic variation in the southern shelf of the Beaufort Sea that appeared to be associated with the western reaches of the Mackenzie River plume. This fine-scale spatial pattern was not associated with kin-associated groups, suggesting larvae cohorts are not remaining together throughout development. We hypothesize that this pattern reflects the intermixing of Pacific and Arctic origin lineages of Arctic cod.

Seagrass meadows provide important ecological services to the marine environment but are declining worldwide. Although eelgrass meadows in the north Pacific are thought to be relatively healthy, few studies have assessed the presence of known disease pathogens in these meadows. In a pilot study to test the efficacy of the methods and to provide foundational disease biodiversity data in the north Pacific, we leveraged metabarcoding of environmental DNA extracted from water, sediment, and eelgrass tissue samples collected from five widely distributed eelgrass meadows in Alaska and one in Japan and uncovered wide prevalence of two classes of pathogenic organisms – Labyrinthula zosterae and other associated strains of Labyrinthula, and the Phytophthora/Halophytophthora blight species complex – known to have caused decline in eelgrass (Zostera marina) elsewhere in the species’ global distribution. Although the distribution of these disease organisms is not well understood in the north Pacific, we uncovered the presence of at least one eelgrass pathogen at every locality sampled.

Accurate and timely data regarding freshwater fish communities is important for informed decision-making by local, state, tribal, and federal land and resource managers; however, conducting traditional gear-based fish surveys can be an expensive and time-consuming process, particularly in remote areas, like those that characterize much of Alaska. To help address this challenge, we developed and tested five multi-species environmental DNA (eDNA) primer sets for the simultaneous detection of up to 37 target fish species in a single sample. Using these primer sets can reduce the cost and time needed to perform future studies of fish communities. Our results comparing multiple samples from multiple lakes and streams using multiple next-generation sequencing runs show the efficacy and reproducibility of these primers.

Natural history collections spanning multiple decades provide fundamental historical baselines to measure and understand changing biodiversity. New technologies such as next generation DNA sequencing have considerably increased the potential of museum specimens to address significant questions regarding the impact of environmental changes on host and parasite/pathogen dynamics. We developed a new technique to identify intestinal helminth parasites and applied it to shrews (Eulipotyphla: Soricidae) because they are ubiquitous, occupy diverse habitats, and host a diverse and abundant parasite fauna. Notably, we included museum specimens preserved in various ways to explore the efficacy of using metabarcoding analyses that may enable identification of helminth symbiont communities from historical archives. We successfully sequenced the parasite communities (using 12S mtDNA, 16S mtDNA, 28S rDNA) of 23 whole gastrointestinal tracts. All gastrointestinal tracts were obtained from the Museum of Southwestern Biology, USA, and from recent field collections, varying both in time since fixation (ranging from 4 months to 16 years) and preservation method (70% or 95% ethanol stored at room temperature, or flash frozen in liquid nitrogen and stored at −80 °C). Our proof of concept demonstrates the feasibility of applying next generation DNA sequencing techniques to authoritatively identify the parasite/pathogen communities within whole gastrointestinal tracts from museum specimens of varying age and fixation, and the value of future preservation of host-associated whole gastrointestinal tracts in public research archives. This powerful approach facilitates future comparative examinations of the distributions and interactions among multiple associated groups of organisms through time and space.

Arctic Cod (Boreogadus saida) serve as an important link in Arctic food webs and are thus considered an important species for environmental monitoring. RNA-Seq was conducted on samples from wild-collected individuals representing various age classes and tissue types to obtain as complete a transcriptome as possible on an Illumina MiSeq, which resulted in a total of 64,457 transcripts with an average length of 295 bp. We identified well-known genes that are associated with temperature change or response to pollutants. This RNA-Seq effort provides the first insight into the B. saida transcriptome, which can be a starting point for investigations identifying genes for local adaptation and genomic responses to future environmental change.

Karst estuaries are unique systems governed by freshwater inputs that flow directly to the sea through karst conduits and/or matrices. Because they are found at the interface between terrestrial and marine environments, they can act as sentinels to climate change and as indicators of aquifer health. The physical and geochemical gradients formed in karst estuaries are a direct result of the interactions between inland hydrological conditions and sea level. To examine the influence these gradients have on microbial communities in the water column and sediment of a karst estuary, we studied the spring-fed Double Keyhole Karst Estuary in west central Florida for a 2-year period. Four sites were monitored within this system starting at the Double Keyhole Spring Conduit extending 2 km west through the estuary toward the Gulf of Mexico. Water column and sediment samples were collected quarterly at all sites from September 2011 through September 2013. Archaeal, bacterial, and microbial eukaryote communities were analyzed using quantitative PCR and length-heterogeneity PCR. The biological communities were analyzed in the context of hydrological, physical, and geochemical parameters in order to determine which factor(s) governed the observed changes of microbial abundance and richness. The major finding of this study was that microbial community change in this karst estuary was primarily driven by the volume of aquifer discharge and associated physical gradients, and less by the geochemical fluctuations within the system.

Summary Karst estuaries represent unique systems created by freshwater inputs that flow directly into the sea through karst conduits and/or matrices. In order to determine the characteristics of a karst estuary resulting from the brackish discharge of Double Keyhole Spring into the Gulf of Mexico, we monitored short-term tidal fluctuations, long-term rainfall patterns, aquifer levels, spring discharge, and multiple geochemical parameters along a transect from the spring through the estuary. We monitored four sites along a spring/estuary transect and a nearby inland freshwater spring to represent the freshwater portion of the Upper Floridan Aquifer. Datasondes were deployed in Double Keyhole Spring to measure discharge volume, tidal fluctuations, and physical water parameters for two years. Water samples were collected quarterly from both springs and the surrounding surface sites over the same time period. An isotopic/trace element mass balance tracer method was used to determine the hydrogeological components of the spring discharge from three possible sources: (1) freshwater from the upper portion of the Upper Floridan aquifer, (2) freshwater from the lower portion of the Upper Floridan aquifer, and (3) saltwater from the Gulf of Mexico. Within the water column of the submarine spring conduit, there were no significant differences of the sampled parameters over short sampling distances (

The genome sequence of the obligate chemolithoautotroph Hydrogenovibrio crunogenus paradoxically predicts a complete oxidative citric acid cycle (CAC). This prediction was tested by multiple approaches including whole cell carbon assimilation to verify obligate autotrophy, phylogenetic analysis of CAC enzyme sequences and enzyme assays. Hydrogenovibrio crunogenus did not assimilate any of the organic compounds provided (acetate, succinate, glucose, yeast extract, tryptone). Enzyme activities confirmed that its CAC is mostly uncoupled from the NADH pool. 2-Oxoglutarate:ferredoxin oxidoreductase activity is absent, though pyruvate:ferredoxin oxidoreductase is present, indicating that sequence-based predictions of substrate for this oxidoreductase were incorrect, and that H. crunogenus may have an incomplete CAC. Though the H. crunogenus CAC genes encode uncommon enzymes, the taxonomic distribution of their top matches suggests that they were not horizontally acquired. Comparison of H. crunogenus CAC genes to those present in other 'Proteobacteria' reveals that H. crunogenus and other obligate autotrophs lack the functional redundancy for the steps of the CAC typical for facultative autotrophs and heterotrophs, providing another possible mechanism for obligate autotrophy.

Water column samples from the island of Mallorca, Spain were collected from one site in Cova des Pas de Vallgornera (Vallgornera) and three sites (Llac Martel, Llac Negre, and Llac de les Delícies) in Coves del Drac (Drac). Vallgornera is located on the southern coast of Mallorca approximately 57 km southwest of Coves del Drac. Drac is Europe's most visited tourist cave, whereas Vallgornera is closed to the public. Water samples were analyzed for water chemistry using spectrophotometric methods, by quantitative PCR for estimated total abundance of microbial communities, and by length heterogeneity PCR for species richness and relative species abundance of Archaea, Bacteria, and microbial eukaryotes. Estimated total abundance was multiplied by relative species abundance to determine the absolute species abundance. All sites were compared to determine spatial distributions of the microbial communities and to determine water column physical and chemical gradients. Water quality and community structure data indicate that both Drac Delícies and Drac Negre have distinct biogeochemical gradients. These sites have communities that are similar to Vallgornera but distinct from Drac Martel, only a few hundred meters away. Drac Martel is accessible to the general public and had the most dissimilar microbial community of all the sites. Similarities among communities at sites in Drac and Vallgornera suggest that these two spatially separated systems are operating under similar ecological constraints.

Double Keyhole Spring is a unique coastal submarine spring with complex and dynamically changing hydrology and water chemistry. It periodically reverses direction of flow, with accompanying changes in water chemistry and microbial communities. Although these transient changes follow the tidal cycle, longer term seasonal changes have also been detected.