Geology topics

Damian M. Menning

Publications and source records attributed to Damian M. Menning.

16 recordsLinked to original sources

USGS2025

Detection of Giardia and Cryptosporidium in surface water of a subarctic city

Giardia and Cryptosporidium spp. are globally distributed protozoan parasites that can cause gastrointestinal disease in humans and animals. These zoonotic parasites and their ecological relationships have been understudied in Alaska and elsewhere, despite being identified as priority zoonotic pathogens. We aimed to detect and characterize Giardia and Cryptosporidium spp. in waterbodies within Anchorage, Alaska, USA using two methods, including the Environmental Protection Agency (EPA) Method 1623 that relies on microscopy and a molecular detection approach. The molecular approach was ultimately unsuccessful and therefore only data obtained using Method 1623 are presented. Giardia or Cryptosporidium spp. was detected from nine of 15 urban streams and lakes sampled (60%), six of which were positive for both parasites (40%). Fewer than 10 cysts or oocysts were detected in 10 L of surface water. Further research to characterize Giardia and Cryptosporidium beyond the genus level would help elucidate the zoonotic potential and ecology of these parasites within the region and more broadly in Alaska.

Alaska↗

USGS2023

Environmental DNA as a tool for better understanding the distribution, abundance, and health of Atlantic and Pacific salmon

The development and application of approaches to detect and quantify environmental DNA (eDNA) have potential to improve our understanding of the distribution, abundance, and health of Atlantic Salmon Salmo salar and Pacific salmon Oncorhynchus spp. Here, we review 61 articles focusing on eDNA applications pertaining to salmon occupying natural habitat and aquaculture facilities in the context of advances, opportunities, and challenges. Given recent advances, eDNA now serves as a useful tool for detecting Atlantic Salmon and Pacific salmon and understanding threats to the health of fish and their habitats. Opportunities exist to apply sensitive and minimally invasive eDNA approaches to detect fish and assess fish habitat, assess range expansions of salmon and salmon pathogens, and detect invasive species that may threaten salmon health and abundance. Near real-time eDNA detection and quantification approaches to inform fisheries management may be on the horizon. Challenges limiting the widespread application of eDNA approaches for informing salmon management include accounting for the many factors affecting detection and quantification of eDNA, limits of data for deriving inference, and expense. Through continued development and refinement, eDNA approaches are anticipated to become increasingly available to, and utilized by, managers of Atlantic Salmon and Pacific salmon fisheries.

Fisheries Magazine↗

USGS2023

Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)

Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass ( Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.

Nature Plants↗

USGS2023

eDNA Metabarcoding Analyses of Diet in Yellow-Billed Loons of Northern Alaska

Environmental DNA is a burgeoning tool used to address wide-ranging scientific questions, including determining diets of difficult-to-sample predators. Loons are large piscivorous diving birds that capture and consume prey underwater, making it nearly impossible to visually determine their diet via observation alone. Identifying species' diets is important for understanding basic life history traits, and revealing key prey species can clarify species' roles in complex trophic webs, aid in understanding population and community dynamics, and help identify critical habitat for protection. Current information about loon diet is largely anecdotal, and traditional non-observational methods for quantifying loon diet have limitations. Analysis of eDNA from loon feces may provide biologists with a non-invasive technique for determining diet without negative sampling effects, and with increased resolution as compared to other techniques. We surveyed lakes in two areas of northern Alaska for Yellow-billed Loons ( Gavia adamsii ). Loon fecal samples were collected opportunistically from latrine sites without disturbing any animals and analyzed using novel marker sets to determine loon species and diet. Fish species were detected in all fecal samples, the most common being Alaska blackfish ( Dallia pectoralis ), and ninespine stickleback ( Pungitius pungitius ). This research demonstrates that eDNA metabarcoding analyses of loon fecal samples can determine the specific loon species that deposited the feces and characterize the piscine portion of their diet with limited disturbance to the animals.

Alaska↗

USGS2023

Fecal DNA metabarcoding shows credible short-term prey detections and explains variation in the gut microbiome of two polar bear subpopulations

This study developed and evaluated DNA metabarcoding to identify the presence of pinniped and cetacean prey DNA in fecal samples of East Greenland (EG) and Southern Beaufort Sea (SB) polar bears Ursus maritimus sampled in the spring of 2015-2019. Prey DNA was detected in half (49/92) of all samples, and when detected, ringed seal Pusa hispida was the predominant prey species, identified in 100% (22/22) of EG and 81% (22/27) of SB polar bear samples with prey DNA detected. Bearded seal Erignathus barbatus DNA was found in 19% (5/27) of SB polar bear samples for which prey DNA was detected. Prey DNA detection frequencies and relative abundances were compared to estimates from quantitative fatty acid signature analysis (QFASA) for a subset of SB polar bears. Ringed seal and bearded seal were the main prey identified by both methods, but QFASA also identified 2 cetacean prey species not found by prey DNA. Differences in DNA metabarcoding vs. QFASA results were likely related to the different dietary timescales captured by each approach, i.e. short-term vs. long-term diet, respectively. Prey DNA detection, sex/age class, and subpopulation significantly explained variation in polar bear gut bacterial composition. Polar bear samples with prey DNA detected were associated with higher abundances of the bacterial classes Clostridia and Bacilli and lower abundances of Negativicutes. Fecal DNA metabarcoding is thus useful for identifying recent prey of polar bears, complementing quantitative and likely longer-term QFASA estimates, and may help understand variation in the polar bear gut microbiome.

Marine Ecology Progress Series (MEPS)↗

USGS2021

Using next generation sequencing of alpine plants to improve fecal metabarcoding diet analysis for Dall’s sheep

Objectives Dall’s sheep ( Ovis dalli dalli ) are important herbivores in the mountainous ecosystems of northwestern North America, and recent declines in some populations have sparked concern. Our aim was to improve capabilities for fecal metabarcoding diet analysis of Dall’s sheep and other herbivores by contributing new sequence data for arctic and alpine plants. This expanded reference library will provide critical reference sequence data that will facilitate metabarcoding diet analysis of Dall’s sheep and thus improve understanding of plant-animal interactions in a region undergoing rapid climate change. Data description We provide sequences for the chloroplast rbcL gene of 16 arctic-alpine vascular plant species that are known to comprise the diet of Dall’s sheep. These sequences contribute to a growing reference library that can be used in diet studies of arctic herbivores.

BMC Research Notes↗

USGS2021

Abundance of a recently discovered Alaskan rhodolith bed in a shallow, seagrass-dominated lagoon

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 presence and biomass were estimated to assess trends and environmental factors that may influence rhodolith distribution and abundance during 4 years spread over a 12-year period (2008–2010, and 2019). Rhodolith presence and biomass were positively associated with percent seaweed cover, as most rhodoliths and seaweeds occurred in subtidal areas, and negatively associated with percent eelgrass cover. 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.

Alaska↗

USGS2021

Metabarcoding of environmental samples suggest wide distribution of eelgrass (Zostera marina) pathogens in the north Pacific

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.

Metabarcoding and Metagenomics↗

USGS2020

Microbiomes from biorepositories? 16S rRNA bacterial amplicon sequencing of archived and contemporary intestinal samples of wild mammals (Eulipotyphla: Soricidae)

Interest in gut microbial community composition has exploded recently as a result of the increasing ability to characterize these organisms and a growing understanding of their role in host fitness. New technologies, such as next generation amplicon (16S rRNA) sequencing, have enabled identification of bacterial communities from samples of diverse origin (e.g., fecal, skin, genital, environmental, etc.). Relatively little work, however, has explored the feasibility of utilizing historical samples (e.g., museum archived samples) of varying age, quality, and preservation type. Because natural history collections span multiple decades, these biorepositories have the potential to provide fundamental historical baselines to measure and better understand biodiversity on a changing planet. Utilizing even a small proportion of museum specimens could provide a means of sampling past microbial communities, allowing for direct comparison to contemporary communities and more complete understanding of dynamic shifts through time. We examined the feasibility of obtaining 16S rRNA amplicon microbiome data from whole gastrointestinal tracts (GIs) of shrews of varying age and preservation method, including 5 freshly collected shrew GIs immediately fixed in liquid nitrogen (LN2), 10 ten-year old shrew GIs frozen at −20°C (whole animal), and 10 shrews of varying ages (4 from 1968, 1 from 1980, 1 from 2001, 1 from 2004, 1 from 2007, 1 from 2011 and 2 from 2013) fixed and stored whole in 70% ethanol. Not surprisingly, results of 16S rDNA amplicon sequencing reveal significantly different bacterial communities between different preservation techniques and age of samples. Ten-year old frozen samples had bacterial communities most similar to freshly collected (LN2) samples, while the bacterial communities of both were significantly different from the 70% ethanol preserved samples of various ages. Amongst those preserved in 70% ethanol, age of samples also influenced bacterial community composition. Additionally, we compare results of OTU based and ASV based analyses. Looking ahead, field collectors and museums should develop and adopt best practices related to frozen preservation to ensure adequate material for future microbiome investigations.

Frontiers in Ecology and Evolution↗

USGS2020

Are migratory waterfowl vectors of seagrass pathogens?

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.

Alaska↗

USGS2020

Environmental DNA: An emerging tool for understanding aquatic biodiversity

Field surveys for aquatic organisms provide critical information that is important for robust resource management. However, such surveys are expensive and labor intensive, particularly in large, remote landscapes like those that characterize much of Alaska. Traditionally, characterizing aquatic biodiversity necessitated the physical capture and identification of individual organisms, which required that field crews have some level of expertise in identifying the species likely to be present. Many other limitations of surveys that rely on direct observation of aquatic organisms have been noted (Evans and Lamberti 2018). However, what if it were possible to identify all of the species present at a site without having to capture or even see them? While we are not there yet, the recent revolution in environmental DNA (eDNA) technology is bringing us closer to that goal (Thomsen and Willerslev 2014).

Alaska↗

USGS2019

Micro-geographic population genetic structure within Arctic cod (Boreogadus saida) in Beaufort Sea of Alaska

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 ( F ST = −0.001). Congruent with this finding, microsatellite loci suggested a panmictic population ( F ST = 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.

Alaska↗

USGS2018

Using redundant primer sets to detect multiple native Alaskan fish species from environmental DNA

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.

Alaska↗

USGS2018

Museum metabarcoding: a novel method revealing gut helminth communities of small mammals across space and time

Natural history collections spanning multiple decades provide fundamental historical baselines to measure and understand changing biodiversity. New technologies such as next generation DNA sequencing (NGS) 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 (GI) tracts. All GI tracts were obtained from the Museum of Southwestern Biology (MSB), 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 NGS techniques to authoritatively identify the parasite/pathogen communities within whole GI tracts from museum specimens of varying age and fixation, and the value of future preservation of host-associated whole GI 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.

International Journal for Parasitology↗

USGS2018

A transcriptome resource for the Arctic Cod (Boreogadus saida)

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.

Marine Genomics↗

USGS2017

Genomics of Arctic cod

The Arctic cod (Boreogadus saida) is an abundant marine fish that plays a vital role in the marine food web. To better understand the population genetic structure and the role of natural selection acting on the maternally-inherited mitochondrial genome (mitogenome), a molecule often associated with adaptations to temperature, we analyzed genetic data collected from 11 biparentally-inherited nuclear microsatellite DNA loci and nucleotide sequence data from from the mitochondrial DNA (mtDNA) cytochrome b (cytb) gene and, for a subset of individuals, the entire mitogenome. In addition, due to potential of species misidentification with morphologically similar Polar cod (Arctogadus glacialis), we used ddRAD-Seq data to determine the level of divergence between species and identify species-specific markers. Based on the findings presented here, Arctic cod across the Pacific Arctic (Bering, Chukchi, and Beaufort Seas) comprise a single panmictic population with high genetic diversity compared to other gadids. High genetic diversity was indicated across all 13 protein-coding genes in the mitogenome. In addition, we found moderate levels of genetic diversity in the nuclear microsatellite loci, with highest diversity found in the Chukchi Sea. Our analyses of markers from both marker classes (nuclear microsatellite fragment data and mtDNA cytb sequence data) failed to uncover a signal of microgeographic genetic structure within Arctic cod across the three regions, within the Alaskan Beaufort Sea, or between near-shore or offshore habitats. Further, data from a subset of mitogenomes revealed no genetic differentiation between Bering, Chukchi, and Beaufort seas populations for Arctic cod, Saffron cod (Eleginus gracilis), or Walleye pollock (Gadus chalcogrammus). However, we uncovered significant differences in the distribution of microsatellite alleles between the southern Chukchi and central and eastern Beaufort Sea samples of Arctic cod. Finally, using ddRAD-Seq data, we identified species-specific markers and in conjunction with mitogenome data, identified an Arctic cod x Polar cod hybrid in western Canadian Beaufort Sea. Overall, the lack of genetic structure among Arctic cod within the Bering, Chukchi and Beaufort seas of Alaska is concordant with the absence of geographic barriers to dispersal and typical among marine fishes. Arctic cod may exhibit a genetic pattern of isolation-by-distance, whereby populations in closer geographic proximity are more genetically similar than more distant populations. As this signal is only found between our two fartherest localities, data from populations elsewhere in the species’ global range are needed to determine if this is a general characteristic. Further, tests for selection suggested a limited role for natural selection acting on the mitochondrial genome of Arctic cod, but do not exclude the possibility of selection on genes involved in nuclear-mitogenome interactions. Unlike previous genetic assessment of Arctic cod sampled from the Chukchi Sea, the high levels of genetic diversity found in Arctic cod assayed in this study, across regions, suggests that the species in the Beaufort and Chukchi seas does not suffer from low levels of genetic variation, at least at neutral genetic markers. The large census size of Arctic cod may allow this species to retain high levels of genetic diversity. In addition, we discovered the presence of hybridization between Arctic and Polar cod (although low in frequency). Hybridization is expected to occur when environmental changes modify species distributions that result in contact between species that were previously separated. In such cases, hybridization may be an evolutionary mechanism that promotes an increase in genetic diversity that may provide species occupying changing environments with locally-adapted genotypes and, therefore, phenotypes. Natural selection can only act on the standing genetic variation present within a population. Therefore, given its higher levels of genetic diversity in combination with a large population size, Arctic cod may be resilient to current and future environmental change, as high genetic diversity is expected to increase opportunities for positive selection to act on genetic variants beneficial in different environments, regardless of the source of that genetic variation.

OCS Study↗