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At least 703 records · Page 39Linked to original sources
USGS2019

North-facing slopes and elevation shape asymmetric genetic structure in the range-restricted salamander Plethodon shenandoah

Species with narrow environmental preferences are often distributed across fragmented patches of suitable habitat, and dispersal among subpopulations can be difficult to directly observe. Genetic data collected at population centers can help quantify gene flow, which is especially important for vulnerable species with a disjunct range. Plethodon shenandoah is a Federally Endangered salamander known only from three mountaintops in Virginia, USA. To reconstruct the evolutionary history and population connectivity of this species, we generated both mitochondrial and nuclear data using sequence capture for all three populations and found strong population structure that was independent of geographic distance. Both the nuclear markers and mitochondrial genome indicated a deep split between the most southern population and the combined central and northern population. Although there was some mitochondrial haplotype-splitting between the central and northern populations, there was complete admixture in nuclear markers. This is indicative of either a recent split or current male-biased dispersal among mountain isolates. Models of landscape resistance found that dispersal across north-facing slopes at mid-elevation levels best explain the observed genetic structure among populations. These unexpected results highlight the importance of landscape features in understanding and predicting movement and fragmentation of salamanders across space.

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

Evaluating wildlife translocations using genomics: A bighorn sheep case study

Wildlife restoration often involves translocation efforts to reintroduce species and supplement small, fragmented populations. We examined the genomic consequences of bighorn sheep ( Ovis canadensis ) translocations and population isolation to enhance understanding of evolutionary processes that affect population genetics and inform future restoration strategies. We conducted a population genomic analysis of 511 bighorn sheep from 17 areas, including native and reintroduced populations that received 0–10 translocations. Using the Illumina High Density Ovine array, we generated datasets of 6,155 to 33,289 single nucleotide polymorphisms and completed clustering, population tree, and kinship analyses. Our analyses determined that natural gene flow did not occur between most populations, including two pairs of native herds that had past connectivity. We synthesized genomic evidence across analyses to evaluate 24 different translocation events and detected eight successful reintroductions (i.e., lack of signal for recolonization from nearby populations) and five successful augmentations (i.e., reproductive success of translocated individuals) based on genetic similarity with the source populations. A single native population founded six of the reintroduced herds, suggesting that environmental conditions did not need to match for populations to persist following reintroduction. Augmentations consisting of 18–57 animals including males and females succeeded, whereas augmentations of two males did not result in a detectable genetic signature. Our results provide insight on genomic distinctiveness of native and reintroduced herds, information on the relative success of reintroduction and augmentation efforts and their associated attributes, and guidance to enhance genetic contribution of augmentations and reintroductions to aid in bighorn sheep restoration.

Montana, Idaho, Wyoming↗
USGS2025

Maintenance of genetic diversity despite population fluctuations in the lesser prairie-chicken (Tympanuchus pallidicinctus)

Assessments of genetic diversity, structure, history, and effective population size ( N e ) are critical for the conservation of imperiled populations. The lesser prairie-chicken ( Tympanuchus pallidicinctus ) has experienced declines due to habitat loss, degradation, and fragmentation in addition to substantial population fluctuations with unknown effects on genetic diversity. Our objectives were to: (i) compare genetic diversity across three temporally discrete sampling periods (2002, 2007-2010, and 2013-2014) that are characterized by low or high population abundance; (ii) examine genetic diversity at lek and lek cluster spatial scales; (ii) identify potential bottlenecks and characterize genetic structure and relatedness; and (iii) estimate the regional N e . We analyzed 194 samples across the shinnery oak prairie region of eastern New Mexico and western Texas using 13 microsatellite loci. Mean heterozygosity, allelic richness, and inbreeding coefficient were not significantly different between discrete sampling periods, suggesting that this population has maintained its genetic diversity across the sampled population fluctuations. We did not detect genetic structure using multiple Bayesian clustering approaches. Furthermore, there was no support for recent genetic bottlenecks, and we estimated that the N e ranged from 229.5 ( p crit = 0.05, 95% CIs = 121.2-1023.1) to 349.1 ( p crit = 0.02, 95% CIs = 176.4-2895.2) during our final sampling period (2013-2014). Although we provide evidence for gene flow within this region, continued habitat loss and fragmentation that leads to population declines and isolation could increase the risk of genetic consequences. Continued monitoring of genetic diversity and increasing available habitat that supports robust populations of lesser prairie-chickens may improve the likelihood of the species' persistence.

New Mexico, Texas↗
USGS2021

Genomic association with pathogen carriage in bighorn sheep (Ovis canadensis)

Genetic composition can influence host susceptibility to, and transmission of, pathogens, with potential population‐level consequences. In bighorn sheep ( Ovis canadensis ), pneumonia epidemics caused by Mycoplasma ovipneumoniae have been associated with severe population declines and limited recovery across North America. Adult survivors either clear the infection or act as carriers that continually shed M. ovipneumoniae and expose their susceptible offspring, resulting in high rates of lamb mortality for years following the outbreak event. Here, we investigated the influence of genomic composition on persistent carriage of M. ovipneumoniae in a well‐studied bighorn sheep herd in the Wallowa Mountains of Oregon, USA. Using 10,605 SNPs generated using RADseq technology for 25 female bighorn sheep, we assessed genomic diversity metrics and employed family‐based genome‐wide association methodologies to understand variant association and genetic architecture underlying chronic carriage. We observed no differences among genome‐wide diversity metrics (heterozygosity and allelic richness) between groups. However, we identified two variant loci of interest and seven associated candidate genes, which may influence carriage status. Further, we found that the SNP panel explained ~55% of the phenotypic variance (SNP‐based heritability) for M. ovipneumoniae carriage, though there was considerable uncertainty in these estimates. While small sample sizes limit conclusions drawn here, our study represents one of the first to assess the genomic factors influencing chronic carriage of a pathogen in a wild population and lays a foundation for understanding genomic influence on pathogen persistence in bighorn sheep and other wildlife populations. Future research should incorporate additional individuals as well as distinct herds to further explore the genomic basis of chronic carriage.

Oregon↗
USGS2021

Gut microbial ecology of the Critically Endangered Fijian crested iguana (Brachylophus vitiensis): Effects of captivity status and host reintroduction on endogenous microbiomes

Animals often exhibit distinct microbial communities when maintained in captivity as compared to when in the wild. Such differentiation may be significant in headstart and reintroduction programs where individuals spend some time in captivity before release into native habitats. Using 16S rRNA gene sequencing, we (i) assessed differences in gut microbial communities between captive and wild Fijian crested iguanas ( Brachylophus vitiensis ) and (ii) resampled gut microbiota in captive iguanas released onto a native island to monitor microbiome restructuring in the wild. We used both cloacal swabs and fecal samples to further increase our understanding of gut microbial ecology in this IUCN Critically Endangered species. We found significant differentiation in gut microbial community composition and structure between captive and wild iguanas in both sampling schemes. Approximately two months postrelease, microbial communities in cloacal samples from formerly captive iguanas closely resembled wild counterparts. Interestingly, microbial communities in fecal samples from these individuals remained significantly distinct from wild conspecifics. Our results indicate that captive upbringings can lead to differences in microbial assemblages in headstart iguanas as compared to wild individuals even after host reintroduction into native conditions. This investigation highlights the necessity of continuous monitoring of reintroduced animals in the wild to ensure successful acclimatization and release.

Ecology and Evolution↗
USGS2022

Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex

The Neosho Bass ( Micropterus velox ), a former subspecies of the keystone top-predator and globally popular Smallmouth Bass ( M. dolomieu ), is endemic and narrowly restricted to small, clear streams of the Arkansas River Basin in the Central Interior Highlands (CIH) ecoregion, USA. Previous studies have detected some morphological, genetic, and genomic differentiation between the Neosho and Smallmouth Basses; however, the extent of neutral and adaptive divergence and patterns of intraspecific diversity are poorly understood. Furthermore, lineage diversification has likely been impacted by gene flow in some Neosho populations, which may be due to a combination of natural biogeographic processes and anthropogenic introductions. We assessed: (1) lineage divergence, (2) local directional selection (adaptive divergence), and (3) demographic history among Smallmouth Bass populations in the CIH using population genomic analyses of 50,828 single-nucleotide polymorphisms (SNPs) obtained through ddRAD-seq. Neosho and Smallmouth Bass formed monophyletic clades with 100% bootstrap support. We identified two major lineages within each species. We discovered six Neosho Bass populations (two nonadmixed and four admixed) and three nonadmixed Smallmouth Bass populations. We detected 29 SNPs putatively under directional selection in the Neosho range, suggesting populations may be locally adapted. Two populations were admixed via recent asymmetric secondary contact, perhaps after anthropogenic introduction. Two other populations were likely admixed via combinations of ancient and recent processes. These species comprise independently evolving lineages, some having experienced historical and natural admixture. These results may be critical for management of Neosho Bass as a distinct species and may aid in the conservation of other species with complex biogeographic histories.

Ecology and Evolution↗
USGS2022

Spatial models can improve the experimental design of field-based transplant gardens by preventing bias due to neighborhood crowding

Field-based transplant gardens, including common and reciprocal garden experiments, are a powerful tool for studying genetic variation and gene-by-environment interactions. These experiments assume that individuals within the garden represent independent replicates growing in a homogenous environment. Plant neighborhood interactions are pervasive across plant populations and could violate assumptions of transplant garden experiments. We demonstrate how spatially explicit models for plant–plant interactions can provide novel insights on genotypes' performance in field-transplant garden designs. We used individual-based models, based on data from a sagebrush ( Artemisia spp.) common garden, to simulate the impact of spatial plant–plant interactions on between-group differences in plant growth. We found that planting densities within the range of those used in many common gardens can bias experimental outcomes. Our results demonstrate that higher planting densities can lead to inflated group differences and may confound genotypes' competitive ability and genetically underpinned variation. Synthesis. We propose that spatially explicit models can help avoid biased results by informing the design and analysis of field-based transplant garden experiments. Alternately, including neighborhood effects in post hoc analyses of transplant garden experiments is likely to provide novel insights into the roles of biotic factors and density dependence in genetic differentiation.

Ecology and Evolution↗
USGS2021

Sea otter population collapse in southwest Alaska: Assessing ecological covariates, consequences, and causal factors

Sea otter ( Enhydra lutris ) populations in southwest Alaska declined substantially between about 1990 and the most recent set of surveys in 2015. Here we report changes in the distribution and abundance of sea otters, and covarying patterns in reproduction, mortality, body size and condition, diet and foraging behavior, food availability, health profiles, and exposure to environmental contaminants over this 25-yr period. The population decline, which resulted in densities on the order of 5% of environmental carrying capacity, ranged from Attu Island in the west to about Castle Cape (on the south side of the Alaska Peninsula) in the east. Remaining sea otters moved closer to shore and into shallow, protected habitats. Reproductive rates appeared unchanged with the decline. Although the demographic cause of the decline was clearly elevated mortality, stranded carcasses were rare or absent. The net rate of energy gain by foraging sea otters, body length and condition, and prey biomass density, all increased after the decline and varied inversely with sea otter population density beyond the area of decline. Sea otters within the area of decline showed no increases in health anomalies, disease, contaminant exposure, or abnormal gene transcription patterns as compared to animals outside the area of decline. These collective findings are inconsistent with nutritional limitation, disease, or environmental contaminants, and consistent with predation (or possibly some other density-independent factor) as the reason for the sea otter population decline. Our approach and analyses provide a broad conceptual template for thinking about and assessing the causes of wildlife population declines.

Alaska↗
USGS2019

A range-wide model of contemporary, omnidirectional connectivity for the threatened Mojave desert tortoise

As habitat destruction leads to species extinctions globally, conservation planning that accounts for population-level connectivity and gene flow is an urgent priority. Models that only approximate habitat potential are incomplete because areas of high habitat potential may be isolated, whereas intermixed areas of lower habitat potential may still be critical for maintaining connectivity between and among populations. We developed a range-wide, omnidirectional (‘coreless’) connectivity model and map for the threatened Mojave desert tortoise at a high spatial resolution (30 m), based on empirical movement data and a circuit-theoretic approach to estimating connectivity. Specifically, we first estimated habitat potential (i.e., quality) for tortoise movement (as distinct from habitat potential more generally) across its range using hypotheses based on the published literature, linear mixed models, multiple environmental factors derived from remotely sensed data, and recent solar and wind development footprints. The resultant raster output was used to represent landscape conductance in a circuit-theoretic model of connectivity, which relates the flow of electrical current through a circuit to the movement of tortoises through the landscape. We then modeled potential connectivity across the range of the tortoise using Circuitscape software and the Julia numerical programming language. Intermediate distances from minor roads, intermediate values of annual average maximum temperature, and increasing density of desert washes were among the strongest predictors of movement habitat quality. There was also strong evidence for increased habitat quality for movement with increasing amounts of vegetation cover. The resulting connectivity model and map was determined to accurately reflect important areas for tortoise movement, but we encourage others to do their own evaluation of the model within local areas of interest and as more data become available. Accordingly, the map can provide an important component to improve management decisions that have the potential to influence the conservation of connected desert tortoise populations throughout the range.

California↗
USGS2022

Average kinship within bighorn sheep populations is associated with connectivity, augmentation, and bottlenecks

Understanding the influence of population attributes on genetic diversity is important to advancement of biological conservation. Because bighorn sheep ( Ovis canadensis ) populations vary in size and management history, the species provides a unique opportunity to observe the response of average pairwise kinship, inversely related to genetic diversity, to a spectrum of natural and management influences. We estimated average pairwise kinship of bighorn sheep herds and compared estimates with population origin (native/indigenous/extant or reintroduced), historical minimum count, connectivity, and augmentation history, to determine which predictors were the most important. We evaluated 488 bighorn sheep from 19 wild populations with past minimum counts of 16–562 animals, including native and reintroduced populations that received 0–165 animals in augmentations. Using the Illumina High Density Ovine array, we generated a dataset of 7728 single nucleotide polymorphisms and calculated average pairwise kinship for each population. Multiple linear regression analysis determined that connectivity between populations via dispersal, greater number of animals received in augmentations, and greater minimum count were correlated with lower average pairwise kinship at the population level, and whether the population was extant or reintroduced was less important. Thus, our results indicated that genetic isolation of populations can result in increased levels of inbreeding. By determining that natural and human-assisted gene flow were likely the most important influences of average pairwise kinship at the population level, this study can serve as a benchmark for future management of bighorn sheep populations and aid in identifying populations of genetic concern to define priorities for conservation of wild populations.

Montana, Wyoming↗
USGS2022

Implications of habitat-driven survival and dispersal on recruitment in a spatially structured piping plover population

Natal survival and dispersal have important consequences for populations through the movement of genes and individuals. Metapopulation theory predicts either balanced natal dispersal among regions or source–sink dynamics, which can dramatically change population structure. For species reliant on dynamic, early-successional habitats, availability and location of habitat will shift from year to year, requiring primiparous individuals to locate an appropriate breeding habitat. We estimated hatch-year survival to adulthood and natal dispersal rates between two breeding groups of Northern Great Plains piping plovers ( Charadrius melodus ) from four cohorts ( n = 2669 total individuals; 2014–2017). Hatch-year survival to adulthood was slightly higher for individuals hatched on the Missouri River than on the US Alkali Wetlands but declined over time. Individuals hatched on the US Alkali Wetlands were more likely to disperse to breed on the Missouri River (0.33 [0.20, 0.48]) than vice versa (0.17 [0.11, 0.24]). When more habitat was available at the natal site than in the prior year, natal dispersal rates increased. However, despite higher recruitment rates as a result of higher natal fidelity, the Missouri River showed lower total recruitment with a declining trend in the number of recruits, largely due to differences in abundance between breeding groups. Overall, unbalanced, high natal dispersal rates within the Northern Great Plains indicate high connectivity among distinct regions with different water regimes on the Missouri River and on the US Alkali Wetlands driven by fluctuating availability of habitat. Our results suggest that plovers in the Northern Great Plains take advantage of dynamic habitats where they are available in a broad geographic area, which is consistent with a spatially structured panmictic population rather than a true metapopulation, but further research on adult breeding dispersal is needed to clarify population structure.

North Dakota, South Dakota↗
USGS2023

Marmots do not drink coffee: Human urine contributions to the nitrogen budget of a popular national park destination

Reactive nitrogen (Nr) concentrations are higher than expected for mountain lakes in Rocky Mountain National Park, and for many years, high Nr concentrations have been attributed to atmospheric Nr deposition from regional and more distant emission sources, including combustion of fossil fuels and agricultural activities. Here, we estimated the contribution from a very local source, that of human urine, related to intensive use by visitors in Loch Vale Watershed (LVWS). Not only does urine convey hormones, pharmaceuticals, antibiotic-resistant bacteria, and antibiotic-resistant genes to the environment, but it also contributes Nr, which contributes to loss of biodiversity and eutrophication. Using caffeine as a specific marker for human urine, we compared the calculated maximum potential input of urine with that from wet atmospheric Nr deposition. The maximum potential input is a worst-case scenario. Nearly 30,000 and 45,000 people hiked the 4.0 km to the Loch, the lowest lake in LVWS, in June–September 2019 and 2020, respectively. Informal trails and informal latrine sites were mapped, and the contribution of human urine was calculated based on several assumptions, including that each visitor voided their bladder on the ground once per visit somewhere in Loch Vale. The resulting Nr input from urine in Loch Vale for the summer months of June through September was 0.02 kg Nr ha −1 , and prorated to a full year, the 2019 potential contribution of human waste was 0.06 kg ha −1 year −1 . These values are compared with June–September 1.2 kg Nr ha −1 from wet atmospheric deposition or annual measured 2019 deposition of 2.5 kg Nr ha −1 year −1 , to indicate a contribution of 2% Nr to the waters of Loch Vale from local human urine. Most Nr in this alpine and subalpine watershed is still attributable to emissions and subsequent wet atmospheric deposition, but a 2% contribution from human waste is not insignificant. In the very broadest sense, our results document an ecological disturbance from an unprecedented level of human activity in a protected and designated wilderness area. Local solutions to this local problem could include greater outreach to visitors of public lands about the consequences of their activities and installation of latrines.

Colorado↗
USGS2023

Geographic isolation reduces genetic diversity of a wide-ranging terrestrial vertebrate, Canis lupus

Genetic diversity is theorized to decrease in populations closer to a species' range edge, where habitat may be suboptimal. Generalist species capable of long-range dispersal may maintain sufficient gene flow to counteract this, though the presence of significant barriers to dispersal (e.g., large water bodies, human-dominated landscapes) may still lead to, and exacerbate, the edge effect. We used microsatellite data for 2421 gray wolves ( Canis lupus ) from 24 subpopulations (groups) to model how allelic richness and expected heterozygosity varied with mainland–island position and two measures of range edge (latitude and distance from range center) across >7.3 million km 2 of northern North America. We expected low genetic diversity both at high latitudes, due to harsh environmental conditions, and on islands, but no change in diversity with distance to the range center due to the species' exceptional dispersal ability and favorable conditions in far eastern and western habitats. We found that allelic richness and expected heterozygosity of island groups were measurably less than that of mainland groups, and that these differences increased with the island's distance to the species' range center in the study area. Our results demonstrate how multiple axes of geographic isolation (distance from range center and island habitation) can act synergistically to erode the genetic diversity of wide-ranging terrestrial vertebrate populations despite the counteracting influence of long-range dispersal ability. These findings emphasize how geographic isolation is a potential threat to the genetic diversity and viability of terrestrial vertebrate populations even among species capable of long-range dispersal.

Alaska↗
USGS2024

Translocation in a fragmented river provides demographic benefits for imperiled fishes

Fragmentation isolates individuals and restricts access to valuable habitat with severe consequences for populations, such as reduced gene flow, disruption of recolonization dynamics, reduced resiliency to disturbance, and changes in aquatic community structure. Translocations to mitigate the effects of fragmentation and habitat loss are common, but few are rigorously evaluated, particularly for fishes. Over six years, we translocated 1215 individuals of four species of imperiled fish isolated below a barrier on the San Juan River, Utah, USA, that restricts access to upstream habitat. We used re-encounter data (both passive integrated transponder tag and telemetry detections and physical recaptures) collected between 2016 and 2023, to inform a spatially explicit multistate mark–recapture model that estimated survival and transition probabilities of translocated and non-translocated individuals, both below and above the barrier. Individuals of all four species moved large (>200 km) distances upstream following translocation, with the maximum upstream encounter distance varying by species. Results from the multistate mark–recapture model suggested translocated fish survived at a higher rate compared with non-translocated fish below the barrier for three of the four species. Above the barrier, translocated individuals survived at similar rates as non-translocated fish for bluehead sucker ( Catostomus discobolus ) and flannelmouth sucker ( Catostomus latipinnis ), while survival rates of translocated endangered Colorado pikeminnow ( Ptychocheilus lucius ; mean, 95% CI: 0.75, 0.55–0.88) and endangered razorback sucker ( Xyrauchen texanus ; 0.86, 0.75–0.92) were higher relative to non-translocated individuals (Colorado pikeminnow: 0.52, 0.51–0.54; razorback sucker: 0.75, 0.74–0.75). Transition probabilities from above the barrier to below the barrier were generally low for three of the four species (all upper 95% CI ≤ 0.23), but they were substantially higher for razorback sucker. Our results suggest translocation to mitigate fragmentation and habitat loss can have demographic benefits for large-river fish species by allowing movements necessary to complete their life history in heterogeneous riverscapes. Further, given the costs or delays in providing engineered fish passage structures or in achieving dam removal, we suggest translocations may provide an alternative conservation strategy in fragmented river systems.

Colorado, New Mexico, Utah↗
USGS2020

Metabarcoding assays for the detection of freshwater mussels (Unionida) with environmental DNA

Freshwater mussels of the order Unionida are a widely distributed taxon that are important in maintaining freshwater ecosystems and are also highly imperiled throughout the world. Monitoring of mussel populations with environmental DNA (eDNA) is an attractive alternative to traditional methods because it is noninvasive and requires less labor and taxonomic knowledge from field personnel. We developed eDNA metabarcoding assays specific to freshwater mussels and tested them at six sites in the Clinch River, located in the southeastern United States. Our objective was to determine the utility of eDNA metabarcoding for future monitoring of mussel populations and restoration efforts in this watershed. Two metabarcoding assays that target the mitochondrial DNA regions of the cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit (ND1) genes were developed and tested. Our assays appear to be order specific, amplifying members from the two families found in North America, Unionidae and Margaritiferidae, while not amplifying nontarget fish or other bivalve species. From the field collected samples, our assays together detected 19 species, eight of which are listed as federally endangered. The assays also detected 42%, 58%, and 54% of the species identified by recent quantitative visual mussel surveys at three sampling sites. Increased sampling effort by processing a greater water volume or number of samples will likely increase species detections. These eDNA metabarcoding assays may enable enhanced monitoring of freshwater mussel assemblages and subsequently inform conservation efforts.

Virginia↗
USGS2021

eDNA metabarcoding outperforms traditional fisheries sampling and reveals fine-scale heterogeneity in a temperate freshwater lake

Understanding biodiversity in aquatic systems is critical to ecological research and conservation efforts, but accurately measuring species richness using traditional methods can be challenging. Environmental DNA (eDNA) metabarcoding, which uses high-throughput sequencing and universal primers to amplify DNA from multiple species present in an environmental sample, has shown great promise for augmenting results from traditional sampling to characterize fish communities in aquatic systems. Few studies, however, have compared exhaustive traditional sampling with eDNA metabarcoding of corresponding water samples at a small spatial scale. We intensively sampled Boardman Lake (1.4 km 2 ) in Michigan, USA, from May to June in 2019 using gill and fyke nets and paired each net set with lake water samples collected in triplicate. We analyzed water samples using eDNA metabarcoding with 12S and 16S fish-specific primers and compared estimates of fish diversity among methods. In total, we set 60 nets and analyzed 180 1 L lake water samples. We captured a total of 12 fish species in our traditional gear and detected 40 taxa in the eDNA water samples, which included all the species observed in nets. The 12S and 16S assays detected a comparable number of taxa, but taxonomic resolution varied between the two genes. In our traditional gear, there was a clear difference in the species selectivity between the two net types, and there were several species commonly detected in the eDNA samples that were not captured in nets. Finally, we detected spatial heterogeneity in fish community composition across relatively small scales in Boardman Lake with eDNA metabarcoding, but not with traditional sampling. Our results demonstrated that eDNA metabarcoding was substantially more efficient than traditional gear for estimating community composition, highlighting the utility of eDNA metabarcoding for assessing species diversity and informing management and conservation.

Michigan↗
USGS2019

Great Lakes Cladophora harbors phylogenetically diverse nitrogen-fixing microorganims

Abstract Nitrogen‐fixing microorganisms are among the epiphytic communities in Cladophora, potentially benefitting the algae in nutrient‐deficient waters, but their abundance and diversity remain unexplored. In this study, we determined the abundance and taxonomic composition of these nitrogen‐fixing microorganisms in Cladophora growing on rocks, breakwall structures, or submerged dreissenid mussel beds around southern Lake Michigan (N = 33) during the summer 2015, using two complementary genomic techniques: quantitative PCR (qPCR) and shotgun metagenomic sequencing. Genomic DNA was extracted from processed algal pellets, and the nitrogen‐fixing microbes were quantified by qPCR by targeting the nifH gene. Mean nifH concentrations (log10 copy numbers/gram algae fresh weight ± SE) were 5.54 ± 0.09, ranging from 4.31 to 6.57. Mean nifH concentrations in water samples (log10 copy numbers/milliliter of water ± SE) were: 3.25 ± 0.06, ranging from 2.41 to 3.90. Shotgun sequencing of a subset of algal samples representing the four sampling locations (N = 10) revealed as many as 267 nifH reads from among the sequences of the 10 shotgun metagenomes (averaging 27 reads per metagenome), ranging from 5 to 91 reads from Jeorse Park (September) and North Beach (September) locations. Taxonomic assignment of nifH sequences identified members from bacteria and archaea domains showing a clear separation of reads at domain and lower taxonomic levels. Bacteria were relatively more abundant than archaea. Anabaena, Bradyrhizobium, Geobacter, Methylocystis, Oscillatoria sp., and Skermanella (all bacteria), and Methanoregula, Methanothrix, and Methanosarcina (archaea) were among the nitrogen‐fixing genera identified by the MEGAN Community Edition program. Collectively, these findings show that phylogenetically diverse nitrogen‐fixing microbial communities are part of the Cladophora microbiome, likely contributing to the algal nitrogen needs.

Environmental DNA↗