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At least 1,387 records · Page 77Linked to original sources
USGS2016

Pranked by Audubon: Constantine S. Rafinesque's description of John James Audubon's imaginary Kentucky mammals

The North American naturalist Constantine S. Rafinesque spent much of the year 1818 engaged in a solo journey down the Ohio River Valley to explore parts of what was then the western United States. Along the way, he visited a number of fellow naturalists, and he spent more than a week at the Henderson, Kentucky, home of artist and ornithologist John James Audubon. During the succeeding two years, Rafinesque published descriptions of new species that resulted from his expedition, including eleven species of fishes that eventually proved to have been invented by Audubon as a prank on the credulous naturalist. Less well known are a number of “wild rats” described by Rafinesque that include one recognized species ( Musculus leucopus ) and ten other, imaginary “species” fabricated by Audubon ( Gerbillus leonurus , G. megalops , Spalax trivittata , Cricetus fasciatus , Sorex cerulescens , S. melanotis , Musculus nigricans , Lemmus albovittatus , L. talpoides , Sciurus ruber ). Rafinesque's unpublished sketches of these animals provide important insight regarding the supposed nature of the animals invented by Audubon and ultimately published by Rafinesque.

Archives of Natural History↗
USGS2020

“Mostri Marini”: Constantine S. Rafinesque's names for three of Antonino Mongitore's Sicilian whales

In 1815, the naturalist Constantine Samuel Rafinesque (1783–1840) previewed three new species of cetaceans – Delphinus dalippus , Physeter urganantus and Oxypterus mongitori – that he intended to describe from Sicily based on illustrations in Antonino Mongitore's published work Della Sicilia ricercata nelle cose più memorabili (1742–1743). Although formal descriptions of the three species were never published, Rafinesque's reference to Mongitore's illustrations made the names available by “indication”. The names, nonetheless, fell into obscurity, most likely a result of contemporary taxonomists' lack of access to Mongitore's work. Rafinesque's names remain relevant to the history of cetacean taxonomy, although they are no longer applicable. Moreover, the animals associated with these names add to the historical record of whale strandings in the Mediterranean. For these reasons, we studied the illustrations Rafinesque indicated for his cetaceans and reviewed Mongitore's accompanying text, which together provide sufficient distinctive characters that two of the three animals can be confidently identified with modern species, namely the sperm whale, Physeter catodon ( Linnaeus, 1758), and the false killer whale, Pseudorca crassidens (Owen, 1846). Had Rafinesque's name D. dalippus been recognized for what it was, it would have had priority over P. crassidens as the earliest scientific name for the false killer whale.

Archives of Natural History↗
USGS2019

One hundred pressing questions on the future of global fish migration science, conservation, and policy

Migration is a widespread but highly diverse component of many animal life histories. Fish migrate throughout the world's oceans, within lakes and rivers, and between the two realms, transporting matter, energy, and other species (e.g., microbes) across boundaries. Migration is therefore a process responsible for myriad ecosystem services. Many human populations depend on the presence of predictable migrations of fish for their subsistence and livelihoods. Although much research has focused on fish migration, many questions remain in our rapidly changing world. We assembled a diverse team of fundamental and applied scientists who study fish migrations in marine and freshwater environments to identify pressing unanswered questions. Our exercise revealed questions within themes related to understanding the migrating individual's internal state, navigational mechanisms, locomotor capabilities, external drivers of migration, the threats confronting migratory fish including climate change, and the role of migration. In addition, we identified key requirements for aquatic animal management, restoration, policy, and governance. Lessons revealed included the difficulties in generalizing among species and populations, and in understanding the levels of connectivity facilitated by migrating fishes. We conclude by identifying priority research needed for assuring a sustainable future for migratory fishes.

Frontiers in Ecology and Evolution↗
USGS2019

Overhauling ocean spatial planning to improve marine megafauna conservation

Tracking data have led to evidence-based conservation of marine megafauna, but a disconnect remains between the many thousands of individual animals that have been tracked and the use of these data in conservation and management actions. Furthermore, the focus of most conservation efforts is within Exclusive Economic Zones despite the ability of these species to move thousands of kilometres across multiple national jurisdictions. To assist the goal of the United Nations General Assembly’s recent effort to negotiate a global treaty to conserve biodiversity on the high seas, we propose the development of a new frontier in dynamic marine spatial management. We argue that a global approach combining tracked movements of marine megafauna and human activities at-sea, and using existing and emerging technologies (e.g., through new tracking devices and big data approaches) can be applied to deliver near real-time diagnostics on existing risks and threats to mitigate global risks for marine megafauna. With technology developments over the next decade expected to catalyse the potential to survey marine animals and human activities in ever more detail and at global scales, the development of dynamic predictive tools based on near real-time tracking and environmental data will become crucial to address increasing risks. Such global tools for dynamic spatial and temporal management will, however, require extensive synoptic data updates and will be dependent on a shift to a culture of data sharing and open access. We propose a global mechanism to store and make such data available in near real-time, enabling a holistic view of space use by marine megafauna and humans that would significantly accelerate efforts to mitigate impacts and improve conservation and management of marine megafauna.

Frontiers in Marine Science↗
USGS2021

Comparison of preservation and extraction methods on five taxonomically disparate coral microbiomes

All animals are host to a multitude of microorganisms that are essential to the animal’s health. Host-associated microbes have been shown to defend against potential pathogens, provide essential nutrients, interact with the host’s immune system, and even regulate mood. However, it can be difficult to preserve and obtain nucleic acids from some host-associated microbiomes, making studying their microbial communities challenging. Corals are an example of this, in part due to their potentially remote, underwater locations, their thick surface mucopolysaccharide layer, and various inherent molecular inhibitors. This study examined three different preservatives (RNAlater, DNA/RNA Shield, and liquid nitrogen) and two extraction methods (the Qiagen PowerBiofilm kit and the Promega Maxwell RBC kit with modifications) to determine if there was an optimum combination for examining the coral microbiome. These methods were employed across taxonomically diverse coral species, including deep-sea/shallow, stony/soft, and zooxanthellate/azooxanthellate: Lophelia pertusa , Paragorgia johnsoni , Montastraea cavernosa , Porites astreoides , and Stephanocoenia intersepta . Although significant differences were found between preservative types and extraction methods, these differences were subtle, and varied in nature from coral species to coral species. Significant differences between coral species were far more profound than those detected between preservative or extraction method. We suggest that the preservative types presented here and extraction methods using a bead-beating step provide enough consistency to compare coral microbiomes across various studies, as long as subtle differences in microbial communities are attributed to dissimilar methodologies. Additionally, the inclusion of internal controls such as a mock community and extraction blanks can help provide context regarding data quality, improving downstream analyses.

Frontiers in Marine Science↗
USGS2023

Monitoring population-level foraging distribution of a marine migratory species from land: Strengths and weaknesses of the isotopic approach on the Northwest Atlantic loggerhead turtle aggregation

Assessing the linkage between breeding and non-breeding areas has important implications for understanding the fundamental biology of and conserving animal species. This is a challenging task for marine species, and in sea turtles a combination of stable isotope analysis (SIA) and satellite telemetry has been increasingly used. The Northwest Atlantic (NWA) loggerhead ( Caretta caretta ) Regional Management Unit, one of the largest sea turtle populations in the world, provides an excellent opportunity to investigate key biological patterns as well as methodological aspects related to the use of stable isotopes to infer spatial distribution of turtles in foraging areas. We provide the first comprehensive assessment of the annual distribution of NWA adult female loggerheads among foraging areas and investigate the efficacy of various analytical approaches as well as the effect of sample size in these types of studies. A total of 5168 individual females were sampled from seven Management Units (MUs) between 2013-2018. We provide the first estimate of the proportion of females originating from each MU that uses each foraging area and show how this proportion varies over time. We also estimate the relative importance (in terms of number of turtles) of each foraging area to the overall loggerhead breeding aggregation nesting in Florida and in the NWA for each year of the study. The foraging area used by reproductively active females differs considerably across MUs. One of these, the Subtropical NWA, is by far the most important foraging area in terms of both number of individuals and genetic diversity, and therefore this region may be considered as a conservation priority. Through simulations, we show that limited sizes of sample groups (unknowns; training; priors) may result in false geographic differentiation and consequently mislead interpretations. We provide thresholds and methodological recommendations for future studies. This study establishes a fundamental baseline for monitoring the annual contribution of foraging area to a terrestrial-based breeding aggregation of a marine animal in a cost-effective way. This type of monitoring allows for early detection of changes in foraging distributions—a possible effect of climate change on marine ecosystems or of area-specific anthropogenic threats.

Frontiers in Marine Science↗
USGS2021

Implications of zoonoses from hunting and use of wildlife in North American arctic and boreal biomes: Pandemic potential, monitoring, and mitigation

The COVID-19 pandemic has re-focused attention on mechanisms that lead to zoonotic disease spillover and spread. Commercial wildlife trade, and associated markets, are recognized mechanisms for zoonotic disease emergence, resulting in a growing global conversation around reducing human disease risks from spillover associated with hunting, trade, and consumption of wild animals. These discussions are especially relevant to people who rely on harvesting wildlife to meet nutritional, and cultural needs, including those in Arctic and boreal regions. Global policies around wildlife use and trade can impact food sovereignty and security, especially of Indigenous Peoples. We reviewed known zoonotic pathogens and current risks of transmission from wildlife (including fish) to humans in North American Arctic and boreal biomes, and evaluated the epidemic and pandemic potential of these zoonoses. We discuss future concerns, and consider monitoring and mitigation measures in these changing socio-ecological systems. While multiple zoonotic pathogens circulate in these systems, risks to humans are mostly limited to individual illness or local community outbreaks. These regions are relatively remote, subject to very cold temperatures, have relatively low wildlife, domestic animal, and pathogen diversity, and in many cases low density, including of humans. Hence, favorable conditions for emergence of novel diseases or major amplification of a spillover event are currently not present. The greatest risk to northern communities from pathogens of pandemic potential is via introduction with humans visiting from other areas. However, Arctic and boreal ecosystems are undergoing rapid changes through climate warming, habitat encroachment, and development; all of which can change host and pathogen relationships, thereby affecting the probability of the emergence of new (and re-emergence of old) zoonoses. Indigenous leadership and engagement in disease monitoring, prevention and response, is vital from the outset, and would increase the success of such efforts, as well as ensure the protection of Indigenous rights as outlined in the United Nations Declaration on the Rights of Indigenous Peoples. Partnering with northern communities and including Indigenous Knowledge Systems would improve the timeliness, and likelihood, of detecting emerging zoonotic risks, and contextualize risk assessments to the unique human-wildlife relationships present in northern biomes.

Frontiers in Public Health↗
USGS2021

If you give a clam an estuary: The story of potamocorbula

When you look at San Francisco Bay, what animals do you see? You may see lots of fish swimming around and birds flying above. What you DON’T see is Potamocorbula, a little clam that has had a big impact. Many years ago, ships accidentally brought Potamocorbula into the Bay. Pretty soon, Potamocorbula spread out all over in large numbers! Clams pump water over their gills and eat small particles of food, like phytoplankton, that pass through with the water. Potamocorbula can pump water much faster than other clams that live in the Bay, and they can eat more than their share of phytoplankton. Sometimes Potamocorbula eats phytoplankton faster than phytoplankton can grow! What problems does that cause for other animals, like birds and fish, that also need phytoplankton? Does Potamocorbula’s invasion only have negative impacts? In this article, we dive to the bottom of the Bay to find some answers. Book series publishing the chapter: https://kids.frontiersin.org/collection/13528/where-the-river-meets-the-ocean-stories-from-san-francisco-estuary

California↗
USGS2018

Bovine tuberculosis management in northwest Minnesota and implications of the Risk Information Seeking and Processing (RISP) model for wildlife disease management

Bovine tuberculosis (bTB) is an infectious, zoonotic disease caused by Mycobacterium bovis that can spread between domestic and wild animals, as well as to humans. The disease is characterized by the progressive development of lesions that compromise the victim's lungs and lymph system. The disease was first identified in northwest Minnesota in both cattle and white-tailed deer ( Odocoileus virginianus ) in 2005. Due to its risks to human and animal health, bTB has numerous implications related to population management, policy outcomes, stakeholder relations, and economic impacts. When dealing with complicated risks, like bTB, individuals often seek out and process information as a method to learn about, and cope, with the risk. We developed a questionnaire that adapted components of the Risk Information Seeking and Processing (RISP) model and surveyed northwest Minnesota deer hunters. Our objectives were to better understand how stakeholders perceive and act on information regarding disease management in wildlife and to understand the utility of the RISP model for such management contexts. We drew a random proportional sample of licensed deer hunters ( n = 2100) from the area affected by bTB and conducted a multi-contact mail survey. We found that 43% of the variability in the information-seeking behaviors of respondents was explained by demographics, hunting importance, personal risk perceptions, attitudes, and subjective norms. However, these results are largely attributable to the factors in the RISP model encompassed by components of the Theory of Planned Behavior (i.e., attitudes, subjective norms, perceived behavioral control, and behavioral intentions). This information can help managers contextualize individuals' perceived risks to better frame communication efforts to address stakeholder concerns and develop best practices for disease communication. While the state of Minnesota is currently considered free of bTB, future outbreaks remain possible in Minnesota and elsewhere. Understanding the key factors in the processes through which deer hunters seek out information pertaining to the disease can help managers collect the data necessary to aid decisions about desired future management outcomes. In addition, testing RISP model performance in applied research improves its future use across a broad spectrum of topics throughout veterinary disease management.

Minnesota↗
USGS2024

Prion seeding activity in plant tissues detected by RT-QuIC

Prion diseases such as scrapie, bovine spongiform encephalopathy (BSE), and chronic wasting disease (CWD) affect domesticated and wild herbivorous mammals. Animals afflicted with CWD, the transmissible spongiform encephalopathy of cervids (deer, elk, and moose), shed prions into the environment, where they may persist and remain infectious for years. These environmental prions may remain in soil, be transported in surface waters, or assimilated into plants. Environmental sampling is an emerging area of TSE research and can provide more information about prion fate and transport once shed by infected animals. In this study, we have developed the first published method for the extraction and detection of prions in plant tissue using the real-time quaking-induced conversion (RT-QuIC) assay. Incubation with a zwitterionic surfactant followed by precipitation with sodium phosphotungstate concentrates the prions within samples and allows for sensitive detection of prion seeding activity. Using this protocol, we demonstrate that prions can be detected within plant tissues and on plant surfaces using the RT-QuIC assay.

Pathogens↗
USGS2020

Comparative performance and trend of remotely sensed phenology and productivity metrics across the Western United States

Vegetation phenology and productivity play a crucial role in surface energy balance, plant and animal distribution, and animal movement and habitat use and can be measured with remote sensing metrics including start of season (SOS), peak instantaneous rate of green-up date (PIRGd), peak of season (POS), end of season (EOS), and integrated vegetation indices. However, for most metrics, we do not yet understand the agreement of remotely sensed data products with near-surface observations. We also need summaries of changes over time, spatial distribution, variability, and consistency in remote sensing dataset metrics for vegetation timing and quality. We compare metrics from 10 leading remote sensing datasets against a network of PhenoCam near-surface cameras throughout the western United States from 2002 to 2014. Most phenology metrics representing a date (SOS, PIRGd, POS, and EOS), rather than a duration (length of spring, length of growing season), better agreed with near-surface metrics but results varied by dataset, metric, and land cover, with absolute value of mean bias ranging from 0.38 (PIRGd) to 37.92 days (EOS). Datasets had higher agreement with PhenoCam metrics in shrublands, grasslands, and deciduous forests than in evergreen forests. Phenology metrics had higher agreement than productivity metrics, aside from a few datasets in deciduous forests. Using two datasets covering the period 1982–2016 that best agreed with PhenoCam metrics, we analyzed changes over time to growing seasons. Both datasets exhibited substantial spatial heterogeneity in the direction of phenology trends. Variability of metrics increased over time in some areas, particularly in the Southwest. Approximately 60% of pixels had consistent trend direction between datasets for SOS, POS, and EOS, with the direction varying by location. In all ecoregions except Mediterranean California, EOS has become later. This study comprehensively compares remote sensing datasets across multiple growing season metrics and discusses considerations for applied users to inform their data choices. des indicators of vegetation timing and quality through metrics such as start of season (SOS), peak instantaneous rate of green-up date (PIRGd), peak of season (POS), end of season (EOS), and integrated vegetation indices. Few comparisons guide users in dataset selection, examine a large spatial extent, and include multiple metrics. This study compares metrics from 10 leading remote sensing datasets against a network of PhenoCam near-surface cameras throughout the Western United States from 2002-2014. Correlation (R2) and mean bias varied substantially by dataset, metric, and land cover. The closest association with PhenoCam measured phenology metrics represented a date (SOS, PIRGd, POS, and EOS) rather than a duration (length of spring, length of growing season), with R2 of individual datasets ranging from 0.03 (SOS) – 0.55 (PIRGd), and absolute value of mean bias ranging from 0.38 (PIRGd) – 37.92 days (EOS). Datasets had higher agreement with PhenoCam metrics in shrublands, grasslands, and deciduous/broadleaf forests than in evergreen forests. Productivity metrics agreed worse than phenology metrics, though some datasets showed high correlations in deciduous/broadleaf forests. Using the two datasets that agreed best with PhenoCam metrics and covered 1982-2016, we conducted a trend analysis to study changes to growing seasons. Trends in phenology exhibited substantial spatial heterogeneity in the direction of trend for both datasets. Variability of metrics increased over time in some areas, particularly in the Southwest. Approximately 60% of pixels had consistent trend direction (both earlier and later) for SOS, POS, and EOS. In all ecoregions except Mediterranean California EOS trended toward a later date. This study provides a comprehensive comparison of remote sensing datasets across many important phenology and productivity metrics and discusses considerations for users to make informed decisions about their data choices.

Arizona, California, Colorado, Idaho, Montana, New↗
USGS2014

Changes in vegetation and biological soil crust communities on sand dunes stabilizing after a century of grazing on San Miguel Island, Channel Island National Park, California

San Miguel Island is the westernmost of the California Channel Islands and one of the windiest areas on the west coast of North America. The majority of the island is covered by coastal sand dunes, which were stripped of vegetation and subsequently mobilized due to droughts and sheep ranching during the late 19th century and early 20th century. Since the removal of grazing animals, vegetation and biological soil crusts have once again stabilized many of the island's dunes. In this study, historical aerial photographs and field surveys were used to develop a chronosequence of the pattern of change in vegetation communities and biological soil crust levels of development (LOD) along a gradient of dune stabilization. Historical aerial photographs from 1929, 1954, 1977, and 2009 were georeferenced and used to delineate changes in vegetation canopy cover and active (unvegetated) dune extent among 5 historical periods (pre-1929, 1929–1954, 1954–1977, 1977–2009, and 2009–2011). During fieldwork, vegetation and biological soil crust communities were mapped along transects distributed throughout San Miguel Island's central dune field on land forms that had stabilized during the 5 time periods of interest. Analyses in a geographic information system (GIS) quantified the pattern of changes that vegetation and biological soil crust communities have exhibited on the San Miguel Island dunes over the past 80 years. Results revealed that a continuing increase in total vegetation cover and a complex pattern of change in vegetation communities have taken place on the San Miguel Island dunes since the removal of grazing animals. The highly specialized native vascular vegetation (sea rocket, dunedelion, beach-bur, and locoweed) are the pioneer stabilizers of the dunes. This pioneer community is replaced in later stages by communities that are dominated by native shrubs (coastal goldenbush, silver lupine, coyote-brush, and giant coreopsis), with apparently overlapping or cyclical succession pathways. Many of the dunes that have been stabilized the longest (since before 1929) are dominated by exotic grasses. Stands of biological soil crusts (cyanobacteria) are found only on dunes where vascular vegetation is already present. Biological soil crusts are not found on dunes exhibiting a closed vascular plant canopy, which may indicate that the role of soil crusts in dune stabilization on the island is transitory. Particle-size analyses of soil samples from the study area reveal that higher biological soil crust LOD is positively correlated with increasing fine grain content. The findings indicate that changes in vegetation communities may be the most rapid at earlier and later stages of dune stabilization and that regular monitoring of dunes may help to identify the interactions between vegetation and soil crusts, as well as the potential transitions between native and exotic plant communities.

California↗
USGS2018

Malassezia vespertilionis sp. nov.: A new cold-tolerant species of yeast isolated from bats

Malassezia is a genus of medically-important, lipid-dependent yeasts that live on the skin of warm-blooded animals. The 17 described species have been documented primarily on humans and domestic animals, but few studies have examined Malassezia species associated with more diverse host groups such as wildlife. While investigating the skin mycobiota of healthy bats, we isolated a Malassezia sp. that exhibited only up to 92 % identity with other known species in the genus for the portion of the DNA sequence of the internal transcribed spacer region that could be confidently aligned. The Malassezia sp. was cultured from the skin of nine species of bats in the subfamily Myotinae ; isolates originated from bats sampled in both the eastern and western United States. Physiological features and molecular characterisation at seven additional loci (D1/D2 region of 26S rDNA, 18S rDNA, chitin synthase, second largest subunit of RNA polymerase II, β-tubulin, translation elongation factor EF-1α, and minichromosome maintenance complex component 7) indicated that all of the bat Malassezia isolates likely represented a single species distinct from other named taxa. Of particular note was the ability of the Malassezia sp. to grow over a broad range of temperatures (7–40 °C), with optimal growth occurring at 24 °C. These thermal growth ranges, unique among the described Malassezia , may be an adaptation by the fungus to survive on bats during both the host's hibernation and active seasons. The combination of genetic and physiological differences provided compelling evidence that this lipid-dependent yeast represents a novel species described herein as Malassezia vespertilionis sp. nov. Whole genome sequencing placed the new species as a basal member of the clade containing the species M. furfur , M. japonica , M. obtusa , and M. yamatoensis . The genetic and physiological uniqueness of Malassezia vespertilionis among its closest relatives may make it important in future research to better understand the evolution, life history, and pathogenicity of the Malassezia yeasts.

Persoonia - Molecular Phylogeny and Evolution of F↗
USGS2023

Wild rodents harbor high diversity of Arthroderma

Arthroderma is the most diverse genus of dermatophytes, and its natural reservoir is considered to be soil enriched by keratin sources. During a study on the diversity of dermatophytes in wild small rodents in the Czech Republic, we isolated several strains of Arthroderma . To explore the diversity and ecological significance of these isolates from rodents (n = 29), we characterised the strains genetically (i.e., sequenced ITS, tubb and tef1α ), morphologically, physiologically, and by conducting mating experiments. We then compared the rodent-derived strains to existing ITS sequence data from GenBank and the GlobalFungi Database to further investigate biogeography and the association of Arthroderma species with different types of environments. In total, eight Arthroderma species were isolated from rodents, including four previously described species ( A. crocatum , A. cuniculi , A. curreyi , A. quadrifidum ) and four new species proposed herein, i.e., A. rodenticum , A. simile , A. zoogenum and A. psychrophilum . The geographical distribution of these newly described species was not restricted to the Czech Republic nor rodents. Additional isolates were obtained from bats and other mammals, reptiles, and soil from Europe, North America, and Asia. Data mining showed that the genus has a diverse ecology, with some lineages occurring relatively frequently in soil, whereas others appeared to be more closely associated with live animals, as we observed in A. rodenticum . Low numbers of sequence reads ascribed to Arthroderma in soil show that the genus is rare in this environment, which supports the hypothesis that Arthroderma spp. are not soil generalists but rather strongly associated with animals and keratin debris. This is the first study to utilise existing metabarcoding data to assess biogeographical, ecological, and diversity patterns in dermatophytes.

Persoonia - Molecular Phylogeny and Evolution of F↗
USGS2011

Rapid diagnosis of avian influenza virus in wild birds: Use of a portable rRT-PCR and freeze-dried reagents in the field

Wild birds have been implicated in the spread of highly pathogenic avian influenza (HPAI) of the H5N1 subtype, prompting surveillance along migratory flyways. Sampling of wild birds for avian influenza virus (AIV) is often conducted in remote regions, but results are often delayed because of the need to transport samples to a laboratory equipped for molecular testing. Real-time reverse transcriptase polymerase chain reaction (rRT-PCR) is a molecular technique that offers one of the most accurate and sensitive methods for diagnosis of AIV. The previously strict lab protocols needed for rRT-PCR are now being adapted for the field. Development of freeze-dried (lyophilized) reagents that do not require cold chain, with sensitivity at the level of wet reagents has brought on-site remote testing to a practical goal. Here we present a method for the rapid diagnosis of AIV in wild birds using an rRT-PCR unit (Ruggedized Advanced Pathogen Identification Device or RAPID, Idaho Technologies, Salt Lake City, UT) that employs lyophilized reagents (Influenza A Target 1 Taqman; ASAY-ASY-0109, Idaho Technologies). The reagents contain all of the necessary components for testing at appropriate concentrations in a single tube: primers, probes, enzymes, buffers and internal positive controls, eliminating errors associated with improper storage or handling of wet reagents. The portable unit performs a screen for Influenza A by targeting the matrix gene and yields results in 2-3 hours. Genetic subtyping is also possible with H5 and H7 primer sets that target the hemagglutinin gene. The system is suitable for use on cloacal and oropharyngeal samples collected from wild birds, as demonstrated here on the migratory shorebird species, the western sandpiper (Calidrus mauri) captured in Northern California. Animal handling followed protocols approved by the Animal Care and Use Committee of the U.S. Geological Survey Western Ecological Research Center and permits of the U.S. Geological Survey Bird Banding Laboratory. The primary advantage of this technique is to expedite diagnosis of wild birds, increasing the chances of containing an outbreak in a remote location. On-site diagnosis would also prove useful for identifying and studying infected individuals in wild populations. The opportunity to collect information on host biology (immunological and physiological response to infection) and spatial ecology (migratory performance of infected birds) will provide insights into the extent to which wild birds can act as vectors for AIV over long distances.

Journal of Visualized Experiments↗
USGS2003

Exopolymer microenvironments of microbial flora: Multiple and interactive effects on trophic relationships

Microbial cells in natural environments are often encased in different types of exopolymer secretions (EPS), ranging from tight capsules surrounding individual cells to the looser slime matrices of biofilms. The different physical and chemical properties of exopolymers could have secondary effects on trophic interactions between microbial cells and consumer animals. Laboratory studies showed that capsule EPS is significantly less digestible to consumers than slime EPS, even when extracted from the same bacterial strain. Bacterial cells with EPS capsules are less efficiently digested than noncapsuled cells, suggesting that capsules protect against digestion. Follow-up experiments determined that polysaccharide-rich fractions of slime EPS are absorbed with very high efficiencies while protein portions, which are more abundant in capsular polymers, are absorbed relatively poorly. Another series of experiments showed that dissolved organic matter (DOM), when adsorbed directly to the mineralogical portions of sediment particles, is available to deposit feeders. However, the further presence of an exopolymer coating on sediments more than doubled the bioavailability of adsorbed DOM to the consumer. Observations using cold-stage scanning electron microscopy indicated that exopolymer microenvironments are a common feature of natural marine sediments. Microbial exopolymers range from easily digestible carbon sources to relatively refractory ones that effectively protect some microbial cells from consumer digestion. Exopolymer microenvironments may also make recently adsorbed DOM highly accessible to particle-ingesting animals.

Limnology and Oceanography↗
USGS2012

Telemetry techniques: A user guide for fisheries research

Telemetry provides a powerful and flexible tool for studying fish and other aquatic animals, and its use has become increasingly commonplace. However, telemetry is gear intensive and typically requires more specialized knowledge and training than many other field techniques. As with other scientific methods, collecting good data is dependent on an understanding of the underlying principles behind the approach, knowing how to use the equipment and techniques properly, and recognizing what to do with the data collected. This book provides a road map for using telemetry to study aquatic animals, and provides the basic information needed to plan, implement, and conduct a telemetry study under field conditions. Topics include acoustic or radio telemetry study design, tag implantation techniques, radio and acoustic telemetry principles and case studies, and data management and analysis. Chapters are written by biologists, technicians, and engineers from the private, academic, and government sectors, with decades of experience using these technologies.

Book↗
USGS2012

Introduction

elemetry provides a powerful and flexible tool for studying aquatic animals, making it possible to repeatedly locate and identify individuals in remote or inaccessible settings—a task that would be difficult (if not impossible) to accomplish using other methods. The use of telemetry has increased dramatically in recent years, and its application is limited only by the capabilities of the equipment and the researcher’s imagination. In spite of these advantages, telemetry is equipment-intensive and generally requires more specialized knowledge and training than many other field techniques. The electronic equipment associated with its use can often dazzle, intimidate, and confuse those just starting out. Even experienced users are often hard-pressed to keep up with the technological advances. Answers to such basic questions as “what equipment do I need?” or “how do I get started?” are not always evident or straightforward. These are valid concerns, since the equipment and methods used can affect the success of the study and the quality of information collected. The purpose of this book is to provide a guide for using telemetry to study aquatic animals—call it a user’s manual or Telemetry 101. Our principal intent is to provide the basic information to plan, implement, and conduct telemetry studies under field conditions. Considerations related to data collection and interpretations are also discussed. As with any scientific procedure, collecting usable information and accurately interpreting study results depends on an understanding of the underlying principles of the methods used. A wide range of telemetry equipment and field techniques are available. Clearly defined research objectives and knowledge of the various options, capabilities, and limitations of the equipment and methods is essential for developing projects that effectively address the research or management questions being asked. Telemetry is a tool, and like any tool it will only function effectively when used properly.

Book chapter↗