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USGS2003

USGS Alaska Tissue Archival Projects: An update on FY02 activities

The banking of environmental specimens under cryogenic conditions for future retrospective analysis has been recognized for many years as an important part of environmental monitoring programs. Since 1987, the Alaska Marine Mammal Tissue Archival Project (AMMTAP) has been collecting tissue samples from marine mammals for archival in the National Biomonitoring Specimen Bank (NBSB) at the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland, USA. The USGS, Alaska Biological Science Center (ABSC), the NOAA Fisheries, Office of Protected Resources (NMFS), and the NIST conduct this partnership project, which began under the Mineral Management Service (MMS) Outer Continental Shelf Environmental Assessment Program. MMS remains the primary client agency for the AMMTAP providing programmatic guidance and review. The purpose of the project is to collect tissue samples from Alaska marine mammals and to store these specimens under the best conditions so that they can be analyzed for environmental contaminants and other constituents. A substantial part of the sample collection is from Arctic species and, since most of the animals sampled are from Alaska Native subsistence harvests, the project relies on cooperation and collaboration with several Alaska Native organizations and local governmental agencies. Although a substantial amount of recent research has been conducted on contaminants in Alaskan marine mammals, few data exists on colonial seabirds nesting in Alaska. Like marine mammals, seabirds are an important group of upper trophic level marine organisms with a potential for accumulating lipophilic contaminants and are identified by MMS as species of interest for monitoring activities. More than 95% of the seabirds breeding in the continental United States nest at colonies in the Bering and Chukchi seas and Gulf of Alaska (see USFWS 1992). Realizing the value of colonial seabirds in environmental monitoring and the lack of recent data from Alaskan seabird colonies, the U.S. Fish and Wildlife Service Alaska Maritime National Wildlife Refuge (USFWS-AMNWR), the U.S. Geological Survey Biological Resources Division (USGS-BRD), and the National Institute of Standards and Technology (NIST) initiated the Seabird Tissue Archival and Monitoring Project (STAMP) in 1998. The project was designed as a 100-year-long program to monitor long-term trends in environmental quality by collecting eggs at nesting colonies using standardized protocols, banking the egg contents under conditions that ensure chemical stability during long-term (decadal) storage, and analyzing subsamples of the stored material to establish baseline levels for persistent bioaccumulative contaminants (e.g., chlorinated pesticides, PCBs, mercury).

Conference Paper↗

USGS2005

Gulf of Mexico Integrated Science - Tampa Bay Study: Examining the Impact of Urbanization on Seafloor Habitats

Seafloor habitats, such as seagrass beds, provide essential habitat for fish and marine mammals. For many years, the study of seagrass vitality has been a priority for scientists and resource managers working in Tampa Bay. Seafloor habitats are extremely sensitive to changes in water quality. Like a canary in a coal mine, seagrass can serve as an ecological indicator of estuary health. Between the 1940s and the 1970s, seagrass gradually died in Tampa Bay. This loss has been attributed to a rise in urbanization and an increase in nutrient loading into the bay. Better treatment of industrial wastewater and runoff beginning in the 1980s resulted in the continuous recovery of seagrass beds. However, in the mid-1990s, the recovery began to level off in areas where good water quality was expected to support continued seagrass recovery, demonstrating that nutrient loading may be only one factor impacting seagrass health. Researchers now are trying to determine what might be affecting the recovery of seagrass in these areas. Currently, little is understood about the effects that other aspects of urbanization and natural change, such as groundwater and sediment quality, might have on seagrass vitality. This segment of the Tampa Bay integrated science study is intended to identify, quantify, and develop models that illustrate the impact that urbanization may have on seafloor habitat distribution, health, and restoration.

Open-File Report↗

USGS2012

2008 Joint United States-Canadian program to explore the limits of the Extended Continental Shelf aboard the U.S. Coast Guard cutter Healy --Cruise HLY0806

In September 2008, the U.S. Geological Survey (USGS), in cooperation with Natural Resources Canada, Geological Survey of Canada (GSC), conducted bathymetric and geophysical surveys in the Arctic Beaufort Sea aboard the U.S. Coast Guard cutter USCGC Healy . The principal objective of this mission to the high Arctic was to acquire data in support of delineation of the outer limits of the U.S. and Canadian Extended Continental Shelf (ECS) in the Arctic Ocean in accordance with the provisions of Article 76 of the Law of the Sea Convention. The Healy was accompanied by the Canadian Coast Guard icebreaker Louis S. St- Laurent . The science parties on the two vessels consisted principally of staff from the USGS ( Healy ), and the GSC and the Canadian Hydrographic Service ( Louis ). The crew included marine mammal and Native-community observers, ice observers, and biologists conducting research of opportunity in the Arctic Ocean. The joint survey proved an unqualified success. The Healy collected 5,528 km of swath (multibeam) bathymetry (38,806 km 2 ) and CHIRP subbottom profile data, with accompanying marine gravity measurements. The Louis acquired 2,817 km of multichannel seismic (airgun) deep-penetration reflection-profile data along 12 continuous lines, as well as 35 sonobuoy refraction stations and accompanying single-beam bathymetry. The coordinated efforts of the two vessels resulted in seismic-reflection profile data of much higher quality and continuity than if the data had been acquired with a single vessel alone. Equipment failure rate of the seismic equipment gear aboard the Louis was greatly improved with the advantage of having a leading icebreaker. When ice conditions proved too severe to deploy the seismic system, the Louis led the Healy , resulting in much improved quality of the swath bathymetry and CHIRP sub-bottom data in comparison with data collected by the Healy in the lead or working alone. Ancillary science objectives, including ice observations, deployment of ice-monitoring buoys and water-column sampling for biologic (phytoplankton) studies, were also successfully accomplished.

Open-File Report↗

USGS2009

Satellite telemetry of marine megavertebrates: The coming of age of an experimental science

Wildlife telemetry research has expanded greatly in the last 2 decades, with the application of satellite tracking and archival logging technologies to study the ecology and conservation of marine mammals, birds, fishes, and turtles. Widespread and expanding use of satellite tracking to study movements and habitats of marine megavertebrates warrants a review of progress to date and a discussion of challenges facing this rapidly evolving research field. To this end, we reviewed the satellite telemetry literature of air-breathing marine taxa (i.e. birds, mammals, turtles) over the 20 yr time period from 1987 to 2006. This review yielded 92 studies with a wide taxonomic representation: 47 seabirds, 23 sea turtles, and 22 marine mammals. Here we critically evaluate these articles to assess progress in satellite tracking of marine megavertebrates in terms of (1) objectives and approach, (2) experimental design, and (3) reporting of results. The overall trends revealed increases in the duration and scope of tracking studies, yet improvements on experimental design and reporting are needed to facilitate comparisons across studies and species. While inherent ecological differences influence the focus and methods of taxon-specific studies, this review highlights specific areas in need of improvement and provides general suggestions for future tracking studies of marine megavertebrates.

Endangered Species Research↗

USGS2016

Toward a national animal telemetry network for aquatic observations in the United States

Animal telemetry is the science of elucidating the movements and behavior of animals in relation to their environment or habitat. Here, we focus on telemetry of aquatic species (marine mammals, sharks, fish, sea birds and turtles) and so are concerned with animal movements and behavior as they move through and above the world’s oceans, coastal rivers, estuaries and great lakes. Animal telemetry devices (“tags”) yield detailed data regarding animal responses to the coupled ocean–atmosphere and physical environment through which they are moving. Animal telemetry has matured and we describe a developing US Animal Telemetry Network (ATN) observing system that monitors aquatic life on a range of temporal and spatial scales that will yield both short- and long-term benefits, fill oceanographic observing and knowledge gaps and advance many of the U.S. National Ocean Policy Priority Objectives. ATN has the potential to create a huge impact for the ocean observing activities undertaken by the U.S. Integrated Ocean Observing System (IOOS) and become a model for establishing additional national-level telemetry networks worldwide.

Animal Biotelemetry↗

USGS2022

Harnessing island–ocean connections to maximize marine benefits of island conservation

Islands support unique plants, animals, and human societies found nowhere else on the Earth. Local and global stressors threaten the persistence of island ecosystems, with invasive species being among the most damaging, yet solvable, stressors. While the threat of invasive terrestrial mammals on island flora and fauna is well recognized, recent studies have begun to illustrate their extended and destructive impacts on adjacent marine environments. Eradication of invasive mammals and restoration of native biota are promising tools to address both island and ocean management goals. The magnitude of the marine benefits of island restoration, however, is unlikely to be consistent across the globe. We propose a list of six environmental characteristics most likely to affect the strength of land–sea linkages: precipitation, elevation, vegetation cover, soil hydrology, oceanographic productivity, and wave energy. Global databases allow for the calculation of comparable metrics describing each environmental character across islands. Such metrics can be used today to evaluate relative potential for coupled land–sea conservation efforts and, with sustained investment in monitoring on land and sea, can be used in the future to refine science-based planning tools for integrated land–sea management. As conservation practitioners work to address the effects of climate change, ocean stressors, and biodiversity crises, it is essential that we maximize returns from our management investments. Linking efforts on land, including eradication of island invasive mammals, with marine restoration and protection should offer multiplied benefits to achieve concurrent global conservation goals.

PNAS↗

USGS1984

Distribution and abundance of manatees along the northern coast of the Gulf of Mexico

A review of historical and recent records of manatee ( Trichechus manatus ) sightings along the coast of the northern Gulf of Mexico indicates that their numbers have declined in Texas, but increased in Louisiana and Mississippi. This is due to their extirpation in Mexico and dramatic increase along the southern Big Bend coast of northwestern peninsular Florida. The distribution of manatees along the southern Big Bend coast is related to their need for warm water and the distribution of fresh water and submerged aquatic and marine food plants. The spring-fed headwaters of Crystal and Homosassa rivers are important warm water winter refuges; nearly 90% of the same individuals return each winter. The estuaries and grass beds associated with these two rivers and the Suwannee, Withlacoochee, and Chasshowitzka rivers are the principal summer habitats. The Suwannee and Crystal rivers are "high-use" rivers, whereas the other three are "low-use" rivers. Low human-caused mortality, high fecundity, some immigration, and high site fidelity are responsible for the increasing numbers of manatees using the southern Big Bend coast. Since this region of Florida has experienced relatively little development compared with the rest of the state, the best long-term future for this endangered marine mammal in the United States lies along the southern Big Bend coast.

Alabama, Florida, Louisiana, Mississippi, Texas↗

USGS2017

Biological and ecological science for Florida—The Sunshine State

Florida is rich in sunshine and other natural resources essential to the State's economy. More than 100 million tourists visit Florida's beaches, wetlands, forests, oceans, lakes, and streams where they generate billions of dollars and sustain more than a million jobs. Florida also provides habitat for several thousand freshwater and marine fish, mammals, birds, and other wildlife that are viewed, hunted, or fished, or that provide valuable ecological services. Fertile soils and freshwater supplies support agriculture and forest industries and generate more than $8 billion of revenue annually and sustain thousands of jobs.

Florida↗

USGS2021

Genetics as a tool for conservation and management of West Indian manatee populations in Brazil

A study conducted by the National Center for Research and Conservation of Aquatic Mammals (CMA), United States Geological Survey Wetland and Aquatic Research Center, and partner researchers found that the marine Antillean manatee ( Trichechus manatus manatus ) has low genetic diversity in regions where there are territorial interfaces with the Amazonian manatee ( Trichechus inunguis ). The study was published as an article in the journal, Frontiers in Marine Science.

Sirenews↗

USGS2026

Agency approach to allocation of human capital and program composition for human-marine mammal interaction management in the United States

Introduction: Marine mammals have served important and diverse roles throughout human history. Once exploited to near extinction, many species in the United States (U.S.) have recovered dramatically under the Marine Mammal Protection Act (MMPA). The U.S. National Marine Fisheries Service (NMFS) has jurisdiction to administer the MMPA for cetaceans and most pinnipeds. While most take is now prohibited, NMFS still dedicates significant time and resources to protecting and conserving marine mammals. As human populations continue to grow and exploit marine environments, opportunities for human-marine mammal interactions (HMMI) have increased. Resources may fail to keep up with growing needs for conservation investments, so that many agencies struggle to adequately meet social and legal requirements. Methods: This study evaluated NMFS’ approach to addressing HMMI through a mixed-methods (semi-structured interviews, quantitative questionnaire, and facilitated workshops) expert elicitation analysis of resource allocation (i.e., staff time) and priorities of NMFS Science Center (SC) and Regional Office (RO) staff across five geographic regions to understand how employee time is allocated, the degree to which employee time allocation is aligned with self-reported job descriptions, and employee perceptions of actions or investments which would improve their ability to mitigate HMMI. Results and Discussion: SC staff reported spending more time on Biological and Administrative tasks , while RO staff allocated more time to Policy, Social science , and Outreach tasks . SC employees spent less time on Biological tasks than specified by their perceived job descriptions, suggesting resource constraints. Participants identified Biological research and monitoring as top priorities, followed by Policy tasks . Identified actions included increasing research capacity, enhancing enforcement, expanding social science expertise, and improving outreach programs. The study reveals mismatches between mandated activities and available resources, suggesting strategic reallocation or increased funding may benefit the agency in effectively addressing growing HMMI challenges.

Frontiers in Marine Science↗

USGS2002

Persistent organochlorine pollutants in ringed seals and polar bears collected from northern Alaska

Blubber samples from ringed seal (Phoca hispida; n=8) and polar bear subcutaneous fat (Ursus maritimus; n=5) were collected near Barrow, Alaska in 1996 as part of the Alaska Marine Mammal Tissue Archival Project (AMMTAP) and retained in the National Biomonitoring Specimen Bank at the National Institute of Standards and Technology in Gaithersburg, Maryland (USA). The samples were analyzed for a variety of persistent organochlorine pollutants (POPs) including polychlorinated biphenyls (PCBs), hexachlorocyclohexanes (HCHs), chlordane and metabolites, hexachlorobenzene (HCB) and DDTs and metabolites. The geometric mean, on a wet mass basis, of ??PCBs (sum of 29 congeners and congener groups) were 732??282 ng/g (1 S.D.) in seals and 3395??1442 ng/g in polar bears. The geometric mean of ??DDTs, ??HCHs (??-, ??- and ??- HCH) and HCB concentrations (wet mass basis) in seals and bears were 562??261 ng/g vs. 74.8??39 ng/g, 380??213 ng/g vs. 515 ng/g, and 17.4??10.1 ng/g vs. 183??153 ng/g, respectively. The geometric mean sum of chlordane (??chlordane, sum of cis- and trans-chlordane, cis- and trans-nonachlor, oxychlordane and heptachlor epoxide) and dieldrin concentrations in ringed seals and polar bears were 753??617 ng/g vs. 720??315 ng/g and 38.6??22.8 ng/g vs. 130??65 ng/g, respectively. Apparent bioaccumulation factors (polar bear/ringed seal POP concentrations) were lower in the animals sampled near Barrow, Alaska than in those from locations in the Canadian Arctic. This suggests that polar bears are also preying on marine mammals from lower trophic levels than the ringed seals with correspondingly lower organochlorine levels, such as bowhead whale carcasses. PCB congener patterns in the samples demonstrated the metabolism of certain PCB congeners in the polar bear relative to the ringed seal in agreement with previous studies. Regional comparisons of animals collected in Alaska and Arctic Canada are presented. Copyright ?? 2002 Elsevier Science B.V.

Science of the Total Environment↗

USGS2022

Categorizing active marine acoustic sources based on their potential to affect marine animals

Marine acoustic sources are widely used for geophysical imaging, oceanographic sensing, and communicating with and tracking objects or robotic vehicles in the water column. Under the U.S. Marine Mammal Protection Act and similar regulations in several other countries, the impact of controlled acoustic sources is assessed based on whether the sound levels received by marine mammals meet the criteria for harassment that causes certain behavioral responses. This study describes quantitative factors beyond received sound levels that could be used to assess how marine species are affected by many commonly deployed marine acoustic sources, including airguns, high-resolution geophysical sources (e.g., multibeam echosounders, sidescan sonars, subbottom profilers, boomers, and sparkers), oceanographic instrumentation (e.g., acoustic doppler current profilers, split-beam fisheries sonars), and communication/tracking sources (e.g., acoustic releases and locators, navigational transponders). Using physical criteria about the sources, such as source level, transmission frequency, directionality, beamwidth, and pulse repetition rate, we divide marine acoustic sources into four tiers that could inform regulatory evaluation. Tier 1 refers to high-energy airgun surveys with a total volume larger than 1500 in 3 (24.5 L) or arrays with more than 12 airguns, while Tier 2 covers the remaining low/intermediate energy airgun surveys. Tier 4 includes most high-resolution geophysical, oceanographic, and communication/tracking sources, which are considered unlikely to result in incidental take of marine mammals and therefore termed de minimis . Tier 3 covers most non-airgun seismic sources, which either have characteristics that do not meet the de minimis category (e.g., some sparkers) or could not be fully evaluated here (e.g., bubble guns, some boomers). We also consider the simultaneous use of multiple acoustic sources, discuss marine mammal field observations that are consistent with the de minimis designation for some acoustic sources, and suggest how to evaluate acoustic sources that are not explicitly considered here.

Journal of Marine Science and Engineering↗

USGS2026

Vessel surveys for marine birds in the Gulf of America (Gulf of Mexico): Protocol manual (2017–2025)

This manual provides contextual background and detailed instructions for survey procedures that were used to collect, enter, archive, and analyze digitally-entered field data collected for marine birds during three large-vessel survey projects in the northern Gulf of America (also Gulf of Mexico, hereafter “Gulf”). Projects using this protocol included the Gulf of Mexico Marine Assessment Program for Protected Species (GoMMAPPS: 2017-2018), the Vessel Surveys for Abundance and Distribution of Marine Mammals and Seabirds (VSAD: 2023-2024), and certain repositioning legs of the Atlantic Marine Assessment Program for Protected Species (AMAPPS: 2021, 2023). Based substantially on Ballance and Force (2011), the protocol used in the Gulf is based on a standardized 300 m wide strip transect using software architecture available in program SeeBird (v.4.3.7), a data collection program developed by Robert Holland at the National Oceanic and Atmospheric Administration (NOAA) Southwest Fisheries Science Center, La Jolla, CA. Survey protocols relied on the digital entering of standardized metadata linked to sightings of seabirds (e.g., species, number, location, distance bin, association[s], behavior, flight direction, flight height, angle from ship, age, sex, plumage, and optional comments) as well as other protected species. SeeBird has additional modules that may be used to input data on mixed-species seabird flocks and flying fish (only the latter was used in the Gulf). SeeBird includes “user-driven” commands issued through the keyboard, touch screen, and/or mouse, many of which are aided by drop-down menus that prompt the user options that are available for input. In addition, the program features “event–driven” inputs updated at intervals selected by the user, and that also record exact time and location of such edits. We describe how SeeBird was adapted in the Gulf both to run directly via serial connections from the ship’s navigation system and to operate independently from the ship through a satellite-derived GPS feed. This user manual also gives information about: procedures used to document flying fish abundance on Gulf surveys; how to use the Beaufort scale for standardizing wind force and sea state environmental conditions; how to make and use a hand-held rangefinder for delimiting strip transect bin distances; additional functionalities in SeeBird for which user guides are not available; file-naming, file-archiving, and file location conventions used on Gulf marine bird surveys; protocols used in the Gulf for describing relative abundance of the macro-alga Sargassum as an environmental covariate; the standardized four-letter taxa codes (summarized in a SpeciesCode.txt file) used in the Gulf for denoting species, other taxonomic, and event categories as inputs to SeeBird; an Excel example spreadsheet that has successfully imported SeeBird’s ASCII text file; procedural steps to import, edit, and archive into Excel ASCII text files from SeeBird; initialization instructions for starting up program SeeBird on a Panasonic ToughBook™ that relies on integrated, satellite-derived GPS, and for writing “S” (seabirds + other taxa) and “E” (flying fish) ASCII files to a folder or subfolder other than the default root location on the laptop that contains program SeeBird; how to trouble-shoot miscellaneous start-up problems with program SeeBird; how to add new four-letter codes (into a SpeciesCode.txt file) when additional taxa or objects of interest are encountered. The primary objective of this manual is to archive a permanent, replicable history of survey methodology to facilitate continuity with comparable future projects that may be conducted in the Gulf. A secondary objective is to describe why and how program SeeBird was applied and adapted specifically for operating in Gulf survey conditions. As of late 2025, user guides for software program SeeBird were no longer readily accessible, so this manual serves also to address that gap.

Northern Gulf of America↗

USGS2018

Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals

Mammals diversified by colonizing drastically different environments, with each transition yielding numerous molecular changes, including losses of protein function. Though not initially deleterious, these losses could subsequently carry deleterious pleiotropic consequences. We have used phylogenetic methods to identify convergent functional losses across independent marine mammal lineages. In one extreme case, Paraoxonase 1 ( PON1 ) accrued lesions in all marine lineages, while remaining intact in all terrestrial mammals. These lesions coincide with PON1 enzymatic activity loss in marine species’ blood plasma. This convergent loss is likely explained by parallel shifts in marine ancestors’ lipid metabolism and/or bloodstream oxidative environment affecting PON1’s role in fatty acid oxidation. PON1 loss also eliminates marine mammals’ main defense against neurotoxicity from specific man-made organophosphorus compounds, implying potential risks in modern environments.

Science↗

USGS2025

U.S. Geological Survey science strategy to address highly pathogenic avian influenza and its effects on wildlife health 2025–29

Executive Summary Highly pathogenic avian influenza (HPAI) is an ecologically and economically important animal disease that can also directly affect humans (a “zoonotic” disease). HPAI was once limited almost exclusively to domestic poultry but has rapidly adapted to diverse animal hosts. Viruses causing HPAI now appear to be maintained and dispersed by wild birds largely independent of poultry, though HPAI continues to cause considerable economic losses and supply chain disruptions in the domestic poultry trade. Coincident with the adaptation of HPAI viruses to wild birds, particularly waterfowl and gulls, increasingly diverse wild bird hosts are becoming exposed to HPAI, often resulting in disease and death. More sporadically, HPAI has caused mass mortality events, particularly among seabirds. Furthermore, viral spillover to wild and domestic mammals has become more common. Spillover to wild mammals has resulted in mortality among diverse terrestrial and marine taxa, including episodic losses of such scale as to represent potential conservation challenges. Since approximately March 2024, HPAI has also affected dairy cows, which represents a new threat to the agricultural economy. Lastly, HPAI has increasingly affected humans through domestic animal exposures, exemplifying the considerable implications of this disease beyond animal health. Rapid changes in the ecology of HPAI are currently outpacing research efforts. For example, it is not entirely clear which newly established hosts may become reservoirs for HPAI viruses (in other words, capable of maintaining HPAI viruses within a broad population indefinitely) and how this may influence viral evolution and dissemination. As a result, there are considerable information gaps regarding HPAI in wildlife that, if filled, would improve the ability of scientists, managers, agricultural industry representatives, and healthcare professionals to understand and to anticipate the effects of HPAI on wild animal, domestic animal, environmental, and human health (“One Health”). The U.S. Geological Survey (USGS) is the lead Federal agency providing scientific research on avian influenza viruses (AIVs), including HPAI viruses, that affect wildlife for which the Department of the Interior (DOI) has management authority. States have jurisdiction over wildlife on Federal lands within their borders (43 CFR § 24.3), so the USGS Ecosystems Mission Area (EMA) coordinates with State natural resource management agencies. The EMA focuses its research on HPAI through priorities identified by the USGS Avian Influenza Science Team ( app. 1 ). Priorities identified by the USGS Avian Influenza Science Team are based on Administration priorities, Congressional direction, and discussions with State, Federal, and Tribal natural resource management agencies that identify specific scientific gaps that need to be filled to inform sound wildlife management decisions. Notable non-DOI Federal partners include the U.S. Department of Agriculture, the lead for the HPAI regulatory response in poultry and livestock, and the Centers for Disease Control and Prevention (CDC), the lead agency for the HPAI response pertaining to human health. The USGS offers unique expertise and capacity pertaining to research on diseases affecting free-ranging wildlife populations. This expertise has been critical to interjurisdictional surveillance and capacity-building efforts, including programs administered by the U.S. Department of Agriculture and the CDC. The USGS also provides resources, guidance, and tools to inform surveillance and interventions conducted by natural resource management agencies. More specifically, the USGS EMA provides objective and rigorous scientific data for inferring (1) the utility of new methods to detect and characterize AIVs, including those maintained in wildlife and the environment; (2) effects of HPAI on wildlife; (3) spatiotemporal patterns of wildlife host and AIV dispersal; (4) the presence and persistence of AIVs in the environment; (5) how HPAI in wildlife influences consumptive and nonconsumptive utilization of wildlife; (6) how new tools and scientific methods may promote sound management decisions for HPAI-affected wildlife, particularly species of conservation concern; and (7) the combined effects of HPAI and other stressors on ecosystem health and resiliency. This science strategy builds upon research outlined in a previous USGS science strategy for HPAI (2016–20) by Harris and others (2016) . This strategy also details research priorities identified by the Administration (for example, U.S. Department of Agriculture, 2025 ) and others based on USGS Avian Influenza Science Team discussions with natural resource management agencies to address HPAI and wildlife health over the next 5 years (2025–29). This strategy presents 7 goals and 26 objectives that focus USGS and partner efforts on priorities that will fill data gaps regarding the effects of HPAI on wildlife managed by or co-managed with the U.S. Department of the Interior such that agencies and partners might anticipate or limit adverse effects on public resources. This strategy also identifies research priorities intended to address HPAI in wildlife and wildlife habitat that are anticipated to support interjurisdictional One Health efforts.

Circular↗

USGS2026

Fatal leptospirosis in southern sea otters from Central California: Pathologic findings and detection of Leptospira interrogans

Leptospira interrogans serovar Pomona infections cause periodic outbreaks in California sea lions (CSLs; Zalophus californianus ) and sporadic deaths in phocids. However, the frequency of infection and associated health impacts remain uncharacterized in sympatric threatened southern sea otters (SSOs; Enhydra lutris nereis ), which serve as important sentinels of coastal health. Given the broad impacts of L. interrogans on other marine mammals, our objective was to screen selected SSOs for infection, determine whether leptospirosis contributes to SSO mortality, and describe leptospiral-associated lesions. A retrospective review (2005–2025) identified 19 candidate cases that underwent detailed review, including Leptospira immunohistochemistry (IHC), serology, and polymerase chain reaction (PCR), with a special focus on renal and hepatic lesions. Kidney samples were PCR-positive for 74% (14/19) of suspected cases. For eight of these, DNA sequence-based serogroup typing detected L. interrogans serogroup Pomona. Seven of the 14 PCR-positive leptospirosis cases were classified as fatal based on positive renal IHC and moderate to severe tubulointerstitial nephritis. All fatal cases had anti- L. interrogans serovar Pomona antibody titers ≥1:25,600. The remaining seven PCR-positive cases were considered nonfatal leptospirosis due to minimal and/or unrelated renal lesions and negative IHC. Nonfatal Leptospira -infected cases ranged from seronegative to low positive (1:400) for serovar Pomona. Antibody titers for Leptospira PCR-negative cases were negative. In fatal cases, gross renal changes were often inapparent or characterized by miliary white cortical foci. Renal histologic lesions included tubulointerstitial nephritis, acute tubular necrosis, and suppurative tubulitis with intratubular bacteria, along with positive IHC staining for leptospiral antigen in the lesions. Gross hepatic changes were also inapparent in fatal cases, and histologic lesions were rare, characterized in one animal by hepatocellular dissociation and in two sea otters by limited leptospiral antigen detection by IHC. Most Leptospira -infected sea otters (71%, 10/14) stranded during higher rainfall months in California, suggesting possible land-to-sea transmission from terrestrial hosts. Given these findings, and because L. interrogans serovar Pomona infections have been confirmed in sympatric CSLs and terrestrial mammals from adjacent watersheds, a focused investigation of potential marine and terrestrial disease transmission dynamics could provide new information to reduce SSO mortalities.

California↗

USGS2003

Sequential megafaunal collapse in the North Pacific Ocean: An ongoing legacy of industrial whaling?

Populations of seals, sea lions, and sea otters have sequentially collapsed over large areas of the northern North Pacific Ocean and southern Bering Sea during the last several decades. A bottom-up nutritional limitation mechanism induced by physical oceanographic change or competition with fisheries was long thought to be largely responsible for these declines. The current weight of evidence is more consistent with top-down forcing. Increased predation by killer whales probably drove the sea otter collapse and may have been responsible for the earlier pinniped declines as well. We propose that decimation of the great whales by post-World War II industrial whaling caused the great whales' foremost natural predators, killer whales, to begin feeding more intensively on the smaller marine mammals, thus "fishing-down" this element of the marine food web. The timing of these events, information on the abundance, diet, and foraging behavior of both predators and prey, and feasibility analyses based on demographic and energetic modeling are all consistent with this hypothesis.

Proceedings of the National Academy of Sciences of↗

USGS2002

Transport of sludge-derived organic pollutants to deep-sea sediments at deep water dump site 106

Linear alkylbenzenes (LABs), coprostanol and epi-coprostanol, were detected in sediment trap and bottom sediment samples at the Deep Water Dump Site 106 located 185 km off the coast of New Jersey, in water depths from 2400 to 2900 m. These findings clearly indicate that organic pollutants derived from dumped sludge are transported through the water column and have accumulated on the deep-sea floor. No significant difference in LABs isomeric composition was observed among sludge and samples, indicating little environmental biodegradation of these compounds. LABs and coprostanol have penetrated down to a depth of 6 cm in sediment, indicating the mixing of these compounds by biological and physical processes. Also, in artificially resuspended surface sediments, high concentrations of LABs and coprostanols were detected, implying that sewage-derived organic pollutants initially deposited on the deep-sea floor can be further dispersed by resuspension and transport processes. Small but significant amounts of coprostanol were detected in the sediment from a control site at which no LABs were detected. The coprostanol is probably derived from feces of marine mammals and sea birds and/or from microbial or geochemical transformations of cholesterol. Polcyclic aromatic hydrocarbons (PAHs) in sediment trap samples from the dump site were largely from the sewage sludge and had a mixed petroleum and pyrogenic composition. In contrast, PAHs in sediments in the dump site were mainly pyrogenic; contributed either from sewage sludge or from atmospheric transport to the overlying waters. & 1994 American Chemical Society.

Environmental Science & Technology↗