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Solutions in microbiome engineering: Prioritizing barriers to organism establishment

Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.

The ISME Journal: Multidisciplinary Journal of Mic

An overview and participatory framework for choosing spatial boundaries in social–ecological systems modeling

A common challenge when modeling social–ecological systems (SESs) is defining the spatial extent of the system. Boundaries that do not adequately capture both social and ecological processes and their interactions can lead to mischaracterization of the system, while expanding boundaries too widely can impact model complexity and required resources. Socially, boundaries can invoke and influence identity, culture, power, and sense of place. Boundary decisions benefit from flexible, iterative approaches and the expertise of local communities. Here, we use a structured database search supplemented with citation searching to identify and review the literature that addresses choosing or defining spatial boundaries in SESs mapping or modeling and, when applicable, how participatory methods were used in the research process. In a review of the resulting 79 studies, we discovered that pre-existing social or ecological boundaries were used most frequently (36 and 18 publications, respectively). Twenty-one publications combined social and ecological boundaries or data to create custom boundaries, and four studies used an alternative approach to conventional boundaries. Informed by the literature review, we present a general framework for defining boundaries at the outset of SES research. We then connect the framework to a specific case study based on a collaborative project with Tribal, university, and federal scientists to develop a social–ecological climate adaptation plan. We present guiding questions alongside candidate boundaries for our study system and explore the tradeoffs of these boundary options, which can function as a useful template for other social–ecological research collaborations.

ISPRS International Journal of Geo-Information

Scientific Framework for resilience research on the Upper Mississippi River System

The goal of this research framework is to outline research that would continue to improve our understanding of ecological resilience of the Upper Mississippi River System (UMRS) and inform management of the system for health and resilience. We provide a broad overview of recently completed and ongoing work that has been funded as a part of the UMRS Ecological Resilience Assessment and related efforts to provide context for how proposed research questions build upon our current knowledge and may inform restoration planning and design. We describe two primary objectives within this research framework - the first objective is to investigate hypothesized drivers and feedbacks related to specified resilience, and the second is to expand our utility of general resilience indicators through further development and evaluation. The intended audience for this framework is the Upper Mississippi River Restoration Program (UMRR). The UMRR partnership is made up of natural resource agencies from five states (Illinois, Iowa, Minnesota, Missouri and Wisconsin) and five federal agencies (U.S. Army Corps of Engineers, U.S. Environmental Protection Agency, U.S. Fish and Wildlife Service, U.S. Geological Survey, and USDA Natural Resources Conservation Service).

Illinois, Iowa, Minnesota, Missouri, Wisconsin

Final Project Memorandum: Ecological implications of mangrove forest migration in the southeastern U.S.

Winter climate change has the potential to have a large impact on coastal wetlands in the southeastern United States. Warmer winter temperatures and reductions in the intensity of freeze events would likely lead to mangrove forest range expansion and salt marsh displacement in parts of the U.S. Gulf of Mexico and Atlantic coast. The objective of this research was to better evaluate the ecological implications of mangrove forest migration and salt marsh displacement. The potential ecological impacts of mangrove migration are diverse ranging from important biotic impacts (e.g., coastal fisheries, land bird migration; colonial-nesting wading birds) to ecosystem stability (e.g., response to sea level rise and drought; habitat loss; coastal protection) to biogeochemical processes (e.g., carbon storage; water quality). This research specifically investigated the impact of mangrove forest migration on coastal wetland soil processes and the consequent implications for coastal wetland responses to sea level rise and carbon storage.

Report

Hierarchical computing for hierarchical models in ecology

Bayesian hierarchical models allow ecologists to account for uncertainty and make inference at multiple scales. However, hierarchical models are often computationally intensive to fit, especially with large datasets, and researchers face trade-offs between capturing ecological complexity in statistical models and implementing these models. We present a recursive Bayesian computing (RB) method that can be used to fit Bayesian models efficiently in sequential MCMC stages to ease computation and streamline hierarchical inference. We also introduce transformation-assisted RB (TARB) to create unsupervised MCMC algorithms and improve interpretability of parameters. We demonstrate TARB by fitting a hierarchical animal movement model to obtain inference about individual- and population-level migratory characteristics. Our recursive procedure reduced computation time for fitting our hierarchical movement model by half compared to fitting the model with a single MCMC algorithm. We obtained the same inference fitting our model using TARB as we obtained fitting the model with a single algorithm. For complex ecological statistical models, like those for animal movement, multi-species systems, or large spatial and temporal scales, the computational demands of fitting models with conventional computing techniques can limit model specification, thus hindering scientific discovery. Transformation-assisted RB is one of the most accessible methods for reducing these limitations, enabling us to implement new statistical models and advance our understanding of complex ecological phenomena.

Article

Can identifying discrete behavioral groups with individual-based acoustic telemetry advance the understanding of fish distribution patterns?

Identifying patterns of organismal distribution can provide valuable insights for basic and applied marine and coastal ecology because understanding where animals are located is foundational to both research and science-based conservation. Understanding variation in distributional patterns can lead to a better assessment of ecological drivers and an improved ability to predict consequences of natural and altered relationships. Here, our purpose is to explore if quantifying coexisting groups of individual fish predators advances our understanding of field distribution patterns. Toward this end, we quantified locations of 59 acoustically tagged striped bass ( Morone saxatilis) within a 26-stationary unit telemetry receiver array in Plum Island Estuary (PIE), MA, United States. We then used cluster analyses on spatial and temporal-spatial metrics from this dataset to (1) assess if distinct groups of individuals coexisted, (2) quantify group characteristics, and (3) test associations between groups and distribution (e.g., physical site type and region). Based on multiple lines of evidence, we identified four groups of striped bass with different space use patterns that persisted across seasons (summer and fall). Similar-sized striped bass clustered at spatial and temporal scales at which individuals within distinct groups could, and did, physically overlap. In addition, distributional groups were linked to components of physical site type and region suggesting that discrete groups of individuals can interact differently with the environment within the same ecological system. The identification of these distinct groups of individuals creates a baseline from which to explore further ecological implications of grouping behavior for research and conservation in geographically large, temporally dynamic, and spatially heterogeneous marine and coastal environments.

Massachusetts

Ecological impacts of non-native species

Non-native species are considered one of the greatest threats to freshwater biodiversity worldwide (Drake et al. 1989; Allen and Flecker 1993; Dudgeon et al. 2005). Some of the first hypotheses proposed to explain global patterns of amphibian declines included the effects of non-native species (Barinaga 1990; Blaustein and Wake 1990; Wake and Morowitz 1991). Evidence for the impact of non-native species on amphibians stems (1) from correlative research that relates the distribution or abundance of a species to that of a putative non-native species, and (2) from experimental tests of the effects of a non-native species on survival, growth, development or behaviour of a target species (Kats and Ferrer 2003). Over the past two decades, research on the effects of non-native species on amphibians has mostly focused on introduced aquatic predators, particularly fish. Recent research has shifted to more complex ecological relationships such as influences of sub-lethal stressors (e.g. contaminants) on the effects of non-native species (Linder et al. 2003; Sih et al. 2004), non-native species as vectors of disease (Daszak et al. 2004; Garner et al. 2006), hybridization between non-natives and native congeners (Riley et al. 2003; Storfer et al. 2004), and the alteration of food-webs by non-native species (Nystrom et al. 2001). Other research has examined the interaction of non-native species in terms of facilitation (i.e. one non-native enabling another to become established or spread) or the synergistic effects of multiple non-native species on native amphibians, the so-called invasional meltdown hypothesis (Simerloff and Von Holle 1999). Although there is evidence that some non-native species may interact (Ricciardi 2001), there has yet to be convincing evidence that such interactions have led to an accelerated increase in the number of non-native species and cumulative impacts are still uncertain (Simberloff 2006). Applied research on the control, eradication, and management of non-native species has only just begun but some promising results have already emerged (see below), giving hope to a very difficult conservation issue. This chapter provides an overview of the role of non-native species in amphibian declines and summarizes the current state of knowledge of non-native species that are known, or considered to be, a threat to amphibian species and populations. The biological and socio-economic issues of non-native species control are examined and brief case studies of successful eradication programmes are provided.

Book chapter

Mysis diluviana and Hemimysis anomala : reviewing the roles of a native and invasive mysid in the Laurentian Great Lakes region

Mysis diluviana and Hemimysis anomala are the only two species of mysid shrimps in the order Mysidacea that are present in the Laurentian Great Lakes of North America. M. diluviana has inhabited the deep, cold waters of this region since Pleistocene-era glacial retreat and is widely considered to have a central role in the functioning of offshore food webs in systems they inhabit. More recently, the Great Lakes were invaded by the Ponto-Caspian native Hemimysis , a species that inhabits warmer water and shallower depths relative to M. diluviana . Hemimysis has rapidly expanded throughout the Great Lakes region and has become integrated into nearshore food webs as both food for planktivorous fish and predators and competitors of zooplankton. This special issue is composed of 14 papers that represent the most recent advances in our understanding of the ecological importance of both species of mysids to lake and river ecosystems in the Great Lakes region of North America. Topics discussed in this special issue will inform future research in all systems influenced by mysid ecology.

Lake Erie;Lake Huron;Lake Michigan;Lake Ontario;La

Ecological effects of pinyon-juniper removal in the Western United States—A synthesis of scientific research, January 2014–March 2021

Executive Summary Increasing density of pinyon ( Pinus spp. ) and juniper ( Juniperus spp. ) woodlands (hereinafter “pinyon-juniper”), as well as expansion of these woodlands into adjacent shrublands and grasslands, has altered ecosystem function and wildlife habitat across large areas of the interior western United States. Although there are many natural and human-caused drivers of woodland infilling and expansion, restoration of sagebrush ( Artemisia spp. ) habitat through removal of pinyon-juniper is considered an urgent management objective in many locations, particularly in support of sagebrush-dependent wildlife species of conservation concern. In December 2020, the Bureau of Land Management (BLM) established the Pinyon-Juniper Management Categorical Exclusion (PJCX) to expedite the regulatory process for pinyon-juniper removal projects on public lands, largely intended to benefit mule deer ( Odocoileus hemionus ) and greater sage-grouse ( Centrocercus urophasianus ) habitats. During final preparation of this report, the BLM discontinued use of the PJCX (as of November, 2022), but the pinyon-juniper tree removal techniques assessed in this report are commonly used and understanding their effects remains relevant to land use planning. To address areas of uncertainty relative to potential ecological effects of the PJCX, we conducted a review of the peer-reviewed science literature to better understand the likely responses of vegetation, environmental (for example, soils), and wildlife variables to specific tree removal techniques permitted by the PJCX. In brief, the PJCX permitted removal of trees by either manual cutting, mechanical cutting, or mastication; allowed certain methods to redistribute or remove resulting tree biomass after treatment; and prohibited broadcast burning, roadbuilding, removal of old-growth, and seeding of non-native species. Specifically, we conducted our review to address the following questions: How will PJCX removal techniques affect plant communities, soils, and abiotic resources? How do these pinyon-juniper removal techniques affect wildlife communities, including both woodland- and sagebrush-dependent species? What are the potential ecological implications of different pinyon-juniper removal treatment types and implementation strategies (for example, treatment sizes) over time? What are the most important gaps in our scientific understanding of how treatments might affect targeted ecosystems over space and time (for example, potential effects of climate change)? To answer these questions, we considered studies related to pinyon-juniper ecosystems, focusing on research that occurred over a large portion of the interior western United States that is the primary focus of the PJCX. We also focused on papers published from 2014 onward, to avoid excessive overlap with other recent reviews on pinyon-juniper management effects. Using strict criteria, including only considering research that tested responses for statistical significance, we identified 48 papers that primarily examined treatment effects on vegetation and other environmental variables (1,709 responses), and 11 papers that addressed effects on wildlife (132 responses). Responses to the PJCX-permitted treatments were summarized as either positive (that is, a significant increase), negative (that is, a significant decrease), or non-significant (that is, no significant difference). Responses were assigned to categories (for example, Native Annual Grass/Forb Abundance) and hierarchical treatment levels. We found that there were large proportions of non-significant responses among all categories combined, with roughly half or more of all responses non-significant (48 percent for wildlife, 60 percent for vegetation-environmental), comparable to other recent systematic reviews of pinyon-juniper treatment effects. However, we also found that when there were significant responses, some important trends potentially emerged. Important undesirable outcomes included far more positive than negative responses of exotic grass and forb abundance among nearly all treatment types. Cutting treatments were also more likely to decrease biocrust cover and microbial activity. Potentially beneficial outcomes included mostly positive responses among sagebrush obligate species, including more positive than negative responses for mule deer and sage-grouse. Some treatment types (for example, mastication) also resulted in more positive than negative responses for native grasses and forbs (although, non-significant responses were the majority). We also highlighted many limitations of this review, including how responses often come from few studies, and how some response-treatment category combinations lack adequate response data. Moreover, the existing research is often insufficient to address many key questions about treatment effects, largely owing to short time-scales and limited spatial extents of observations, which do not match the size of treatments being implemented by land managers, nor capture long-term, post-treatment ecological dynamics. We also identify a lack of research that addresses key interactions that could undermine restoration objectives, including potential effects of climate change and grazing on post-treatment environments. Thus, we emphasize the importance of integrating these factors into future pinyon-juniper treatment research, and we stress the need for use of monitoring programs and research studies that partake in data collection and analysis over long durations and broad spatial scales.

Open-File Report

Three decades of World Recreational Fishing Conferences: What have we learned about the dynamics of recreational fisheries?

Recreational fishing extends beyond catching fish, connecting individuals with nature, generating environmental stewards and contributing significantly to both local, regional and national economies. Assessing potential impacts on ecosystems and social-ecological systems requires dedicated multi- and interdisciplinary research and integrative management and policy approaches. Managing recreational fisheries effectively also necessitates transdisciplinary thinking, yet this poses continued challenges, as researchers and managers balance specialized expertise with innovative, boundary-crossing perspectives in light of limited funding in a rapidly changing social-ecological environment. The World Recreational Fishing Conference (WRFC) serves as the leading global scientific forum for addressing these challenges, fostering interdisciplinary exchange among scientists, managers, policy makers and stakeholders. The papers in this special issue represent the output of the last WRFC in Melbourne, Australia in 2023. By reviewing the content of the papers published in the present special issue, we illustrate the critical role of collaborative spaces, such as the WRFC, in bridging different expertise and approaches and fostering innovation, thereby securing adaptive management and conservation of recreational fisheries in response to global changes. Evaluating the development of the WRFC over three decades highlights how this conference series represents a leading think tank serving the entire network of recreational fisheries professionals globally.

Fisheries Management and Ecology

Effects of fire on threatened and endangered plants: an annotated bibliography

This bibliography presents basic information about the effects of fm on plants that the U.S. Fish and Wildlife Service lists as endangered or threatened or as category-one (Cl) candidates for federal listing. We searched 23 databases for publications, unpublished reports, and records with pertinent information; summarized and compiled information on the effects of fire from all final rulings on endangered and threatened plants and from endangered species recovery plans for plants; and solicited information from key researchers and agencies involved in fire ecology. The bibliography includes 126 references to the effect of fire on 172 federally listed plant species, or on 26% of the total number of federally listed plant species in these categories. Our study revealed that the total number of relevant articles has been increasing since the 1970s and more rapidly since the 1980s. Although research on fire and rare plants is increasing, an absence of information on many species persists. We hope that this document will facilitate and encourage research in this increasingly important field of botanical conservation.

Information and Technology Report

Beyond exposure, sensitivity and adaptive capacity: A response based ecological framework to assess species climate change vulnerability

As the impacts of global climate change on species are increasingly evident, there is a clear need to adapt conservation efforts worldwide. Species vulnerability assessments (VAs) are increasingly used to summarize all relevant information to determine a species’ potential vulnerability to climate change and are frequently the first step in informing climate adaptation efforts. VAs commonly integrate multiple sources of information by utilizing a framework that distinguishes factors relevant to species exposure, sensitivity, and adaptive capacity. However, this framework was originally developed for human systems, and its use to evaluate species vulnerability has serious practical and theoretical limitations. By instead defining vulnerability as the degree to which a species is unable to exhibit any of the responses necessary for persistence under climate change (i.e., toleration of projected changes, migration to new climate-compatible areas, enduring in microrefugia, and evolutionary adaptation), we can bring VAs into the realm of ecological science without applying borrowed abstract concepts that have consistently challenged species-centric research and management. This response-based framework to assess species vulnerability to climate change allows better integration of relevant ecological data and past research, yielding results with much clearer implications for conservation and research prioritization.

Climate Change Responses

Using citizen scientists to collect oxygen and hydrogen isotope data in southern Nevada

What is Citizen Science? Citizen science programs provide a means for Federal and non-Federal government agencies to make science more engaging, transparent, and accessible by partnering with the public for the purpose of problem solving, data collection, and monitoring. Public volunteers become directly involved in local research, thereby engaging in scientific projects. The public has already been included in existing citizen science programs that cover a broad range of disciplines, such as ecology, hydrology, and tectonics. Citizen science advances research while simultaneously fostering a sense of involvement and interest from the public. Beginning in 2017, the U.S. Geological Survey (USGS), U.S. Forest Service, Bureau of Land Management, U.S. Fish and Wildlife Service, and National Park Service collaborated with private, non-profit partners to inventory, survey, and rehabilitate springs in Clark County, Nevada. The USGS maintains the National Water Information System (NWIS), a publicly available online database of water-resources data for the Nation, and the agency is interested in using citizen science to add geochemical data from springs in southern Nevada. From 2021 to 2023, the USGS directly worked with citizen science partners, including the Springs Stewardship Institute and the Friends of Nevada Wilderness, to collect stable isotope and tritium samples from southern Nevada springs. The citizen science volunteers were provided the training and supplies for proper sample collection by USGS staff. As the citizen science partners traveled and hiked to the remote spring sites to complete spring surveys and perform restoration activities, they collected stable isotope and tritium samples for the USGS. Samples were shipped to national USGS laboratories for analysis, and the results were uploaded to the NWIS database (U.S. Geological Survey, 2024).

Nevada

An integrated framework for ecological drought across riverscapes of North America

Climate change is increasing the severity and extent of extreme droughts events, posing a critical threat to freshwater ecosystems, particularly with increasing human demands for diminishing water supplies. Despite the importance of drought as a significant driver of ecological and evolutionary dynamics, current understanding of drought consequences for freshwater biodiversity is very limited. We describe key barriers that hinder integrative drought research and monitoring across riverscapes. The primary constraint limiting understanding of ecological drought is an existing monitoring framework focused on human water consumption and flood risk in mainstem rivers. This approach is misaligned with escalating needs for research and data collection that illuminate exposure, sensitivity, and adaptive capacity (i.e., vulnerability) of biota to drought across entire riverscapes. We present a hierarchical framework for integrated ecological drought monitoring and research that addresses drought vulnerability across riverscapes, and describe how this approach can directly inform natural-resource management.

BioScience

Co-producing coastal bird research on the Gulf Coast through structured decision making (SDM) and constructed value of information (CVoI)

Conservation practitioners face the complex challenge of addressing global biodiversity threats within social-ecological systems with multiple jurisdictions, numerous interest groups, and changing environmental conditions. Bridging the research-to-implementation gap between scientists and managers, which integrates diverse perspectives that represent the variety of considerations impacting management outcomes can help to inform efficient and effective conservation. Avian conservation programs along the U.S. Gulf Coast exemplify these challenges, as management decisions must address diverse threats to declining coastal bird populations across large breeding, wintering, and migratory ranges while facing uncertainty surrounding the efficacy of large-scale strategies. This provides opportunities for improving management through co-produced research with structured decision making (SDM). We present a case study that demonstrates the application of co-production principles and SDM to collaboratively develop high-priority research questions informing effective avian conservation and management. Additionally, we applied a constructed value of information (CVoI) framework to identify and prioritize which uncertainties to reduce and better understand how research questions impact management actions. The integration of SDM’s five-step decision making framework ensured key principles of co-production were met, while co-production enhanced SDM outcomes by incorporating diverse perspectives and knowledge bases. CVoI further allowed participants to collectively determine final high-priority research questions in the face of complexity and uncertainty. Together, these approaches supported co-produced knowledge-generation, strategic hypothesis prioritization, and identification of research questions most likely to improve conservation decisions. This case study from the U.S. Gulf Coast demonstrates how co-produced research through SDM offers a broadly applicable approach for navigating ecological complexity and bridging the research-to-implementation gap in avian conservation.

Gulf Coast

Identifying recruitment sources across trophic levels in a large river food web

Assemblages are connected through the movement of physical and biological resources including recruits. Identifying recruitment sources for predators and their prey could help us understand how assemblages use connectivity across multiple trophic levels and whether predator and prey recruitment is coupled. Recruitment sources of organisms across multiple trophic levels can be quantified by trace element analysis of stomach contents. We used trace element analysis of otoliths to determine recruitment contributions from tributaries of predatory largemouth bass ( Micropterus salmoides ) and bowfin ( Amia calva ) and their consumed prey collected from Pools 4, 8, and 13 of the Upper Mississippi River. We used laser ablation inductively coupled mass spectrometry to quantify strontium:calcium of the core of each otolith and classified each fish to a natal origin (i.e., tributary or potential resident). We compared patterns of natal origin across study reaches, collection years, and species and with previously published origins of independently sampled prey fish. Predator and prey assemblages across all study reaches recruited from tributaries. More prey (44%) than predators (17%) recruited from tributaries. Of fishes originating from tributaries, individuals recruited from various rivers including the large Minnesota and Wisconsin Rivers and several small tributaries. Patterns in natal origin were similar among predators and prey families and among reaches, across sampling years, and between consumed prey and independently sampled prey. Tributaries consistently contributed recruits to both prey and predator fishes, leading to a coupling of predator and prey recruitment sources across space and time. Predators directly and indirectly used tributaries for recruitment and persistence through their own and their prey's recruitment. We further highlighted the utility of using consumed prey to simultaneously study the ecology of prey and predator assemblages, thereby reducing research sampling needs.

Illinois, Iowa, Minnesota, Wisconsin

Restoration research actions to address rapid change in drylands: Insights from the Colorado Plateau

The rapid intensification of ecological extremes in response to climate change and human land use is perhaps nowhere more apparent than in drylands, including the semiarid region of the Colorado Plateau in the southwestern United States. Here, we describe research directions to aid in the restoration of Colorado Plateau ecosystems during the UN Decade on Ecosystem Restoration (2021–2030) that 1) address high levels of heterogeneity 2) explore simultaneous global change drivers 3) are co-produced with a broad range of partners and 4) center Indigenous ways of knowing. We highlight restoration research efforts led by early career scientists grappling with informing management actions in a region where a rapidly changing climate intersects with historic grazing and continued land use pressures to create novel ecological extremes. We highlight restoration research efforts led by early career researchers grappling with informing management actions in a region where novel ecological extremes are the result of historic grazing, continued land-use pressures, and a rapidly changing climate.

Arizona, Colorado, New Mexico, Utah

Identifying management-relevant research priorities for responding to disease-associated amphibian declines

A research priority can be defined as a knowledge gap that, if resolved, identifies the optimal course of conservation action. We (a group of geographically distributed and multidisciplinary research scientists) used tools from nominal group theory and decision analysis to collaboratively identify and prioritize information needs within the context of disease-associated amphibian decline , in order to develop a strategy that would support US management agency needs. We developed iterated influence diagrams to create and assess a unified research strategy. We illustrated a transparent process for identifying specific knowledge gaps in amphibian disease ecology relevant to environmental management, and then constructed a research plan to address these uncertainties. The resulting priorities include a need to: (1) understand the drivers of the community-disease relationship, (2) determine the mechanisms by which exposure to contaminants influence disease outcomes, (3) identify elements of terrestrial and aquatic habitats that stabilize host-pathogen dynamics, (4) discuss how metapopulations may be managed to reduce the speed and intensity of disease outbreaks, and (5) define the relationship between habitat management and the environmental and host microbiomes. Along with identifying research priorities for disease management, we present the details of the process used to develop a consensus plan for addressing disease-related declines in amphibians on federally managed lands of the United States.

Global Ecology and Conservation