Biological impacts of minor shoreline structures on the coastal environment: state-of-the-art review. Vol. I, 156 pp. Vol. II,
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Characterization of Plasmodium relictum, a cosmopolitan agent of avian malaria
Background Microscopic research has shown that Plasmodium relictum is the most common agent of avian malaria. Recent molecular studies confirmed this conclusion and identified several mtDNA lineages, suggesting the existence of significant intra-species genetic variation or cryptic speciation. Most identified lineages have a broad range of hosts and geographical distribution. Here, a rare new lineage of P. relictum was reported and information about biological characters of different lineages of this pathogen was reviewed, suggesting issues for future research. Methods The new lineage pPHCOL01 was detected in Common chiffchaff Phylloscopus collybita, and the parasite was passaged in domestic canaries Serinus canaria . Organs of infected birds were examined using histology and chromogenic in situ hybridization methods. Culex quinquefasciatus mosquitoes, Zebra finch Taeniopygia guttata, Budgerigar Melopsittacus undulatus and European goldfinch Carduelis carduelis were exposed experimentally. Both Bayesian and Maximum Likelihood analyses identified the same phylogenetic relationships among different, closely-related lineages pSGS1, pGRW4, pGRW11, pLZFUS01, pPHCOL01 of P. relictum. Morphology of their blood stages was compared using fixed and stained blood smears, and biological properties of these parasites were reviewed. Results Common canary and European goldfinch were susceptible to the parasite pPHCOL01, and had markedly variable individual prepatent periods and light transient parasitaemia. Exo-erythrocytic and sporogonic stages were not seen. The Zebra finch and Budgerigar were resistant. Neither blood stages nor vector stages of all examined P. relictum lineages can be distinguished morphologically. Conclusion Within the huge spectrum of vertebrate hosts, mosquito vectors, and ecological conditions, different lineages of P. relictum exhibit indistinguishable, markedly variable morphological forms. Parasites of same lineages often develop differently in different bird species. Even more, the variation of biological properties (parasitaemia dynamics, blood pathology, prepatent period) in different isolates of the same lineage might be greater than the variation in different lineages during development in the same species of birds, indicating negligible taxonomic value of such features. Available lineage information is excellent for parasite diagnostics, but is limited in predictions about relationships in certain host-parasite associations. A combination of experiments, field observations, microscopic and molecular diagnostics is essential for understanding the role of different P. relictum lineages in bird health.
Malaria Journal↗
The role of the diagnostic laboratory in fish disease control
The diagnostic laboratory is becoming increasingly important to the productivity and profitability of hatcheries, fish farms, and aquaculture stations. The basic function of the laboratory personnel is to isolate and identify viral, bacterial, protozoan, and other fish pathogens present in cultured and feral fish stocks. New, rapid and accurate methods for the detection and identification of fish disease agents based on immunological, biochemical, and physiological assays are becoming commonly used. Nearly every North American state or province and many foreign countries have fish health regulations that require inspection of stocks for certain disease agents before the fish are shipped into their areas. Decisions from the diagnostic laboratory on identification, treatment, guaranteed isolation, immunization, and disposal of fish populations affect administrative directives, hatchery placement, and national and international transportation of fish and fish products. This paper reviews concepts and describes the equipment, supplies, biologics, and media needed for the basic diagnostic laboratory. Information management, including training of staff, certification procedures, and quality control are also discussed.
Annual Review of Fish Diseases↗
Incidence of pollution, bioaccumulation, biomagnification, and toxic effects of per- and polyfluoroalkyl substances (PFAS) in aquatic ecosystems: A review
Per- and polyfluoroalkyl substances (PFAS) are persistently accumulated in both environmental media and biological systems, leading to significant toxicological effects. Although research on PFAS has expanded in recent years, systematic reviews on its concentration distribution in aquatic environments and biota, as well as its toxicological effects, remain scarce. Moreover, existing literature lacks systematic analyses of diverse aquatic environments and organisms. This review investigates the contamination levels of PFAS in aquatic environments. It also provides a systematic analysis of bioaccumulation in planktonic, swimming, and benthic organisms, including bioaccumulation factors (BAF), biomagnification factors (BMF), trophic magnification factors (TMF), and biota-sediment accumulation factors (BSAF), and evaluates the potential toxic effects on aquatic ecosystems. This study aims to provide theoretical support for the environmental regulation and management of PFAS. Additionally, it seeks to offer data references and potential research directions for future studies, thereby promoting the advancement of PFAS-related research and policy development.
Aquatic Toxicology↗
Identifying key stressors driving biological impairment in freshwater streams in the Chesapeake Bay watershed, USA
Biological communities in freshwater streams are often impaired by multiple stressors (e.g., flow or water quality) originating from anthropogenic activities such as urbanization, agriculture, or energy extraction. Restoration efforts in the Chesapeake Bay watershed, USA seek to improve biological conditions in 10% of freshwater tributaries and to protect the biological integrity of existing healthy watersheds. To achieve these goals, resource managers need to better understand which stressors are most likely driving biological impairment. Our study addressed this knowledge gap through two approaches: 1) reviewing and synthesizing published multi-stressor studies, and 2) examining 303(d) listed impairments linked to biological impairment as identified by jurisdiction regulatory agencies (the states within the watershed and the District of Columbia). Results identified geomorphology (i.e., physical habitat), salinity, and toxic contaminants as important for explaining variability in benthic community metrics in the literature review. Geomorphology (i.e., physical habitat and sediment), salinity, and nutrients were the most reported stressors in the jurisdictional impairment analysis. Salinity is likely a major stressor in urban and mining settings, whereas geomorphology was commonly reported in agricultural settings. Toxic contaminants, such as pesticides, were rarely measured; more research is needed to quantify the extent of their effects in the region. Flow alteration was also highlighted as an important urban stressor in the literature review but was rarely measured in the literature or reported by jurisdictions as a cause of impairment. These results can be used to prioritize stressor monitoring by managers, and to improve stressor identification methods for identifying causes of biological impairment.
Chesapeake Bay Watershed↗
The potential roles of biological soil crusts in dryland hydrologic cycles
Biological soil crusts (BSCs) are the dominant living cover in many drylands of the world. They possess many features that can influence different aspects of local hydrologic cycles, including soil porosity, absorptivity, roughness, aggregate stability, texture, pore formation, and water retention. The influence of biological soil crusts on these factors depends on their internal and external structure, which varies with climate, soil, and disturbance history. This paper presents the different types of biological soil crusts, discusses how crust type likely influences various aspects of the hydrologic cycle, and reviews what is known and not known about the influence of biological crusts on sediment production and water infiltration versus runoff in various drylands around the world. Most studies examining the effect of biological soil crusts on local hydrology are done by comparing undisturbed sites with those recently disturbed by the researchers. Unfortunately, this greatly complicates interpretation of the results. Applied disturbances alter many soil features such as soil texture, roughness, aggregate stability, physical crusting, porosity, and bulk density in ways that would not necessarily be the same if crusts were not naturally present. Combined, these studies show little agreement on how biological crusts affect water infiltration or runoff. However, when studies are separated by biological crust type and utilize naturally occurring differences among these types, results indicate that biological crusts in hyperarid regions reduce infiltration and increase runoff, have mixed effects in and regions, and increase infiltration and reduce runoff in semiarid cool and cold drylands. However, more studies are needed before broad generalizations can be made on how biological crusts affect infiltration and runoff. We especially need studies that control for sub-surface soil features such as bulk density, micro- and macropores, and biological crust structure. Unlike the mixed effects of biological crusts on infiltration and runoff among regions, almost all studies show that biological crusts reduce sediment production, regardless of crust or dryland type.
Hydrological Processes↗
What is a biocrust? A refined, contemporary definition for a broadening research community
Studies of biological soil crusts (biocrusts) have proliferated over the last few decades. The biocrust literature has broadened, with more studies assessing and describing the function of a variety of biocrust communities in a broad range of biomes and habitats and across a large spectrum of disciplines, and also by the incorporation of biocrusts into global perspectives and biogeochemical models. As the number of biocrust researchers increases, along with the scope of soil communities defined as ‘biocrust’, it is worth asking whether we all share a clear, universal, and fully articulated definition of what constitutes a biocrust. In this review, we synthesize the literature with the views of new and experienced biocrust researchers, to provide a refined and fully elaborated definition of biocrusts. In doing so, we illustrate the ecological relevance and ecosystem services provided by them. We demonstrate that biocrusts are defined by four distinct elements: physical structure, functional characteristics, habitat, and taxonomic composition. We describe outgroups, which have some, but not all, of the characteristics necessary to be fully consistent with our definition and thus would not be considered biocrusts. We also summarize the wide variety of different types of communities that fall under our definition of biocrusts, in the process of highlighting their global distribution. Finally, we suggest the universal use of the Belnap, Büdel & Lange definition, with minor modifications: Biological soil crusts (biocrusts) result from an intimate association between soil particles and differing proportions of photoautotrophic (e.g. cyanobacteria , algae , lichens , bryophytes) and heterotrophic (e.g. bacteria , fungi , archaea) organisms , which live within , or immediately on top of , the uppermost millimetres of soil. Soil particles are aggregated through the presence and activity of these often extremotolerant biota that desiccate regularly , and the resultant living crust covers the surface of the ground as a coherent layer. With this detailed definition of biocrusts, illustrating their ecological functions and widespread distribution, we hope to stimulate interest in biocrust research and inform various stakeholders (e.g. land managers, land users) on their overall importance to ecosystem and Earth system functioning.
Biological Reviews↗
Wildlife ecological risk assessment in the 21st century: Promising technologies to assess toxicological effects
Despite advances in toxicity testing and development of new approach methodologies (NAMs) for hazard assessment, the ecological risk assessment (ERA) framework for terrestrial wildlife (i.e., air-breathing amphibians, reptiles, birds, and mammals) has remained unchanged for decades. While survival, growth, and reproductive endpoints derived from whole animal toxicity tests are central to hazard assessment, non-standard measures of biological effects at multiple levels of biological organization (e.g., molecular, cellular, tissue, organ, organism, population, community, ecosystem) have potential to enhance the relevance of prospective and retrospective wildlife ERAs. Other factors (e.g., indirect effects of contaminants on food supplies and infectious disease processes) are influenced by toxicants at individual, population, and community levels, and need to be factored into chemically-based risk assessments to enhance the “eco” component of ERAs. Regulatory and logistical challenges often relegate such non-standard endpoints and indirect effects to post-registration evaluations of pesticides and industrial chemicals, and contaminated site evaluations. While NAMs are being developed, to date their applications in ERAs focused on wildlife have been limited. No single magic tool or model will address all uncertainties in hazard assessment. Modernizing wildlife ERAs will likely entail combinations of laboratory and field-derived data at multiple levels of biological organization, knowledge collection solutions (e.g., systematic review, adverse outcome pathway frameworks), and inferential methods that facilitate integrations and risk estimations focused on species, populations, interspecific extrapolations, and ecosystem services modeling, with less dependence on whole animal data and simple hazard ratios.
Integrated Environmental Assessment and Management↗
Presettlement and modern disturbance regimes in coast redwood forests: Implications for the conservation of old-growth stands
Coast redwood ( Sequoia sempervirens ), a western North American conifer of ancient lineage, has a paradoxical combination of late-successional characteristics and strong adaptations to disturbance. Despite its shade tolerance and heavy dominance of the canopy on many sites, redwood saplings are uncommon in upland old-growth stands. Information needed to ensure the conservation of old-growth redwood forests has been limited. In this review paper, we integrate evidence on redwood biology with data on the historic and modern disturbance regimes to help clarify the degree to which key attributes of redwood forests may have been dependent upon periodic disturbance. Available evidence suggests that episodes of fire, flooding, and slope failure prior to European settlement were frequent but predominantly of low to moderate severity and extent, resulting in broadly uneven-aged forests. The majority of fires prior to European settlement were apparently of human origin. Frequency and severity of the major disturbance agents have been radically changed in modern times. Fires have been largely excluded, and flooding has been altered in ways that have often been detrimental to old-growth redwoods on alluvial terraces. However, because of the apparent anthropogenic origin of most presettlement fires, the long-term evolutionary role of fire for coast redwood is ecologically ambiguous. With fire exclusion, redwood possibly could be displaced to some extent on upland sites by increasing abundance of fire-sensitive competitors. Alternatively, redwood may be able to maintain dominance by vegetative sprouting and new seedling establishment on root-wad mounds, fallen logs, and on soil exposed by slope failure. Future research priorities are suggested that will help resolve some of the current ambiguities.
Forest Ecology and Management↗
An annotated bibliography for lamprey habitat in the White Salmon River, Washington
The October 2011 decommissioning of Condit Dam on the White Salmon River at river kilometer (rkm) 5.3 removed a significant fish passage barrier from the White Salmon River basin for the first time in nearly a century. This affords an opportunity to regain a potentially important drainage basin for Pacific lamprey ( Entosphenus tridentatus ) production. In anticipation of Pacific lamprey recolonization or reintroduction, aquatic resource managers, such as the Yakama Nation (YN), are planning to perform surveys in the White Salmon River and its tributaries. The likely survey objectives will be to investigate the presence of lamprey, habitat conditions, and habitat availability. In preparation for this work, a compilation and review of the relevant aquatic habitat and biological information on the White Salmon River was conducted. References specific to the White Salmon River were collected and an annotated bibliography was produced including reports containing: •Spatial information about where various habitat surveys or monitoring have occurred over the past 20 years; •Database information relevant to habitat attributes (for example, pools, riffles, or glides); •Riparian surveys along major tributary streams; •Water temperature and sediment information; •Lamprey surveys, observations, and collections; •Spawning gravel surveys; and •Surveys that inventory habitat degradation or other environmental factors that may limit potential future productivity of lamprey.
Washington↗
[Book review] Pheasants of the World . . . Again
Review of: The Pheasants of the World: Biology and Natural History, 2nd edition. Paul A. Johnsgard. 1999. Smithsonian Institution Press, Washington, D.C. 398 pages.$50.00 (cloth).
Prairie Naturalist↗
Contaminant Hazard Reviews. [Reports No. 1-28 on CD-ROM.]
This compact disc (CD) contains the first 28 reports in the Contaminant Hazard Reviews (CHR) that were published originally between 1985 and 1994 in the U.S. Department of the Interior Biological Report series. The CD was produced because printed supplies of these reviews--a total of 84,000--became exhausted and demand remained high. Each review was prepared at the request of environmental specialists of the U.S. Fish and Wildlife Service and each contained specific information on mirex, cadmium, carbofuran, toxaphene, selenium, chromium, polychlorinated biphenyls, dioxins, diazinon, mercury, polycyclic aromatic hydrocarbons, arsenic, chlorpyrifos, lead, tin, index issue, pentachlorophenol, atrazine, molybdenum, boron, chlordane, paraquat, cyanide, fenvalerate, diflubenzuron, zinc, famphur, or acrolein. Each report reviewed and synthesized the technical literature on a single contaminant and its effects on terrestrial plants and invertebrates, aquatic plants and animals, avian and mammalian wildlife, and other natural resources. The subtopics include contaminant sources and uses; physical, chemical, and metabolic properties; concentrations in field collections of abiotic materials and living organisms; deficiency effects, where appropriate; lethal and sublethal effects, including effects on survival, growth, reproduction, metabolism, mutagenicity, teratogenicity, and carcinogenicity; proposed criteria for the protection of human health and sensitive natural resources; and recommendations for additional research.
Book↗
Contaminant Hazard Reviews (compilation)
This compact disc (CD) contains the 35 reports in the Contaminant Hazard Reviews (CHR) that were published originally between 1985 and 1999 in the U.S. Department of the Interior Biological Report series. The CD was produced because printed supplies of these reviews--a total of 105,000--became exhausted and demand remained high. Each review was prepared at the request of environmental specialists of the U.S. Fish and Wildlife Service and each contained specific information on the following: mirex, cadmium, carbofuran, toxaphene, selenium, chromium, polychlorinated biphenyls, dioxins, diazinon, mercury, polycyclic aromatic hydrocarbons, arsenic, chlorpyrifos, lead, tin, index issue, pentachlorophenol, atrazine, molybdenum, boron, chlordane, paraquat, cyanide, fenvalerate, diflubenzuron, zinc, famphur, acrolein, radiation, sodium monofluoroacetate, planar PCBs, silver, copper, nickel, and a cumulative index to chemicals and species. Each report reviewed and synthesized the technical literature on a single contaminant and its effects on terrestrial plants and invertebrates, aquatic plants and animals, avian and mammalian wildlife, and other natural resources. The subtopics include contaminant sources and uses; physical, chemical, and metabolic properties; concentrations in field collections of abiotic materials and living organisms; deficiency effects, where appropriate; lethal and sublethal effects, including effects on survival, growth, reproduction, metabolism, mutagenicity, teratogenicity, and carcinogenicity; proposed criteria for the protection of human health and sensitive natural resources; and recommendations for additional research.
Contaminant Hazard Reviews↗
Arsenic and selenium in microbial metabolism
Arsenic and selenium are readily metabolized by prokaryotes, participating in a full range of metabolic functions including assimilation, methylation, detoxification, and anaerobic respiration. Arsenic speciation and mobility is affected by microbes through oxidation/reduction reactions as part of resistance and respiratory processes. A robust arsenic cycle has been demonstrated in diverse environments. Respiratory arsenate reductases, arsenic methyltransferases, and new components in arsenic resistance have been recently described. The requirement for selenium stems primarily from its incorporation into selenocysteine and its function in selenoenzymes. Selenium oxyanions can serve as an electron acceptor in anaerobic respiration, forming distinct nanoparticles of elemental selenium that may be enriched in (76)Se. The biogenesis of selenoproteins has been elucidated, and selenium methyltransferases and a respiratory selenate reductase have also been described. This review highlights recent advances in ecology, biochemistry, and molecular biology and provides a prelude to the impact of genomics studies.
Annual Review of Microbiology↗
Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory-Processing, taxonomy, and quality control of benthic macroinvertebrate samples
Qualitative and quantitative methods to process benthic macroinvertebrate (BMI) samples have been developed and tested by the U.S. Geological Survey?s National Water Quality Laboratory Biological Group. The qualitative processing method is based on visually sorting a sample for up to 2 hours. Sorting focuses on attaining organisms that are likely to result in taxonomic identifications to lower taxonomic levels (for example, Genus or Species). Immature and damaged organisms are also sorted when they are likely to result in unique determinations. The sorted sample remnant is scanned briefly by a second person to determine if obvious taxa were missed. The quantitative processing method is based on a fixed-count approach that targets some minimum count, such as 100 or 300 organisms. Organisms are sorted from randomly selected 5.1- by 5.1-centimeter parts of a gridded subsampling frame. The sorted remnant from each sample is resorted by a second individual for at least 10 percent of the original sort time. A large-rare organism search is performed on the unsorted remnant to sort BMI taxa that were not likely represented in the sorted grids. After either qualitatively or quantitatively sorting the sample, BMIs are identified by using one of three different types of taxonomic assessment. The Standard Taxonomic Assessment is comparable to the U.S. Environmental Protection Agency Rapid Bioassessment Protocol III and typically provides Genus- or Species-level taxonomic resolution. The Rapid Taxonomic Assessment is comparable to the U.S. Environmental Protection Agency Rapid Bioassessment Protocol II and provides Familylevel and higher taxonomic resolution. The Custom Taxonomic Assessment provides Species-level resolution whenever possible for groups identified to higher taxonomic levels by using the Standard Taxonomic Assessment. The consistent use of standardized designations and notes facilitates the interpretation of BMI data within and among water-quality studies. Taxonomic identifications are quality assured by verifying all referenced taxa and randomly reviewing 10 percent of the taxonomic identifications performed weekly by Biological Group taxonomists. Taxonomic errors discovered during this review are corrected. BMI data are reviewed for accuracy and completeness prior to release. BMI data are released phylogenetically in spreadsheet format and unprocessed abundances are corrected for laboratory and field subsampling when necessary.
Open-File Report↗
Application of genetics and genomics to wildlife epidemiology
Wildlife diseases can have significant impacts on wildlife conservation and management. Many of the pathogens that affect wildlife also have important implications for domestic animal and human health. However, management interventions to prevent or control wildlife disease are hampered by uncertainties about the complex interactions between pathogens and free-ranging wildlife. We often lack crucial knowledge about host ecology, pathogen characteristics, and host–pathogen dynamics. The purpose of this review is to familiarize wildlife biologists and managers with the application of genetic and genomic methodologies for investigating pathogen and host biology to better understand and manage wildlife diseases. The genesis of this review was a symposium at the 2013 annual Wildlife Society Conference. We reviewed the scientific literature and used our personal experiences to identify studies that illustrate the application of genetic and genomic methods to advance our understanding of wildlife epidemiology, focusing on recent research, new techniques, and innovative approaches. Using examples from a variety of pathogen types and a broad array of vertebrate taxa, we describe how genetics and genomics can provide tools to detect and characterize pathogens, uncover routes of disease transmission and spread, shed light on the ways that disease susceptibility is influenced by both host and pathogen attributes, and elucidate the impacts of disease on wildlife populations. Genetic and increasingly genomic methodologies will continue to contribute important insights into pathogen and host biology that will aid efforts to assess and mitigate the impacts of wildlife diseases on global health and conservation of biodiversity.
Journal of Wildlife Management↗
Mesocarnivores of western rangelands
There are 22 species of mesocarnivores (carnivores weighing < 15 kg) belonging to five families that live in rangelands of the western United States. Mesocarnivores are understudied relative to large carnivores but can have significant impacts on ecosystems and human dimensions. In this chapter, we review the current state of knowledge about the biology, ecology, and human interactions of the mesocarnivores that occupy the rangelands of the central and western United States. In these two regions, mesocarnivores may serve as the apex predator in areas where large carnivores no longer occur, and can have profound impacts on endemic prey, disease ecology, and livestock production. Some mesocarnivore species are valued because they are harvested for food and fur, while others are considered nuisance species because they can have negative impacts on ranching. Many mesocarnivores have flexible life history strategies that make them well-suited for future population growth or range expansion as western landscapes change due to rapid human population growth, landscape development, and alterations to ecosystems from climate change; however other mesocarnivores continue to decline. More research on this important guild is needed to understand their role in western working landscapes.
Book chapter↗
How plants influence resilience of salt marsh and mangrove wetlands to sea-level rise
This review evaluates the importance of plants and associated biological processes in determining the vulnerability of coastal wetlands to sea-level rise. Coastal wetlands occur across a broad sedimentary continuum from minerogenic to biogenic, providing an opportunity to examine the relative importance of biological processes in wetland resilience to sea-level rise. We explore how plants influence sediment accretion, elevation capital (vertical position in the tidal frame), and compaction or erosion of deposited material. We focus on salt marsh and mangrove wetlands, which occupy a similar physiographic niche and display similar physical and biological controls on resilience to sea-level rise. In both habitats, plants stabilize emergent mudflats and help sustain the wetland position in the tidal frame relative to ocean height through both surface and subsurface process controls on soil elevation. Plants influence soil elevations by modifying (1) mineral sediment deposition and retention, (2) organic matter contributions to soil volume, and (3) resistance to compaction and erosion. Recognition of the importance of plants in coastal wetland resilience to sea-level rise is key to accurate predictions about the future fate of salt marshes and mangrove forests and for development of effective management and restoration plans.
Estuaries and Coasts↗