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Enhancing and restoring habitat for the desert tortoise

Habitat has changed unfavorably during the past 150 y for the desert tortoise Gopherus agassizii , a federally threatened species with declining populations in the Mojave Desert and western Sonoran Desert. To support recovery efforts, we synthesized published information on relationships of desert tortoises with three habitat features (cover sites, forage, and soil) and candidate management practices for improving these features for tortoises. In addition to their role in soil health and facilitating recruitment of annual forage plants, shrubs are used by desert tortoises for cover and as sites for burrows. Outplanting greenhouse-grown seedlings, protected from herbivory, has successfully restored (>50% survival) a variety of shrubs on disturbed desert soils. Additionally, salvaging and reapplying topsoil using effective techniques is among the more ecologically beneficial ways to initiate plant recovery after severe disturbance. Through differences in biochemical composition and digestibility, some plant species provide better-quality forage than others. Desert tortoises selectively forage on particular annual and herbaceous perennial species (e.g., legumes), and forage selection shifts during the year as different plants grow or mature. Nonnative grasses provide low-quality forage and contribute fuel to spreading wildfires, which damage or kill shrubs that tortoises use for cover. Maintaining a diverse “menu” of native annual forbs and decreasing nonnative grasses are priorities for restoring most desert tortoise habitats. Reducing herbivory by nonnative animals, carefully timing herbicide applications, and strategically augmenting annual forage plants via seeding show promise for improving tortoise forage quality. Roads, another disturbance, negatively affect habitat in numerous ways (e.g., compacting soil, altering hydrology). Techniques such as recontouring road berms to reestablish drainage patterns, vertical mulching (“planting” dead plant material), and creating barriers to prevent trespasses can assist natural recovery on decommissioned backcountry roads. Most habitat enhancement efforts to date have focused on only one factor at a time (e.g., providing fencing) and have not included proactive restoration activities (e.g., planting native species on disturbed soils). A research and management priority in recovering desert tortoise habitats is implementing an integrated set of restorative habitat enhancements (e.g., reducing nonnative plants, improving forage quality, augmenting native perennial plants, and ameliorating altered hydrology) and monitoring short- and long-term indicators of habitat condition and the responses of desert tortoises to habitat restoration.

Mojave Desert

Assessment and management of dead-wood habitat

The Bureau of Land Management (BLM) is in the process of revising its resource management plans for six districts in western and southern Oregon as the result of the settlement of a lawsuit brought by the American Forest Resource Council. A range of management alternatives is being considered and evaluated including at least one that will minimize reserves on O&C lands. In order to develop the bases for evaluating management alternatives, the agency needs to derive a reasonable range of objectives for key issues and resources. Dead-wood habitat for wildlife has been identified as a key resource for which decision-making tools and techniques need to be refined and clarified. Under the Northwest Forest Plan, reserves were to play an important role in providing habitat for species associated with dead wood (U.S. Department of Agriculture Forest Service and U.S. Department of the Interior Bureau of Land Management, 1994). Thus, the BLM needs to: 1) address the question of how dead wood will be provided if reserves are not included as a management strategy in the revised Resource Management Plan, and 2) be able to evaluate the effects of alternative land management approaches. Dead wood has become an increasingly important conservation issue in managed forests, as awareness of its function in providing wildlife habitat and in basic ecological processes has dramatically increased over the last several decades (Laudenslayer et al., 2002). A major concern of forest managers is providing dead wood habitat for terrestrial wildlife. Wildlife in Pacific Northwest forests have evolved with disturbances that create large amounts of dead wood; so, it is not surprising that many species are closely associated with standing (snags) or down, dead wood. In general, the occurrence or abundance of one-quarter to one-third of forest-dwelling vertebrate wildlife species, is strongly associated with availability of suitable dead-wood habitat (Bunnell et al., 1999; Rose et al., 2001). In Oregon and Washington, approximately 150 species of wildlife are reported to use dead wood in forests (O’Neil et al., 2001). Forty-seven sensitive and special-status species are associated with dead wood (Appendix A). These are key species for management consideration because concern over small or declining populations is often related to loss of suitable dead-wood habitat (Marshall et al., 1996). Primary excavators (woodpeckers) also are often the focus of dead-wood management, because they perform keystone functions in forest ecosystems by creating cavities for secondary cavity-nesters (Martin and Eadie, 1999; Aubry and Raley, 2002). A diverse guild of secondary cavity-users (including swallows, bluebirds, several species of ducks and owls, ash-throated flycatcher, flying squirrel, bats, and many other species) is unable to excavate dead wood, and therefore relies on cavities created by woodpeckers for nesting sites. Suitable nest cavities are essential for reproduction, and their availability limits population size (Newton, 1994). Thus, populations of secondary cavity-nesters are tightly linked to the habitat requirements of primary excavators. Although managers often focus on decaying wood as habitat for wildlife, the integral role dead wood plays in ecological processes is an equally important consideration for management. Rose et al. (2001) provide a thorough review of the ecological functions of dead wood in Pacific Northwest forests, briefly summarized here. Decaying wood functions in: soil development and productivity, nutrient cycling, nitrogen fixation, and carbon storage. From ridge tops, to headwater streams, to estuaries and coastal marine ecosystems, decaying wood is fundamental to diverse terrestrial and aquatic food webs. Wildlife species that use dead wood for cover or feeding are linked to these ecosystem processes through a broad array of functional roles, including facilitation of decay and trophic interactions with other organisms (Marcot, 2002; Marcot, 2003). For example, by puncturing bark and fragmenting sapwood, woodpeckers create sites favorable for wood-decaying organisms (Farris et al., 2004), which in turn create habitat for other species and facilitate nutrient cycling. Small mammals that use down wood for cover function in the dispersal of plant seeds and fungal spores (Carey et al., 1999). Resident cavitynesting birds may regulate insect populations by preying on overwintering arthropods (Jackson, 1979; Kroll and Fleet, 1979). These examples illustrate how dead wood not only directly provides habitat for a large number of wildlife species, but also forms the foundation of functional webs that critically influence forest ecosystems (Marcot, 2002; Marcot, 2003). The important and far-reaching implications of management of decaying wood highlight the need for conservation of dead-wood resources in managed forests. Consideration of the key ecological functions of species associated with dead wood can help guide management of dead wood in a framework consistent with the paradigm of ecosystem management (Marcot and Vander Heyden, 2001; Marcot, 2002.) As more information is revealed about the ecological and habitat values of decaying wood, concern has increased over a reduction in the current amounts of dead wood relative to historic levels (Ohmann and Waddell, 2002). Past management practices have tended to severely reduce amounts of dead wood throughout all stages of forest development (Hansen et al., 1991). The large amounts of legacy wood that characterize young post-disturbance forests are not realized in managed stands, because most of the wood volume is removed at harvest for economic and safety reasons. Mid-rotation thinning is used to “salvage” some mortality that might otherwise occur due to suppression, so fewer snags are recruited in mid-seral stages. Harvest rotations of 80 years or less truncate tree size in managed stands, and thus limit the production of large-diameter wood. As a consequence of these practices, dead wood has been reduced by as much as 90% after two rotations of managed Douglas-fir (Rose et al., 2001). Large legacy deadwood is becoming a scarce, critical habitat that will take decades to centuries to replace. Furthermore, management continues to have important direct and indirect effects on the amount and distribution of dead wood in forests. Current guidelines for managing dead wood may be inadequate to maintain habitat for all associated species because they largely focus on a single use of dead wood (nesting habitat) by a small suite of species (cavity-nesting birds), and may under represent the sizes and amounts of dead wood used by many wildlife species (Rose et al., 2001, Wilhere, 2003).

Open-File Report

A quantitative soil-geomorphic framework for developing and mapping ecological site groups

Land management decisions need context about how landscapes will respond to different circumstances or actions. As ecologists’ understanding of nonlinear ecological dynamics has evolved into state-and-transition models (STMs), they have put more emphasis on defining and mapping the soil, geomorphological, and climate parameters that mediate these dynamics. The US Department of Agriculture Natural Resources Conservation Service ecological site descriptions (ESDs) have become the foremost system in classifying lands into ecological units based on STMs. However, an exhaustive inventory of ESDs has proved challenging to complete in the United States, and there have been questions about the consistency of detail in areas completed and the ability to objectively support some assertions made in existing ESDs. To address these issues, this study examines ESDs in the diverse Upper Colorado River region, where ESDs are only partially complete, to look at quantitative approaches to generalizing ecological site concepts based on unifying underlying soil, geomorphology, and climate patterns. Using existing ESDs and vegetation monitoring plot data, results show that a simple hierarchical soil geomorphic unit (SGU) framework based on topographic mediation of moisture, soil salinity, soil depth, slope, rock content, and soil texture can represent much of the ecological dynamics cataloged in ESDs. Analyses of reference plant production data, ecological state attribution, and regional monitoring data show that the new SGUs represent more variation than common climate parameters. This study also included predictively mapping SGUs at 30-m resolution (Kappa of 0.53, 74% agreement with top two predictions in validation). An optimized combination of SGUs with climate zones derived from an aridity index and maximum temperature of the hottest month resulted in an ecological site group framework that condensed over 826 unique ecological site records at various stages of completeness in the regional soil survey down to 35 intuitive and mappable ecological site groups.

Rangeland Ecology and Management

An approach for assessment of water quality using semipermeable membrane devices (SPMDs) and bioindicator tests

As an integral part of our continued development of water quality assessment approaches, we combined integrative sampling, instrumental analysis of widely occurring anthropogenic contaminants, and the application of a suite of bioindicator tests as a specific part of a broader survey of ecological conditions, species diversity, and habitat quality in the Santa Cruz River in Arizona, USA. Lipid-containing semipermeable membrane devices (SPMDs) were employed to sequester waterborne hydrophobic chemicals. Instrumental analysis and a suite of bioindicator tests were used to determine the presence and potential toxicological relevance of mixtures of bioavailable chemicals in two major water sources of the Santa Cruz River. The SPMDs were deployed at two sites; the effluent weir of the International Wastewater Treatment Plant (IWWTP) and the Nogales Wash. Both of these systems empty into the Santa Cruz River and the IWWTP effluent is a potential source of water for a constructed wetland complex. Analysis of the SPMD sample extracts revealed the presence of organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polycyclic aromatic hydrocarbons (PAHs). The bioindicator tests demonstrated increased liver enzyme activity, perturbation of neurotransmitter systems and potential endocrine disrupting effects (vitellogenin induction) in fish exposed to the extracts. With increasing global demands on limited water resources, the approach described herein provides an assessment paradigm applicable to determining the quality of water in a broad range of aquatic systems.

Chemosphere

22 years of aquatic plant spatiotemporal dynamics in the upper Mississippi River

Macrophyte (aquatic plant) recovery has occurred in rivers worldwide, but assemblage patterns and habitat requirements are generally not well understood. We examined patterns of species composition and macrophyte abundance in the Upper Mississippi River (UMR), spanning 22 years of monitoring and a period of vegetation recovery. Non-metric multidimensional scaling (NMDS) ordination revealed a gradient of macrophyte abundance and diversity for 25 species, which were associated with water velocity, depth, wind fetch, and water clarity. Three macrophyte genera of ecological and restoration interest ( Zizania aquatica , Vallisneria americana , and Sagittaria spp.) occupied different ecological niches. Trends of NMDS values showed that Z. aquatica first co-occurred in shallow areas with Sagittaria spp. but then expanded into deeper, lotic habitats where V. americana often resided. Curve Fit regression analysis identified large areas of significant increases in the relative abundance of V. americana and percent cover of Z. aquatica in several reaches of the UMR from 1998–2019. Sagittaria spp. were more spatiotemporally dynamic, which may indicate specific habitat requirements and sensitivity to environmental gradients. Our analyses showed that these three ecologically important genera are spatiotemporally dynamic but have somewhat predictable habitat associations, which can guide macrophyte management and restoration in the UMR and other large, floodplain rivers.

Iowa, Minnesota, Wisconsin

Plant water-use strategies predict restoration success across degraded drylands

Plant strategies for coping with water limitation are likely to mediate restoration outcomes in degraded dryland ecosystems. Trade-offs in traits related to water acquisition and use can intensify in more arid environments, making their effects on dryland restoration success even more salient. However, isolating the effects of drought responses from those of other environmental factors, as well as identifying the specific drought resistance traits that influence restoration success, can be difficult. In the present study, we couple a controlled dry-down experiment with a cross-site restoration field trial of out-planted seedlings (RestoreNet) using a suite of dryland herbaceous plant species from the same seed sources. We quantified interspecific variation in physiological responses to drought, specifically reductions in stomatal conductance ( g s ) and stem water potential (SWP), by comparing well-watered control plants to those experiencing decreasing soil moisture. Drought responses of SWP and g s varied independently among species, but both were related to survival in the cross-site restoration field trial when effect sizes were aggregated across all sites. Responses were consistent with acquisitive water-use strategies resulting in greater success, where species with greater declines in SWP or weaker declines in g s under drought had greater survival. The correlation between SWP drought response and survival also intensified in sites with lower accumulated precipitation following restoration. Differences among functional groups revealed two different paths to restoration success: forbs that maintain high g s and narrow safety margins to maximize exploitation of moisture pulses before going into drought dormancy, or C 4 grasses that maintain efficient water uptake in drying soils while risking cavitation. C 3 grass species varied between these two strategies. Synthesis and applications . Taken together, the results of this study and others conducted at RestoreNet sites indicate that while a diversity of physiological responses to drought may exist in dryland plant communities, successfully restoring herbaceous species through out-planting in degraded conditions is likely to be achieved with species that maximize water uptake via one of two strategies, with tolerance of low SWP being particularly important in the most arid settings.

Journal of Applied Ecology

Shifting hotspots: Climate change projected to drive contractions and expansions of invasive plant abundance habitats

Aim Preventing the spread of range-shifting invasive species is a top priority for mitigating the impacts of climate change. Invasive plants become abundant and cause negative impacts in only a fraction of their introduced ranges, yet projections of invasion risk are almost exclusively derived from models built using all non-native occurrences and neglect abundance information. Location Eastern USA. Methods We compiled abundance records for 144 invasive plant species from five major growth forms. We fit over 600 species distribution models based on occurrences of abundant plant populations, thus projecting which areas in the eastern United States (U.S.) will be most susceptible to invasion under current and +2°C climate change. Results We identified current invasive plant hotspots in the Great Lakes region, mid-Atlantic region, and along the northeast coast of Florida and Georgia, each climatically suitable for abundant populations of over 30 invasive plant species. Under a +2°C climate change scenario, hotspots will shift an average of 213 km, predominantly towards the northeast U.S., where some areas are projected to become suitable for up to 21 new invasive plant species. Range shifting species could exacerbate impacts of up to 40 invasive species projected to sustain populations within existing hotspots. On the other hand, within the eastern U.S., 62% of species will experience decreased suitability for abundant populations with climate change. This trend is consistent across five plant growth forms. Main Conclusions We produced species range maps and state-specific watch lists from these analyses, which can inform proactive regulation, monitoring, and management of invasive plants most likely to cause future ecological impacts. Additionally, areas we identify as becoming less suitable for abundant populations could be prioritized for restoration of climate-adapted native species. This research provides a first comprehensive assessment of risk from abundant plant invasions across the eastern U.S.

Diversity and Distributions

Effects of flow diversion on Snake Creek and its riparian cottonwood forest, Great Basin National Park

Snake Creek flows east from the southern Snake Range in Nevada over complex lithology before leaving Great Basin National Park. The river travels over a section of karst limestone where some surface water naturally recharges the groundwater flow system. In 1961 a water diversion pipeline was constructed by downstream water users to transport surface water through the groundwater recharge zone to reduce potential water losses. The diversion pipeline dewaters a 5-km reach for most of the year by transporting water past the recharge zone then returning it to the channel downstream. Snake Creek was incorporated into the newly established Great Basin National Park in 1986, and today park managers and visitors are concerned that the diversion has destabilized Snake Creek’s riparian ecosystem in this arid region where it has high ecological value. The objectives of this study were to 1) document riparian cottonwood forest conditions in the pipeline-dewatered (DW) reach, 2) evaluate Snake Creek water availability and whether it can support a healthy riparian ecosystem, and 3) determine if dewatering has shifted the fluvial system into an unnatural and poorly functioning state. We pursued these ecohydrological study objectives in 11 research investigations of Snake Creek’s DW reach and nearby reference reaches. The research investigations analyzed: 1) riparian forest condition, tree age, growth, and death; 2) tree ring chronologies through time and space; 3) hydroclimatic drivers of tree growth; 4) stable carbon isotopes extracted from tree rings; 5) cottonwood ecophysiology related to water transport and water stress; 6) historical aerial photography; 7) stand-level riparian forest production; 8) groundwater availability as related to surface water and plant rooting zones; 9) near-surface geophysics using electrical resistivity imaging; 10) channel and valley geomorphology; and 11) in-channel wood jams caused by fallen trees. Integrating these diverse research topics provided a full perspective of historical and modern conditions along Snake Creek. We found that modern hydrological conditions in Snake Creek’s DW reach could not maintain the drought-sensitive ecosystem. The riparian cottonwoods ( Populus angustifolia and P. angustifolia x P. trichocarpa ) have experienced significant dieback. Tree mortality was 2.4 times higher in the DW reach than in reference reaches, and surviving trees supported only 60% of the live canopy compared to trees in reference reaches. Changes in the DW reach forest began in the 1960s and became more severe during the last two decades. Stable carbon isotope ratios and branch dieback analyses both demonstrated initial forest adjustments related to water stress beginning in the early 1960s. Tree ring width chronologies indicated two periods of growth decline in the DW relative to control reaches. The first decline in the 1960s represented an immediate adjustment to the modified flow regime, and the second decline in the 2000s demonstrated reduced resilience to atmospheric drought. Aerial photos and stand-level forest production calculations indicated that substantial riparian forest decline occurred in the 1990s–2010s in the DW reach compared to reference reaches. Stable carbon isotope ratios and leaf water potentials revealed that trees in the DW reach experienced greater drought stress than those in reference reaches. Monitoring wells and electrical resistivity surveys both showed riparian water tables to be largely supported by in-channel surface water flow, indicating that the flow diversion removed water that recharges alluvial groundwater and sustains riparian plants. Areas of widespread tree mortality in the DW reach also corresponded to a larger and more unstable channel with a high instream wood load from fallen trees. Modern conditions of Snake Creek in the DW reach robustly suggest that dewatering the river and its associated riparian corridor adversely affected the riparian ecosystem. The degraded condition is likely to persist and intensify unless water is returned to the channel. As we documented during the wet 1980s and the scientific literature suggest, a partial recovery of the riparian ecosystem is likely possible with restored flows.

Nevada

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 × 10 6 reads revealed >3 × 10 6 genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), 4 × 10 6 reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria , predominantly Comamonadaceae . The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3 % of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Taken together, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae , pathogenic Pseudomonadaceae , and ‘ Vibrionales' ) and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River.

Virginia

Soil ecology of a rock outcrop ecosystem: Abiotic stresses, soil respiration, and microbial community profiles in limestone cedar glades

Limestone cedar glades are a type of rock outcrop ecosystem characterized by shallow soil and extreme hydrologic conditions—seasonally ranging from xeric to saturated—that support a number of plant species of conservation concern. Although a rich botanical literature exists on cedar glades, soil biochemical processes and the ecology of soil microbial communities in limestone cedar glades have largely been ignored. This investigation documents the abiotic stress regime of this ecosystem (shallow soil, extreme hydrologic fluctuations and seasonally high soil surface temperatures) as well as soil physical and chemical characteristics, and relates both types of information to ecological structures and functions including vegetation, soil respiration, and soil microbial community metabolic profiles and diversity. Methods used in this investigation include field observations and measurements of soil physical and chemical properties and processes, laboratory analyses, and microbiological assays of soil samples. Stress factors quantified by this research include shallow soil (depth to bedrock ranging from 2.4 to 22.6 cm), volumetric soil water content levels seasonally ranging from xeric (below 5%) to saturated (above 50%), and seasonally extreme ground-surface temperatures (above 48°C). Findings from this research indicate that spatial and temporal heterogeneity exists in limestone cedar glades in terms of abiotic stress factors and soil physical and chemical properties. Several such soil properties (e.g. soil depth, organic matter levels, pH, and particle size distribution) are spatially correlated. These soil properties were statistically related to ecological structures and functions such as vegetation patterns, soil respiration, the density of culturable heterotrophic microbes in soil and metabolic diversity of soil microbial community profiles. In general, zones within limestone cedar glades that had relatively shallow soil, alkaline pH, low levels of organic matter and high levels of silt also tended to have depressed rates of soil respiration and reduced densities and metabolic diversity of culturable heterotrophic soil microbes. Additionally, seasonally-relevant stress factors including soil water content and temperatures at or near the soil surface were related to the same set of ecological structures and functions.

Tennessee

Natural resource condition assessment: Olympic National Park

The Natural Resource Assessment Program aims to document condition and trends of selected park resources while identifying emerging issues and information needs. This information is intended to serve as a platform for natural resource managers to use in developing future resource stewardship priorities and planning. Olympic National Park (OLYM) on Washington’s Olympic Peninsula protects remarkable examples of several Pacific Northwestern ecosystems, including the glacier-capped Olympic Mountains, oldgrowth temperate rainforests, pristine river systems, and wild Pacific coastline and islands. The park provides habitat for numerous plants and animals, including at least 16 animal and eight plant taxa endemic to the Olympic Peninsula. The park’s lakes and rivers support over 70 stocks of Pacific salmonids and 29 native freshwater fish species. The rocky intertidal community is one of the most complex and diverse shorelines in the United States. Although we conducted in-depth assessments on a limited number of resources, the general condition of several other physical and biological components of OLYM ecosystems is described in Chapter 2, along with an overview of park history and ecology. In Chapter 3, we describe how we chose our focal resources and measures, as well as our protocol for conducting the assessment. In Chapter 4, we provide a detailed assessment of each resource, with a summary of condition and trends. In Chapter 5, we further interpret and discuss the implications of each focal resource status, highlighting future areas for monitoring and research. We summarize the general findings from our assessments below.

Washington

Bright spots for inland fish and fisheries to guide future hydropower development

Hydropower production is one of the greatest threats to fluvial ecosystems and freshwater biodiversity. Now that we have entered the Anthropocene , there is an opportunity to reflect on what might constitute a ‘sustainable’ Anthropocene in the context of hydropower and riverine fish populations. Considering elements of existing practices that promote favorable social-ecological outcomes (i.e., ‘bright spots’) is timely given that there are plans to expand hydropower capacity in previously undammed rivers, intensify dam development in some of the world's largest river systems, and re-license existing facilities. We approach this from a pragmatic perspective: for the foreseeable future, hydropower will likely remain an important source of renewable electricity. To offer support for moving toward a more ‘sustainable’ Anthropocene, we provide syntheses of best practices during the siting, design, construction, operation, and compensation phases of hydropower development to minimize impacts on inland fish. For each phase, we offer positive examples (or what might be considered ‘bright spots’) pertaining to some of the approaches described within our syntheses, acknowledging that these projects may not be viewed as without ecological and (or) societal detriment by all stakeholders. Our findings underscore the importance of protecting critical habitat and free-flowing river reaches through careful site selection and basin-scale planning, infrastructure designs that minimize reservoir effects and facilitate safe passage of fish, construction of hydropower plants using best practices that minimize long-term damage, operating guidelines that mimic natural flow conditions, and compensation that is lasting, effective, inclusive, and locally relevant. Learning from these ‘bright spots’ may require engagement of diverse stakeholders, professionals, and governments at scales that extend well beyond a given site, river, or even basin. Indeed, environmental planning that integrates hydropower development into broader discussions of conserving regional biodiversity and ecosystem services will be of utmost importance.

Water Biology and Security

Periphyton biomass and community compositions as indicators of water quality in the Lower Grand River hydrologic unit, Missouri and Iowa, 2011–18

Biological communities, including periphyton, are continuously affected by chemical, physical, and other biological factors, and the health of these communities can reflect the overall health of the aquatic system. A diverse community is more robust, and communities with lower richness and evenness often indicate a degraded community dominated by few taxa tolerant to the degraded conditions, which makes the community more susceptible to ecological changes. Water-quality nutrient samples were collected at sites in the Lower Grand River during 2010 through 2018 and periphyton sample collections began in 2011 to describe the periphyton community and overall ecological health. Nutrient sample concentrations were generally elevated at these sites, which can lead to eutrophication, excessive plant and algae growth, drinking-water taste and odor problems, low dissolved-oxygen concentrations, and harmful algal blooms. Concentrations of total nitrogen were greater than acceptable as described by the U.S. Environmental Protection Agency, and total phosphorus concentrations were greater than reference concentrations. Periphyton communities were dominated by taxa that are tolerant to or indicative of elevated nutrient concentrations; and nuisance algae, or harmful algal bloom producers, were identified at all sites, except one. The presence of these producers indicates that harmful algal blooms may have high potential during optimal conditions at these sites. Chlorophyll concentrations that exceed 100 milligrams per square meter are considered nuisance and were determined in 11 percent of the samples and at every site during September 2012. Samples were collected during low-flow conditions when nutrient concentrations are generally lower than during high-flow and runoff conditions. Elevated nutrient concentrations during low-flow conditions indicate nutrient concentrations are likely elevated throughout most of the year. Agriculture is the primary land use within the Lower Grand River and is likely a primary source of nutrients and sediments. Conservation practices intended to reduce nutrient loss from agriculture fields have increased because of the Mississippi River Basin Healthy Watersheds Initiative and will potentially increase the ecological, chemical, and physical health of these waterways.

Iowa, Missouri

Biodiversity of Fungi : Inventory and Monitoring Methods

Biodiversity of Fungi is essential for anyone collecting and/or monitoring any fungi. Fascinating and beautiful, fungi are vital components of nearly all ecosystems and impact human health and our economy in a myriad of ways. Standardized methods for documenting diversity and distribution have been lacking. An wealth of information, especially regrading sampling protocols, compiled by an international team of fungal biologists, make Biodiversity of Fungi an incredible and fundamental resource for the study of organismal biodiversity. Chapters cover everything from what is a fungus, to maintaining and organizing a permanent study collection with associated databases; from protocols for sampling slime molds to insect associated fungi; from fungi growing on and in animals and plants to mushrooms and truffles. The chapters are arranged both ecologically and by sampling method rather than by taxonomic group for ease of use. The information presented here is intended for everyone interested in fungi, anyone who needs tools to study them in nature including naturalists, land managers, ecologists, mycologists, and even citizen scientists and sophiscated amateurs. Fungi are among the most important organisms in the world; they play vital roles in ecosystem functions and have wide-ranging effects, both positive and negative, on humans and human-related activities. There are about 1.5 million species of fungi. The combination of fungal species and abundances in an ecosystem are often used as indicators of ecosystem health and as indicators of the effects of pollution and of different management and use plans. Because of their significance, it is important that these organisms be monitored. This book is the first comprehensive treatment of fungal inventory and monitoring, including standardized sampling protocols as well as information on study design, sample preservation, and data analysis.

Book

Lianas as invasive species in North America

Liana diversity is typically low in the temperate zones; however, the influx of non-native invasive liana species in North America has increased local diversity at the expense of native habitats and species. Some of the most illustrative studies of invasive lianas in temperate North America compared the biological traits of invasive lianas with native congeners or ecological analogs. The majority of these studies focused on two species, Celastrus orbiculatus (oriental bittersweet) and Lonicera japonica (Japanese honeysuckle). Temperate zone lianas generally have higher photosynthetic rates than other early successional species and their host trees. Invasive lianas are having an increasing impact on the dynamics and trajectories of North American plant communities. They often exhibit superior growth and survival compared to their native counterparts, and in some cases, invasive lianas may directly contribute to the decline of their native correlates.

Book chapter

Free tropospheric transport of microorganisms from Asia to North America

Microorganisms are abundant in the troposphere and can be transported vast distances on prevailing winds. This study measures the abundance and diversity of airborne bacteria and fungi sampled at the Mt. Bachelor Observatory (located 2.7 km above sea level in North America) where incoming free tropospheric air routinely arrives from distant sources across the Pacific Ocean, including Asia. Overall deoxyribonucleic acid (DNA) concentrations for microorganisms in the free troposphere, derived from quantitative polymerase chain reaction assays, averaged 4.94 × 10(-5) ng DNA m(-3) for bacteria and 4.77 × 10(-3) ng DNA m(-3) for fungi. Aerosols occasionally corresponded with microbial abundance, most often in the springtime. Viable cells were recovered from 27.4 % of bacterial and 47.6 % of fungal samples (N = 124), with 49 different species identified by ribosomal DNA gene sequencing. The number of microbial isolates rose significantly above baseline values on 22-23 April 2011 and 13-15 May 2011. Both events were analyzed in detail, revealing distinct free tropospheric chemistries (e.g., low water vapor, high aerosols, carbon monoxide, and ozone) useful for ruling out boundary layer contamination. Kinematic back trajectory modeling suggested air from these events probably originated near China or Japan. Even after traveling for 10 days across the Pacific Ocean in the free troposphere, diverse and viable microbial populations, including presumptive plant pathogens Alternaria infectoria and Chaetomium globosum, were detected in Asian air samples. Establishing a connection between the intercontinental transport of microorganisms and specific diseases in North America will require follow-up investigations on both sides of the Pacific Ocean.

Microbial Ecology

Exotic plant species invade hot spots of native plant diversity

Some theories and experimental studies suggest that areas of low plant species richness may be invaded more easily than areas of high plant species richness. We gathered nested-scale vegetation data on plant species richness, foliar cover, and frequency from 200 1-m 2 subplots (20 1000-m 2 modified-Whittaker plots) in the Colorado Rockies (USA), and 160 1-m 2 subplots (16 1000-m 2 plots) in the Central Grasslands in Colorado, Wyoming, South Dakota, and Minnesota (USA) to test the generality of this paradigm. At the 1-m 2 scale, the paradigm was supported in four prairie types in the Central Grasslands, where exotic species richness declined with increasing plant species richness and cover. At the 1-m 2 scale, five forest and meadow vegetation types in the Colorado Rockies contradicted the paradigm; exotic species richness increased with native-plant species richness and foliar cover. At the 1000-m 2 plot scale (among vegetation types), 83% of the variance in exotic species richness in the Central Grasslands was explained by the total percentage of nitrogen in the soil and the cover of native plant species. In the Colorado Rockies, 69% of the variance in exotic species richness in 1000-m 2 plots was explained by the number of native plant species and the total percentage of soil carbon. At landscape and biome scales, exotic species primarily invaded areas of high species richness in the four Central Grasslands sites and in the five Colorado Rockies vegetation types. For the nine vegetation types in both biomes, exotic species cover was positively correlated with mean foliar cover, mean soil percentage N, and the total number of exotic species. These patterns of invasibility depend on spatial scale, biome and vegetation type, spatial autocorrelation effects, availability of resources, and species-specific responses to grazing and other disturbances. We conclude that: (1) sites high in herbaceous foliar cover and soil fertility, and hot spots of plant diversity (and biodiversity), are invasible in many landscapes; and (2) this pattern may be more closely related to the degree resources are available in native plant communities, independent of species richness. Exotic plant invasions in rare habitats and distinctive plant communities pose a significant challenge to land managers and conservation biologists.

Ecological Monographs

Wildlife species associated with non-coniferous vegetation in Pacific Northwest conifer forests: A review

Non-coniferous vegetation, including herbs, shrubs, and broad-leaved trees, makes a vital contribution to ecosystem function and diversity in Pacific Northwest conifer forests. However, forest management has largely been indifferent or detrimental to shrubs and trees that have low commercial value, in spite of a paradigm shift towards more holistic management in recent decades. Forest management practices that are detrimental to broad-leaved trees and shrubs are likely to decrease habitat diversity for wildlife, but the number of species that may be affected has not previously been enumerated. I reviewed life history accounts for forest-dwelling vertebrate wildlife species and derived a list of 78 species in Oregon and Washington that are associated with non-coniferous vegetation. The diversity of direct and indirect food resources provided was the primary functional basis for associations of most species with non-coniferous vegetation. Thus, a diversity of herbs and broad-leaved trees and shrubs provides the foundation for food webs that contribute to diversity at multiple trophic levels in Pacific Northwest conifer forests. Given the number of species associated with non-coniferous vegetation in conifer-dominated forests, maintaining habitats that support diverse plant communities, particularly broad-leaved trees and shrubs, will be an important component of management strategies intended to foster biodiversity. Silvicultural practices such as modified planting densities, and pre-commercial and commercial thinning, can be used to control stand density in order to favor the development of understory herbs, shrubs, and a diversity of tree species within managed stands. Allowing shrubs and hardwood trees to develop and persist in early seral stands by curtailing vegetation control also would benefit many species associated with non-coniferous vegetation.

Forest Ecology and Management