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Virginia flow-ecology modeling results—An initial assessment of flow reduction effects on aquatic biota

Background The U.S. Geological Survey (USGS), in cooperation with the Virginia Department of Environmental Quality (DEQ), reviewed a previously compiled set of linear regression models to assess their utility in defining the response of the aquatic biological community to streamflow depletion. As part of the 2012 Virginia Healthy Watersheds Initiative (HWI) study conducted by Tetra Tech, Inc., for the U.S. Environmental Protection Agency (EPA) and Virginia DEQ, a database with computed values of 72 hydrologic metrics, or indicators of hydrologic alteration (IHA), 37 fish metrics, and 64 benthic invertebrate metrics was compiled and quality assured. Hydrologic alteration was represented by simulation of streamflow record for a pre-water-withdrawal condition (baseline) without dams or developed land, compared to the simulated recent-flow condition (2008 withdrawal simulation) including dams and altered landscape to calculate a percent alteration of flow. Biological samples representing the existing populations represent a range of alteration in the biological community today. For this study, all 72 IHA metrics, which included more than 7,272 linear regression models, were considered. This extensive dataset provided the opportunity for hypothesis testing and prioritization of flow-ecology relations that have the potential to explain the effect(s) of hydrologic alteration on biological metrics in Virginia streams.

Virginia↗

Using a food web model to inform the design of river restoration—An example at the Barkley Bear Segment, Methow River, north-central Washington

With the decline of Chinook salmon ( Oncorhynchus tshawytscha ) and steelhead ( O. mykiss ), habitat restoration actions in freshwater tributaries have been implemented to improve conditions for juveniles. Typically, physical (for example, hydrologic and engineering) based models are used to design restoration alternatives with the assumption that biological responses will be improved with changes to the physical habitat. Biological models rarely are used. Here, we describe simulations of a food web model, the Aquatic Trophic Productivity (ATP) model, to aid in the design of a restoration project in the Methow River, north-central Washington. The ATP model mechanistically links environmental conditions of the stream to the dynamics of river food webs, and can be used to simulate how alternative river restoration designs influence the potential for river reaches to sustain fish production. Four restoration design alternatives were identified that encompassed varying levels of side channel and floodplain reconnection and large wood addition. Our model simulations suggest that design alternatives focused on reconnecting side channels and the adjacent floodplain may provide the greatest increase in fish capacity. These results were robust to a range of discharge and thermal regimes that naturally occur in the Methow River. Our results suggest that biological models, such as the ATP model, can be used during the restoration planning phase to increase the effectiveness of restoration actions. Moreover, the use of multiple modeling efforts, both physical and biological, when evaluating restoration design alternatives provides a better understanding of the potential outcome of restoration actions.

Washington↗

Using the STARS model to evaluate the effects of the proposed action for the reinitiation of consultation on the coordinated long-term operation of the Central Valley and State Water Project

In 2016, the U.S. Bureau of Reclamation (USBR) and California Department of Water Resources requested a reinitiation of consultation under Section 7 of the Endangered Species Act on the coordinated long-term operations of the Central Valley and State Water Projects. This resulted in a Biological Assessment released by USBR in 2019. In its analysis of the Biological Assessment for its Biological Opinion on the proposed action, the National Marine Fisheries Service (NMFS) requested assistance from the U.S. Geological Survey to describe the effect of the proposed action on juvenile Chinook salmon ( Oncorhynchus tshawytscha ) populations migrating through the Sacramento-San Joaquin River Delta (henceforth called “the Delta”). Therefore, in this report we analyzed an 82-year time series of simulated river flows and Delta Cross Channel (DCC) gate operations under two scenarios constructed for the Biological Assessment: the proposed-action (PA) scenario and the continuing-operations scenario (COS). To evaluate the proposed action, we used the STARS model ( S urvival, T ravel time, A nd R outing S imulation model), a stochastic, individual-based simulation model designed to predict survival of a cohort of fish that experiences variable daily river flows as the fish migrate through the Delta. The STARS model uses parameter estimates from a Bayesian mark-recapture model that jointly estimates travel time and survival in eight discrete reaches of the Delta and migration routing at two key river junctions. By applying the STARS model to the two 82-year scenarios, we found that the proposed action had negative effects on survival, travel time, and routing in October–December but positive effects in April–June. In October–December, there was a high probability that survival in the PA scenario was less than that in the COS, and that travel time and routing to the Interior Delta for the PA scenario was greater than that for the COS. The magnitude of the difference in survival between scenarios was larger in some years than in others. For example, we quantified that survival under the PA scenario was 10 percent lower than under the COS in 25 percent of the water years from October through December. During this period, inflow to the Delta tended to be lower under the PA scenario, and the DCC gate was open more frequently under the PA scenario than during the COS. Lower inflow reduces survival, and more frequent operation of the DCC gate 1) increases the proportion of fish entering the Interior Delta, where survival is low, and thus 2) reduces survival in the Sacramento River in reaches downstream of the DCC. In contrast, during the period April–June, survival was higher, travel times were lower, and routing to the Interior Delta was lower under the PA scenario relative to the COS, although the magnitude of the increase in survival was relatively small in most years (less than a 3-percent difference in survival). This difference between scenarios was driven by higher river flows in some years under the PA scenario relative to the COS. Overall, the differences in survival, travel time, and routing distance between the two operational scenarios were primarily driven by the timing and magnitude of the annual high river flows.

California↗

Effects of urbanization on stream ecosystems in the Willamette River basin and surrounding area, Oregon and Washington

This report describes the effects of urbanization on physical, chemical, and biological characteristics of stream ecosystems in 28 watersheds along a gradient of urbanization in the Willamette River basin and surrounding area, Oregon and Washington, from 2003 through 2005. The study that generated the report is one of several urban-effects studies completed nationally by the U.S. Geological Survey National Water-Quality Assessment Program. Watersheds were selected to minimize natural variability caused by factors such as geology, elevation, and climate, and to maximize coverage of different stages of urban development among watersheds. Because land use or population density alone often are not a complete measure of urbanization, a combination of land use, land cover, infrastructure, and socioeconomic variables were integrated into a multimetric urban intensity index (UII) to represent the degree of urban development in each watershed. Physical characteristics studied include stream hydrology, stream temperature, and habitat; chemical characteristics studied include sulfate, chloride, nutrients, pesticides, dissolved and particulate organic and inorganic carbon, and suspended sediment; and biological characteristics studied include algal, macroinvertebrate, and fish assemblages. Semipermeable membrane devices, passive samplers that concentrate trace levels of hydrophobic organic contaminants such as polycyclic aromatic hydrocarbons and polychlorinated biphenyls, also were used. The objectives of the study were to (1) examine physical, chemical, and biological responses along the gradient of urbanization and (2) determine the major physical, chemical, and landscape variables affecting the structure of aquatic communities. Common effects documented in the literature of urbanization on instream physical, chemical, and biological characteristics, such as increased contaminants, increased streamflow flashiness, increased concentrations of chemicals, and changes in aquatic community structure toward a more tolerant community associated with organically enriched conditions, generally were observed in this study. The strongest correlations to the UII and to many of the algal, macroinvertebrate, and fish assemblage metrics and community ordination involved water-chemistry metrics including the total pesticide concentration, toxic equivalents (extract assay from semipermeable membrane devices), and dissolved oxygen. Hydrologic variability metrics, such as flashiness, that normally are considered to be one of the main processes of urban disturbance had a strong association to the algal and fish assemblages in this study; however, the hydrologic variables for macroinvertebrates were secondary to the water-chemistry metrics mentioned above. Generally, the high urban intensity sites had high abundances of eutrophic and lower dissolved oxygen-indicating diatoms, high abundances of noninsects and tolerant insects, and high abundances of nonnative fish species. On the other hand, the low urban intensity sites had higher abundances of pollution sensitive diatoms, larger numbers of the sensitive macroinvertebrate EPT taxa (Ephemeroptera, Plecoptera and Trichoptera Orders), and fish assemblages with higher abundances of sensitive salmonids. The percent salmonid and macroinvertebrate EPT richness metrics plotted against the UII indicated a possible threshold response at about 25 on the UII, which is equivalent to an impervious surface value of about 5 percent. However, due to the added agricultural land use at sites within the 25 to 60 UII range, this possible threshold probably is not solely due to urbanization, but a combination of urban and agricultural land use. The effects of agricultural and urban land use could not be distinguished from each other, yet combined they provide a good assessment of overall watershed disturbance.

Oregon, Washington↗

Breakpoint analysis and assessment of selected stressor variables on benthic macroinvertebrate and fish communities in Indiana streams: Implications for developing nutrient criteria

Water chemistry, periphyton and seston chlorophyll a (CHL a ), and biological community data were collected from 321 sites from 2001 through 2005 to (1) determine statistically and ecologically significant relations among the stressor (total nitrogen, total phosphorus, periphyton and seston CHL a , and turbidity) variables and response (biological community) variables; and, (2) determine the breakpoint of biological community attributes and metrics in response to changes in stressor variables. Because of the typically weak relations among the stressor and response variables, methods were developed to reduce the effects of non-nutrient biological stressors that could mask the effect of nutrients. Stressor variable concentrations ranged from 0.30 to 11.0 milligrams per liter (mg/L) for total nitrogen, 0.025 to 1.33 mg/L for total phosphorus, 2.9 to 768 milligrams per square meter (mg/m 2 ) for periphyton CHL a , and 0.37 to 42 micrograms per liter (µg/L) for seston CHL a . Turbidity, another stressor variable, ranged from 0.8 to 65.4 Nephelometric turbidity units (NTUs). When the nutrient and CHL a data were compared to Dodds’ trophic classifications, 75.0 percent of the values for total nitrogen, 46.6 percent of the values for total phosphorus, 35.8 percent of the values for periphyton CHL a , and 3.5 percent of the values for seston CHL a , were eutrophic. The invertebrate communities were dominated by families considered highly nutrient tolerant, Chironimidae, (41.7 percent relative abundance), Hydropsychidae, (17.3 percent relative abundance), and Baetidae, (10.2 percent relative abundance). Fish communities were dominated by algivores and nutrient-tolerant species, specifically central stonerollers (13.3 percent relative abundance), creek chubs (9.9 percent relative abundance), and bluntnose minnows (9.3 percent relative abundance). Although not the dominant taxa, white sucker, spotted sucker, green sunfish, and bluegill species were correlated (p ‹0.05) with the stressor variables. The median breakpoints ranged from 2.4 to 3.3 mg/L for total nitrogen, from 0.042 to 0.129 mg/L for total phosphorus, from 54 to 68 mg/m 2 for periphyton CHL a , from 4.5 to 7.5 µg/L for seston CHL a , and from 14.1 to 16.1 NTU for turbidity. The breakpoints determined in this study, in addition to Dodds’ trophic classifications, were used as multiple lines of evidence to show changes in fish and invertebrate community and attributes based on annual exposure to nutrients.

Indiana↗

Aquatic assessment of the Ely Copper Mine Superfund site, Vershire, Vermont

The Ely Mine, which operated from 1821 to 1905, and its area of downstream impact constitute the Ely Copper Mine Superfund site. The site was placed on the National Priorities List in 2001. The mine comprises underground workings, foundations from historical structures, several waste-rock piles, roast beds associated with the smelting operation, and slag piles resulting from the smelting. The mine site is drained by Ely Brook, which includes several tributaries, one of which drains a series of six ponds. Ely Brook empties into Schoolhouse Brook, which flows 3.3 kilometers and joins the Ompompanoosuc River. The aquatic ecosystem at the site was assessed using a variety of approaches that investigated surface-water quality, sediment quality, and various ecological indicators of stream-ecosystem health. The degradation of surface-water quality is dominated by copper with localized effects caused by iron, aluminum, cadmium, and zinc. Chronic water-quality criteria for copper are exceeded in the surface water of four of the six ponds on the Ely Brook tributary, and all of Ely Brook and Schoolhouse Brook, and of the Ompompanoosuc River downstream of the confluence with Schoolhouse Brook. Comparison of hardness-based and Biotic Ligand Model-based water-quality criteria for copper yields similar results with respect to extent of impairment. However, the Biotic Ligand Model criteria are mostly lower than the hardness-based criteria and thus suggest a greater degree of impairment, particularly in the Ely Brook watershed, where dissolved organic carbon concentrations and pH values are lower. Surface-water toxicity testing correlates strongly with the extent of impact. Likewise, riffle-habitat benthic invertebrate richness and abundance data support these results through the stream environment. Similarly, the index of biotic integrity for the fish community in Schoolhouse Brook and the Ompompanoosuc River document degraded habitats throughout Schoolhouse Brook from Ely Brook down to the Ompompanoosuc River. The sediment environment shows similar extents of impairment also dominated by copper, although localized degradation due to chromium, nickel, lead, and zinc was documented on the basis of probable effects concentrations. In contrast, equilibrium-partitioning sediment benchmarks indicate no toxic effects would be expected in sediments at the reference sites, and uncertain toxic effects throughout Ely Brook and Schoolhouse Brook, except for the reference sites and site EB-600M. The results for site EB-600M indicate predicted toxic effects. Acute toxicity testing of in situ pore waters using Hyalella azteca indicates severe impacts in Ely Brook reaching 100 percent lethality at site EB-90M. Acute toxicity testing of in situ pore waters using Chironomus dilutus shows similar, but not as severe, toxicity. Neither set of in situ pore-water toxicity tests showed significant impairment in Schoolhouse Brook or the Ompompanoosuc River. Chronic sediment toxicity testing using Hyalella azteca indicated significant toxicity in Ely Brook, except at site EB-90M, and in Schoolhouse Brook. The low toxicity of EB-90M may be a reflection of the low lability of copper in that sediment as indicated by a low proportion of extractable copper (1.1 percent). Depositional-targeted habitat invertebrate richness and abundance data support these conclusions for the entire watershed, as do the index of biotic integrity data from the fish community. The information was used to develop an overall assessment of the impact on the aquatic system that appears to be a result of the acid rock drainage at the Ely Mine. More than 700 meters of Ely Brook, including two of the six ponds, were found to be severely impacted, on the basis of water-quality data and biological assessments. The reference location was of good quality based on the water quality and biological assessment. More than 3,125 meters of Schoolhouse Brook are also severely impacted, on the basis of water-quality data and biological assessments. The biological community begins to recover near the confluence with the Ompompanoosuc River. The evidence is less conclusive regarding the Ompompanoosuc River. The sediment data suggest that the sediments could be a source of toxicity in Ely Brook and Schoolhouse Brook. The surface-water assessment is consistent with the outcome of a surface-water toxicity testing program performed by the U.S. Environmental Protection Agency for Ely Brook and Schoolhouse Brook and a surface-water toxicity testing program and in situ amphibian testing program for the ponds.

Vermont↗

Breakpoint analysis and relations of nutrient and turbidity stressor variables to macroinvertebrate integrity in streams in the Crawford-Mammoth Cave Uplands Ecoregion, Kentucky, for the development of nutrient criteria

To assist Kentucky in refining numeric nutrient criteria in the Pennyroyal Bioregion, the U.S. Geological Survey and the Kentucky Division of Water collected and analyzed water chemistry, turbidity, and biological-community data from 22 streams throughout the Crawford-Mammoth Cave Upland ecoregion (U.S. Environmental Protection Agency Level IV Ecoregion, 71a) within the Pennyroyal Bioregion from September 2007 to May 2008. Statistically significant and ecologically relevant relations among the stressor (total phosphorus, total nitrogen, and turbidity) variables and response (macroinvertebrate-community attributes) variables and the breakpoint values of biological-community attributes and metrics in response to changes in stressor variables were determined. Thirteen of 18 macroinvertebrate attributes were significantly and ecologically correlated (p-value < 0.10) with at least one nutrient measure. Total number of individuals, Ephemeroptera-Plecoptera-Trichoptera richness, and average tolerance value were macroinvertebrate measures that most strongly correlated with the concentrations of nutrients. Comparison of the average macroinvertebrate-breakpoint value for the median concentration of total phosphorus (TP, 0.033 mg/L) and for median concentration of total nitrogen (TN, 1.1 mg/L) to Dodds' trophic classification for TP and TN indicates streams in the Crawford-Mammoth Cave Uplands ecoregion within the Pennyroyal Bioregion would be classified as mesotrophic-eutrophic. The biological breakpoint relations with median concentrations of TP in this study were similar to the U.S. Environmental Protection Agency proposed numeric TP criteria (0.037 mg/L), but were 1.5 times higher than the proposed numeric criteria for concentrations of TN (0.69 mg/L). No sites were impacted adversely using median turbidity values based on a 25 Formazin nephelometric turbidity unit biological threshold. The breakpoints determined in this study, in addition to Dodds' trophic classifications, were used as multiple lines of evidence to show changes in macroinvertebrate community and attributes based on exposure to nutrients.

Kentucky↗

Seasonal patterns in nutrients, carbon, and algal responses in wadeable streams within three geographically distinct areas of the United States, 2007-08

The U.S. Geological Survey determined seasonal variability in nutrients, carbon, and algal biomass in 22 wadeable streams over a 1-year period during 2007 or 2008 within three geographically distinct areas in the United States. The three areas are the Upper Mississippi River Basin (UMIS) in Minnesota, the Ozark Plateaus (ORZK) in southern Missouri and northern Arkansas, and the Upper Snake River Basin (USNK) in southern Idaho. Seasonal patterns in some constituent concentrations and algal responses were distinct. Nitrate concentrations were greatest during the winter in all study areas potentially because of a reduction in denitrification rates and algal uptake during the winter, along with reduced surface runoff. Decreases in nitrate concentrations during the spring and summer at most stream sites coincided with increased streamflow during the snowmelt runoff or spring storms indicating dilution. The continued decrease in nitrate concentrations during summer potentially is because of a reduction in nitrate inputs (from decreased surface runoff) or increases in biological uptake. In contrast to nitrate concentrations, ammonia concentrations varied among study areas. Ammonia concentration trends were similar at UMIS and USNK sampling sites with winter peak concentrations and rapid decreases in ammonia concentrations by spring or early summer. In contrast, ammonia concentrations at OZRK sampling sites were more variable with peak concentrations later in the year. Ammonia may accumulate in stream water in the winter under ice and snow cover at the UMIS and USNK sites because of limited algal metabolism and increased mineralization of decaying organic matter under reducing conditions within stream bottom sediments. Phosphorus concentration patterns and the type of phosphorus present changes with changing hydrologic conditions and seasons and varied among study areas. Orthophosphate concentrations tended to be greater in the summer at UMIS sites, whereas total phosphorus concentrations at most UMIS and USNK sites peaked in the spring during runoff and then decreased through the remainder of the sampling period. Total phosphorus and orthophosphate concentrations in OZRK streams peaked during summer indicating a runoff-based source of both nutrients. Orthophosphate concentrations may increase in streams in the late summer when surface runoff composes less of total streamflow, and when groundwater containing orthophosphate becomes a more dominant source in streams during lower flows. Seston chlorophyll a concentrations were greatest early in the growing season (spring), whereas the spring runoff events coincided with reductions in benthic algal chlorophyll a biomass likely because of scour of benthic algae from the channel bottom that are entrained in the water column during that period. Nitrate, ammonia, and orthophosphate concentrations also decreased during that same period, indicating dilution in the spring during runoff events. The data from this study indicate that the source of water (surface runoff or groundwater) to a stream and the intensity of major runoff events are important factors controlling instream concentrations. Biological processes appear to affect nutrient concentrations during more stable lower flow periods in later summer, fall, and winter when residence time of water in a channel is longer, which allows more time for biological uptake and transformations. Management of nutrient conditions in streams is challenging and requires an understanding of multiple factors that affect in-stream nutrient concentrations and biological uptake and growth.

Scientific Investigations Report↗

Aquatic assessment of the Pike Hill Copper Mine Superfund site, Corinth, Vermont

The Pike Hill Copper Mine Superfund site in Corinth, Orange County, Vermont, includes the Eureka, Union, and Smith mines along with areas of downstream aquatic ecosystem impairment. The site was placed on the U.S. Environmental Protection Agency (USEPA) National Priorities List in 2004. The mines, which operated from about 1847 to 1919, contain underground workings, foundations from historical structures, several waste-rock piles, and some flotation tailings. The mine site is drained to the northeast by Pike Hill Brook, which includes several wetland areas, and to the southeast by an unnamed tributary that flows to the south and enters Cookville Brook. Both brooks eventually drain into the Waits River, which flows into the Connecticut River. The aquatic ecosystem at the site was assessed using a variety of approaches that investigated surface-water quality, sediment quality, and various ecological indicators of stream-ecosystem health. The degradation of surface-water quality is caused by elevated concentrations of copper, and to a lesser extent cadmium, with localized effects caused by aluminum, iron, and zinc. Copper concentrations in surface waters reached or exceeded the USEPA national recommended chronic water-quality criteria for the protection of aquatic life in all of the Pike Hill Brook sampling locations except for the location farthest downstream, in half of the locations sampled in the tributary to Cookville Brook, and in about half of the locations in one wetland area located in Pike Hill Brook. Most of these same locations also contained concentrations of cadmium that exceeded the chronic water-quality criteria. In contrast, surface waters at background sampling locations were below these criteria for copper and cadmium. Comparison of hardness-based and Biotic Ligand Model (BLM)-based criteria for copper yields similar results with respect to the extent or number of stations impaired for surface waters in the affected area. However, the BLM-based criteria are commonly lower values than the hardness-based criteria and thus suggest a greater degree or magnitude of impairment at the sampling locations. The riffle-habitat benthic invertebrate richness and abundance data correlate strongly with the extent of impact based on water quality for both brooks. Similarly, the fish community assessments document degraded conditions throughout most of Pike Hill Brook, whereas the data for the tributary to Cookville Brook suggest less degradation to this brook. The sediment environment shows similar extents of impairment to the surface-water environment, with most sampling locations in Pike Hill Brook, including the wetland areas, and the tributary to Cookville Brook affected. Sediment impairment is caused by elevated copper concentrations, although localized degradation due to elevated cadmium and zinc concentrations was documented on the basis of exceedances of probable effects concentrations (PECs). In contrast to impairment determined by exceedances of PECs, equilibrium-partitioning sediment benchmarks (based on simultaneously extracted metals, acid volatile sulfides, and total organic carbon) predict no toxic effects in sediments at the background locations and uncertain toxic effects throughout Pike Hill Brook and the tributary to Cookville Brook, with the exception of the most downstream Cookville Brook location, which indicated no toxic effects. Acute laboratory toxicity testing using the amphipod Hyalella azteca and the midge Chironomus dilutus on pore waters extracted from sediment in situ indicate impairment (based on tests with H. azteca ) at only one location in Pike Hill Brook and no impairment in the tributary to Cookville Brook. Chronic laboratory sediment toxicity testing using H. azteca and C. dilutus indicated toxicity in Pike Hill Brook at several locations in the lower reach and two locations in the tributary to Cookville Brook. Toxicity was not indicated for either species in sediment from the most acidic metal-rich location, likely due to the low lability of copper in that sediment, as indicated by a low proportion of extractable copper (simultaneously extracted metal (SEM) copper only 5 percent of total copper) and due to the flushing of acidic metal-rich pore water from experimental chambers as overlying test water was introduced before and replaced periodically during the toxicity tests. Depositional habitat invertebrate richness and abundance data generally agreed with the results of toxicity tests and with the extent of impact in the watersheds on the basis of sediment and pore waters. The information was used to develop an overall assessment of the impact of mine drainage on the aquatic system downstream from the Pike Hill copper mines. Most of Pike Hill Brook, including several wetland areas that are all downstream from the Eureka and Union mines, was found to be impaired on the basis of water-quality data and biological assessments of fish or benthic invertebrate communities. In contrast, only one location in the tributary to Cookville Brook, downstream from the Smith mine, is definitively impaired. The biological community begins to recover at the most downstream locations in both brooks due to natural attenuation from mixing with unimpaired streams. On the basis of water quality and biological assessment, the reference locations were of good quality. The sediment toxicity, chemistry, and aquatic community survey data suggest that the sediments could be a source of toxicity in Pike Hill Brook and the tributary to Cookville Brook. On the basis of water quality, sediment quality, and biologic communities, the impacts of mine drainage on the aquatic ecosystem health of the watersheds in the study area are generally consistent with the toxicity suggested from laboratory toxicity testing on pore water and sediments.

Vermont↗

Nutrient attenuation in rivers and streams, Puget Sound Basin, Washington

Nutrients such as nitrogen and phosphorus are important for aquatic ecosystem health. Excessive amounts of nutrients, however, can make aquatic ecosystems harmful for biota because enhanced growth and decay cycles of aquatic algae can reduce dissolved oxygen in the water. In Puget Sound marine waters, low dissolved oxygen concentrations are observed in a number of marine nearshore areas, and nutrients have been identified as a major stressor to the local ecosystem. Delivery of nutrients from major rivers in the Puget Sound Basin to the marine environment can be large. Therefore, it is important to identify factors related to how nutrients are retained (attenuated) within streams and rivers in the Puget Sound Basin. Physical, chemical, and biological factors related to nutrient attenuation were identified through a review of related scientific literature. Numerous empirical modeling approaches for estimating nutrient attenuation in streams and rivers also were compiled, and a subset of these models was applied to the Puget Sound Basin. In particular, models based on the physical characteristics of a river reach (RivR-N model) and on the physical and biological features of a river reach (v f model) were used and compared for the 17 major rivers draining to the Puget Sound. Data on the relative amount of instream attenuation (the fraction of nutrient input removed per kilometer of stream reach) showed some common and general themes. Firstly, headwater reaches throughout the Puget Sound Basin tend to be better than the main stems of the major rivers at attenuating nitrate and orthophosphorus (ortho-P). Secondly, rivers are more efficient at attenuating nitrate than ortho-P, probably because of the close relation between phosphorus and suspended sediment, which was not captured fully in the models. Thirdly, when comparing the RivR-N and v f models for nitrate, physical characteristics of the channel may be more effective predictors of relative nitrate attenuation for main stem reaches, whereas biological factors may be more effective predictors in headwater reaches. These results are explained in terms of four primary factors of attenuation: sinuosity, channel slope, specific discharge, and uptake velocity (v f ) of the reach. A simple scoring procedure based on these four factors showed that reaches where attenuation scores were high had higher relative attenuation of nutrients from the RivR-N and v f models. This attenuation "scorecard" can be used to quickly assess the potential for a given reach to attenuate nutrients. Seasonal relative attenuation at three case studies was greater in summer months (July through September) and much lower and almost constant from January through June. An analysis of relative attenuation across a range of nutrient concentrations showed that, at some point, relative instream attenuation is minimized. For nitrate, relative attenuation reached a minimum value greater than 3 milligrams of nitrogen per liter (mg N/L) during low flow and 1 mg N/L during high flow. For orthophosphate, minimum relative attenuation was observed at about 0.1 milligram of phosphorus per liter (mg P/L) for both low- and high-flow conditions. Generally, the temporal dynamics of nutrient attenuation are dependent on the travel time through a given reach, the proportion of flow in contact with the sediment, and the amount of biological activity. Improved understanding of nutrient attenuation in Puget Sound Basin will benefit from the compilation of more detailed data for specific discharge, channel slope, and channel sinuosity in Puget Sound streams and rivers. Additionally, field studies examining upstream-downstream changes in nutrient load and field-based measurements of v f are needed. From a management perspective, preservation and improvement of instream nutrient attenuation should focus on increasing the travel time through a reach and contact time of water sediment (reactive) surfaces and lowering nutrient concentrations (and loads) to avoid saturation of instream attenuation and increase attenuation efficiency. These goals can be reached by maintaining and restoring channel-flood plain connectivity, maintaining and restoring healthy riparian zones along streams, managing point and nonpoint nutrient loads to streams and rivers, and restoring channel features that promote attenuation such as the addition of woody debris and maintaining pool-riffle morphologies. Many of these management approaches are already being undertaken during projects aimed to restore quality salmon habitat. Therefore, there is a dual benefit to these projects that also may lead to enhanced potential for nitrogen and phosphorus attenuation.

Washington↗

An international borderland of concern: Conservation of biodiversity in the Lower Rio Grande Valley

The Lower Rio Grande Valley (LRGV) of southern Texas is located on the United States-Mexico borderland and represents a 240-kilometer (150-mile) linear stretch that ends at the Gulf of Mexico. The LRGV represents a unique transition between temperate and tropical conditions and, as such, sustains an exceptionally high diversity of plants and animals—some of them found in few, or no other, places in the United States. Examples include Leopardus pardalis albescens (northern ocelot) and Falco femoralis septentrionalis (northern aplomado falcon)—both endangered in the United States and emblematic of the LRGV. The U.S. Fish and Wildlife Service (USFWS) manages three national wildlife refuges (Santa Ana, Lower Rio Grande Valley, and Laguna Atascosa) that together make up the South Texas Refuge Complex, which actively conserves biodiversity in about 76,006 hectares (187,815.5 acres) of native riparian and upland habitats in the LRGV. These diminished habitats harbor many rare, threatened, and endangered species. This report updates the widely used 1988 USFWS biological report titled “Tamaulipan Brushland of the Lower Rio Grande Valley of South Texas: Description, Human Impacts, and Management Options” by synthesizing nearly 400 peer-reviewed scientific publications that have resulted from biological and sociological research conducted specifically in the four Texas counties of the LRGV in the past nearly 30 years. This report has three goals: (1) synthesize scientific insights gained since 1988 related to the biology and management of the LRGV and its unique biota, focusing on flora and fauna of greatest conservation concern; (2) update ongoing challenges facing Federal and State agencies and organizations that focus on conservation or key natural resources in the LRGV; and (3) redefine conservation opportunities and land-acquisition strategies that are feasible and appropriate today, given the many new and expanding constraints that challenge conservation activities in the LRGV. The LRGV faces every contemporary conservation challenge of the 21st century, but ongoing human population growth and its associated demands, international border issues, and oil, gas, and alternative energy development dominate impacts that affect conservation in the LRGV. Continued careful syntheses of existing and future information collected in the LRGV are needed on many biological and sociological topics to guide conservation activities. Quick response will no doubt be necessary to face contemporary and difficult-to-predict challenges such as climate change, diminished water availability and quality, spread of invasive species, and habitat loss and fragmentation. Complexities of a guarded international borderland add pressure to small patches of native habitat that remain in many places of the LRGV, particularly along the Rio Grande. Large connected corridors of restored native habitat could be the best option to maintain, and even enhance, the exceptional biodiversity of the LRGV in the face of exceptional human demand.

Texas↗

Ecological status of aquatic communities in selected streams in the Milwaukee Metropolitan Sewerage District planning area of Wisconsin, 2004–13

A total of 14 wadable streams in urban or urbanizing watersheds near Milwaukee, Wisconsin, were sampled in 2004, 2007, 2010, and 2013 to assess the ecological status of aquatic communities (biota), including benthic algae and invertebrates, and fish. To assess temporal variation, additional community sampling was also done at a subset of three sites in 2011 and 2012. Relative abundances of each type of organism were used to calculate biological metrics, such as richness and diversity, percentages of intolerant and tolerant organisms, and indexes of biotic integrity for invertebrates and fish. Selected environmental (physical and chemical) data in the streams were collected to evaluate potential relations to the biota and the ecological health of the stream. Physical and chemical data included land use/land cover, stream discharge from U.S. Geological Survey (USGS) streamgages (except at 2 creeks that were not gaged), stream habitat, microhabitat at invertebrate collection locations, water quality (except at 2 creeks that were not gaged), field measurements of several water-quality constituents, measures of benthic algal biomass, and toxicity and chemical tests on extracts from passive samplers deployed at a subset of 6 sites. Relative abundances of organisms and biological metrics were compared among sampling years and with environmental metrics to evaluate the ecological status of these streams and determine primary stressors on the aquatic communities, with the aim of helping resource managers understand and work toward improving the ecological health of these and other urban and urbanizing rivers in the study area. Biological metrics for most sites indicated some level of diminished ecological status when compared across all sampled sites and when compared with rating scales for selected metrics. The least degraded sites among all those sampled—indicated by aggregate bioassessments for algae, invertebrates, and fish metrics and in order starting with the best overall condition—were the Milwaukee River near Cedarburg, Menomonee River at Menomonee Falls, Jewel Creek, and Milwaukee River at Milwaukee. The most degraded sites were Menomonee River at Wauwatosa, Root River at Greenfield, Lincoln Creek, and the Kinnickinnic River. Differences in aggregate bioassessments indicate that aquatic communities at the Menomonee River at Wauwatosa site and the Root River at Greenfield site were worse in 2013 than in 2004; however, Oak Creek and Honey Creek sites were better. In 2013, several sites had less than 30-percent pollution-sensitive diatoms indicating degraded algal assemblages. Invertebrate metrics for most of the 14 sites in 2013 were lower than in 2004 and indicate that invertebrate assemblages at most sampled sites were more degraded in 2013. Tolerant fish taxa made up more than 40 percent of assemblages at most sites and nearly 100 percent of assemblages at four sites. At times, in some smaller streams, too few fish were captured to compute an Index of Biotic Integrity with confidence, and invertebrates provided a better means for assessing the ecological status and water quality. With these few exceptions, the use of all three groups of biota provided the most robust assessments at the 14 sites in 2004–13. Physical and chemical stressors were correlated to adverse effects on aquatic biota at the sampled streams. Passive samplers were deployed at a subset of six sites in 2013. Microtox results indicated there was little or no toxicity at the Milwaukee River near Cedarburg site and at the Oak Creek site, slight toxicity at the Lincoln Creek and Honey Creek sites, and moderate toxicity at the Milwaukee River at Milwaukee site and the Little Menomonee River site; however, based on cytochrome-P450 reporter gene system toxicity tests, potential toxicity from hydrophobic organic contaminants was measured at all six sites. For all 14 sites, physical and chemical stressors related to urbanization correlated with biological metrics for algae, invertebrates, and fish. Most stressors for aquatic biota reflected an urban signature. Stressors related to ecological condition in our study were chemical and physical, such as developed land, impervious surface in the watershed, urban land in a buffer area around the stream (a 100-foot [30-meter]-wide area on each side of the stream, and maximum instantaneous discharge normalized by drainage area (a measure of flood and scour effects). Chemical stressors included low waterborne concentrations of dissolved oxygen and high concentrations of chloride, zinc and other metals, nutrients (nitrite and phosphorus), and fecal coliform bacteria. Although algae, invertebrates, and fish did not always demonstrate a significant response to the same stressors, higher abundances of high total phosphorus-indicator diatoms, lower ratings for invertebrate biotic integrity indexes and percentages of mayflies-stoneflies-caddisflies, and lower values for fish biotic integrity indexes underscored possible adverse effects of even low levels of developed land. Developed land is typically associated with more rapid runoff, which washes chemicals from impervious surfaces into area waterways and degrades stream habitat for aquatic communities. However, with respect to at least chloride from road salt, diatoms tolerant to dissolved salts were significantly lower with as little as 1-percent mixed forest in the watershed. Lower percentages of urban land in the stream buffer correlated with healthier aquatic assemblages of algae, invertebrates, and fish. The assessment of algal, invertebrate, and fish assemblages coupled with physical and chemical data were highly useful in evaluating the ecological status of aquatic communities at the 14 sites and for determining environmental stressors that may be contributing to reduced stream condition. Some of the stressors could potentially be removed or lessened with stream rehabilitation or changes in watershed management.

Wisconsin↗

Water-quality and aquatic-community characteristics of selected reaches of the St. Croix River, Minnesota and Wisconsin, 2000

Synoptic sampling was used to determine chemical and biological characteristics of the St. Croix River within a study reach that extended from near Danbury, Wisconsin to the confluence with the Mississippi River at Prescott, Wisconsin. The study was conducted August 7- September 25, 2000 during summer low flow. Dissolved-residue concentrations were found to increase gradually as the river flows downstream, with an abrupt increase downstream of the confluence with the Sunrise River that was primarily attributed to an increase in calcium and magnesium. Dissolved residue concentrations were further augmented by increased yields of chloride and sulfate in the part of the St. Croix Basin between Nevers Dam near St. Croix Falls, Wisconsin and Marine on St. Croix, Minnesota. Nearly all of the nitrogen in transport was in the form of nitrate and organic nitrogen. Organic nitrogen, mainly in particulate form, accounted for most of the gain in total nitrogen load within the study reach. Nitrogen loading to the mainstem indicated relatively uniform nitrogen inputs from the Clam River, Kettle River, and Snake River watersheds. The rate of nitrogen load accrual increased downstream of the confluence with the Sunrise River and in the subreach extending from Nevers Dam through St. Croix Falls to Franconia, Minnesota. Nitrogen load also increased, primarily because of nitrate input, in the part of Lake St. Croix downstream of the confluence with the Kinnickinnic River. Total phosphorus concentrations and loads reflected variations in the amount of particulate phosphorus in transport. Phosphorus loading increased in the part of the St. Croix River that includes Danbury and the confluences of the Yellow River and Clam River. Phosphorus loading also increased downstream of the confluence with the Sunrise River, but the greatest load increase occurred between Nevers Dam and Franconia. Phosphorus load decreased substantially as the river flowed through the pooled reach of Lake St. Croix downstream of Stillwater. Suspended-sediment concentrations were low, ranging from 4.0 to 36 milligrams per liter. The small amount of sediment in transport was reflected in turbidity measurements that ranged from 0.5 to 3.6 Nephelometry Turbidity Units, and transparency tube measurements that were greater than 60 centimeters at all sites. Biological measures of resource quality change in the St. Croix River along its course from Danbury to Prescott. Changes in the biological indicators of resource quality (fish and invertebrate community composition) are most notable just upstream and downstream of the dam at St. Croix Falls, Wisconsin. Aquatic communities in the upper St. Croix River, from near Danbury to near Rush City, Minnesota, indicate minimal physical and chemical disturbance as evidenced by relatively high taxa richness and greater proportions of taxa intolerant to physical and chemical disturbance. In contrast, aquatic communities downstream of the Sunrise River to Marine on St. Croix indicate both physical and chemical disturbance. Resource monitoring, consisting of short-term diagnostic studies, may be needed in parts of the St. Croix River mainstem and tributaries where results from this study indicate constituent loading is greatest and where the aquatic community composition indicates disturbance. Longer-term trend monitoring may be needed to detect physical, chemical and biological responses to natural processes and human activities in the St. Croix River Basin.

Minnesota, Wisconsin↗

Resurvey of quality of surface water and bottom material of the Barataria Preserve of Jean Lafitte National Historical Park and Preserve, Louisiana, 1999-2000

The quality of water and bottom material in the Barataria Preserve of Jean Lafitte National Historical Park and Preserve, Louisiana, was surveyed from March 1999 to May 2000. Organochlorine, chlorophenoxy acid, and organophosphorus pesticides; polychlorinated biphenyls (PCB's); and trace elements were analyzed in surface water and bottom material from three sites previously sampled in a 1981-82 survey. Surface water at six sites was sampled and analyzed for selected nutrients and major inorganic ions based on their importance to human health, the health of the marshes of the Barataria Preserve, or their usefulness in tracking the circulation of Mississippi River water in the Barataria Preserve. Southern Louisiana was in a moderate to severe drought during most of the sampling period, which elevated salinity in the Barataria Preserve for at least 8 months. Specific conductance values were less than 3,000 µS/cm (microsiemens per centimeter at 25 degrees Celsius) in surface water throughout the Barataria Preserve from March through September 1999. Specific conductance values increased over the next 2 months and then remained between 5,000 and 6,000 µS/cm. The herbicide 2,4-D was detected in water at the two sites sampled in August 1999 but not at any site during the two other sampling times. Iron, manganese, and the trace elements copper, nickel, and zinc were detected in dissolved and whole-water samples at all three sites. Nitrite+ nitrate, as nitrogen, concentrations ranged from less than 0.002 to 0.19 mg/L (milligrams per liter). Ammonia, as nitrogen, concentrations ranged from less than 0.01 to 0.16 mg/L. Orthophosphate, as phosphorus, concentrations ranged from less than 0.002 to 0.14 mg/L. Calcium, magnesium, potassium, sulfate, and chloride concentrations in surface water were elevated due to the marine influence on the composition of surface water in the Barataria Preserve during the sampling period. Sulfate and chloride concentrations reached 379 and 2,830 mg/L, respectively. Polychlorinated biphenyls, chlordane, and DDT were detected in bottom material. Trace elements were detected in bottom material at all three of the sampled sites. Arsenic concentrations ranged from 4 to 9 µg/g (micrograms per gram) and lead concentrations from 20 to 31 µg/g. Mercury concentrations also were above laboratory reporting levels (LRL's) for bottom material at all three sites. The herbicide 2,4-D was detected in surface water during both surveys. Other organic compounds were not detected in surface water. Mercury and chromium were detected in surface water at all three sites during the 1981-82 survey but were below LRL?s during the 1999-2000 survey. Changes in chemical characteristics of bottom material occurred during the years between the 1981-82 and 1999-2000 surveys. DDT decreased in the bottom material at Bayou Segnette near Barataria. DDE, a degradation product, increased at this site, indicating that over time, DDT concentrations are decreasing in bottom material. PCB's were present in similar concentrations (Bayou Segnette near Barataria) or increased (Bayou Segnette 4.6 miles below Westwego) from 1981-82 to 1999-2000. Cadmium concentrations consistently decreased by half or more at all three sites from 1981-82 to 1999-2000. Mercury concentrations were consistently lower at all three sites in the 1999-2000 survey, but the differences from the 1981-82 survey were small. Chromium concentrations increased at two of the three sites from 1981-82 to the present survey. At the third site, no chromium value was available for the earlier survey. Concentrations of copper and nickel increased in bottom material at the two sites on Bayou Segnette, but decreased at Kenta Canal northwest of Westwego. Probable Effects Levels (PEL's) and Interim Sediment Quality Guidelines (ISQG's) concentrations, as tabulated by the Canadian Council of Ministers of the of the Environment, were used to assess the probability of biological impairment in the Barataria Preserve. PEL’s are concentrations of a chemical at or above which some biological impairment is likely. ISQG concentrations are those at or below which biological impairment is unlikely. Concentrations of 2,4-D and trace elements, when detected in surface water, were substantially lower than levels at which biological impairment could be expected. Concentrations of organic compounds in bottom material were at most less than 25 percent of PEL’s, and usually much lower. Arsenic, cadmium, copper, and lead concentrations in bottom material were generally slightly above or lower than ISQG concentrations in both surveys, although arsenic was as high as 53 percent of PEL’s at one site in the 1999-2000 survey. All other trace elements in bottom material were present in concentrations lower than ISQG concentrations.

Louisiana↗

Characteristics of water-quality data for Lake Houston, selected tributary inflows to Lake Houston, and the Trinity River near Lake Houston (a potential source of interbasin transfer), August 1983-September 1990

Lake Houston, a reservoir completed in 1954 about 25 miles east-northeast of Houston, Texas, is a principal surface-water source for the city of Houston. The increase in water supply to meet future demands is expected to be accommodated by supplementing surface-water inflows to Lake Houston. The Trinity River is considered a potential source for interbasin transfer of water to Lake Houston. Before beginning to supplement inflows, the City needs to better understand the potential effects on Lake Houston water quality from streams that flow into or might contribute water to Lake Houston. During 1983&ndash;90, the USGS collected 3,727 water-quality samples from 27 sites in Lake Houston, 6 of the 7 main tributaries to the lake, and the Trinity River at Romayor. Longitudinal profiles of water temperature, dissolved oxygen, specific conductance, pH, and nutrients from the dam to the East and West Forks of Lake Houston constructed for a winter day and a summer day indicate that in general the lake water is mixed in the winter and stratified in the summer. The results of Mann-Whitney rank-sum tests to determine whether there were significant differences between summer and non-summer field measurements, 5-day biological oxygen demand, bacteria, physical and aesthetic properties, nutrients, organic carbon, chlorophyll a, and trace elements in the lake nearest the dam, the East Fork of the lake, and the West Fork of the lake at the same relative depth showed significant differences between summer and non-summer samples for at least one of the three locations at the same relative depth for all 15 properties and constituents tested except specific conductance. The test results indicate that in general Lake Houston is well mixed in the non-summer period and stratified with respect to selected properties and constituents in the summer. The results of rank-sum tests to determine whether there were significant differences between field measurements, 5-day biological oxygen demand, physical and aesthetic properties, nutrients, organic carbon, and chlorophyll a in the lake nearest the dam, the East Fork of the lake, and the West Fork of the lake for samples collected during the same season at the same relative depth showed that significant differences were common; generally, the West Fork had the largest median concentrations among the three locations. The tests comparing trace element concentrations between the lake nearest the dam and the East Fork showed mixed results&mdash;large median dissolved manganese concentrations in lake bottom samples in the summer and in East Fork near-surface samples in the non-summer period. The results of rank-sum tests comparing selected properties, 5-day biological oxygen demand, bacteria, nutrients, and total organic carbon in the eastern tributaries with those in the western tributaries, in the eastern tributaries with those in the Trinity River, and in the western tributaries with those in the Trinity River during the same season (summer or non-summer) at the same relative streamflow (low-medium or high) showed that significant differences were more common than not. In the comparisons of the eastern tributaries with the western tributaries that resulted in significant differences, medians of the western tributaries were larger for all properties and constituents except total organic carbon; in the comparisons of the eastern tributaries with the Trinity River that resulted in significant differences, medians were larger for the Trinity River in about 60 percent of the tests; and in the comparisons of the western tributaries with the Trinity River that resulted in significant differences, medians were larger for the western tributaries in about 60 percent of the tests. In the tests comparing trace elements between the eastern and western tributaries during the same season at the same relative streamflow, five of the eight tests showed no significant differences; between the eastern tributaries and the Trinity River, all eight tests showed significant differences, with eastern tributary medians larger in all tests; and between the western tributaries and the Trinity River, seven of the eight tests showed significant differences, with western tributary medians larger in all seven tests. The tests comparing selected properties, 5-day biological oxygen demand, nutrients, and total organic carbon between the eastern tributaries and the East Fork of Lake Houston, between the western tributaries and the West Fork of Lake Houston, and between the Trinity River and the lake nearest the dam, the East Fork, and the West Fork during the same season (summer or nonsummer) yielded significant differences in about 60 percent of the tests. No discernible pattern emerged to associate significant differences with season. In the tests comparing trace elements between the tributaries and the respective forks of the lake to which the tributaries drain, iron concentrations were significantly different in three of the four tests, with median concentrations larger in the tributaries. All the tests comparing manganese between the Trinity River and the three locations in the lake yielded significant differences, with larger median concentrations in the lake.

Texas↗

Global research priorities for sea turtles: Informing management and conservation in the 21st century

Over the past 3 decades, the status of sea turtles and the need for their protection to aid population recovery have increasingly captured the interest of government agencies, non-governmental organisations (NGOs) and the general public worldwide. This interest has been matched by increased research attention, focusing on a wide variety of topics relating to sea turtle biology and ecology, together with the interrelations of sea turtles with the physical and natural environments. Although sea turtles have been better studied than most other marine fauna, management actions and their evaluation are often hindered by the lack of data on turtle biology, human–turtle interactions, turtle population status and threats. In an effort to inform effective sea turtle conservation a list of priority research questions was assembled based on the opinions of 35 sea turtle researchers from 13 nations working in fields related to turtle biology and/or conservation. The combined experience of the contributing researchers spanned the globe as well as many relevant disciplines involved in conservation research. An initial list of more than 200 questions gathered from respondents was condensed into 20 metaquestions and classified under 5 categories: reproductive biology, biogeography, population ecology, threats and conservation strategies.

Endangered Species Research↗

Seabirds as indicators of marine ecosystems: Introduction: A modern role for seabirds as indicators

A key requirement for implementing ecosystem-based management is to obtain timely information on significant fluctuations in the ecosystem (Botsford et al. 1997). However, obtaining all necessary information about physical and biological changes at appropriate temporal and spatial scales is a daunting task. Intuitively, one might assume that physical data are more important for the interpretation of ecosystem changes than biological data, but analyses of time series data suggest otherwise: physical data are more erratic and often confusing over the short term compared to biological data, which tend to fluctuate less on annual time scales (Hare & Mantua 2000). Even so, biological time-series may also be confusing when coexisting marine species respond differently to ecosystem variability. For example, while warming temperatures in the Gulf of Alaska following the 1976 to 1977 regime shift favored an increase in gadoids and flatfish, a variety of forage fish and pandalid shrimp species virtually disappeared (Anderson & Piatt 1999). Zooplankton communities in the Gulf of Alaska also demonstrated similar patterns of response (Francis et al. 1998). At the basin scale, favorable conditions for salmon in Alaska following the regime shift were matched inversely by poor conditions in the California Current (Francis et al. 1998). In marine birds, subtropical species increased, while subarctic ones decreased during a warming phase in the southern California Bight. Clearly, no single index can tell the whole story accurately. Multi-species, multi-region, and multi-trophic level approaches are needed to quantify fluctuations in marine ecosystem processes and in the distribution and abundance of its inhabitants, to determine critical parameter thresholds and to use this information in management and marine conservation.

Marine Ecology Progress Series↗

Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland

Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata - Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing of ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0–0.5 or 0–10 cm) across the N-amendment gradient (0, 7, and 15 kg ha −1 yr −1 ). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Given the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.

Frontiers in Microbiology↗