SEARCH · Geology Reports

Results for “Biological Invasions”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

714 records · Page 40Linked to original sources

USGS2021

Weed-suppressive bacteria effects differ in culture compared to in soils and with or without microbial competition and separation of active ingredient

Weed-suppressive bacteria (WSB), specifically the D7 and ACK55 strains of Pseudomonas fluorescens , were previously reported to selectively inhibit growth of invasive annual grasses (IAGs) that have caused severe ecosystem degradation across much of the western US. However, recent studies show highly mixed evidence for WSB effectiveness in field settings. We evaluated how the effectiveness of WSB, specifically selective inhibition of exotic annual but not native perennial grasses, was altered by (1) growth media (soil vs. agar culture), (2) pre-sterilization to remove competing microbes, and (3) WSB concentration, reduced by centrifuging with and without filtration. WSB had no effects in soil microcosms with or without pre-sterilization, but WSB did have effects in agar cultures. On agar, WSB effects were amplified by pre-sterilizing seeds prior to treatment with WSB inoculum – but effects were non-selective (i.e., native and exotic plants were equally inhibited) with or without pre-sterilization at high WSB concentration. The only selective effects of WSB were observed on agar at low WSB concentrations, made possible by centrifuging WSB cells out of the inoculum prior to treatment application (from ~10 7 to ~10 5 live cells/ml). Completely removing WSB cells from inoculum by filtration led to no WSB effects. While these results suggest the desired effects of WSB can be reproduced on agar with a supernatant containing the putative active agent and a low density of WSB cells, the effect is still not reproducible for plants in soil, even when competing microbes are removed. Thus, additional research is needed to determine if, when, where, and how WSB could be effective in field settings.

Biological Control↗

USGS2025

Application of fin tissue for nonlethal stable isotope analysis of small-bodied fishes

Stable isotopes are commonly used to characterize food web structure and resource use by aquatic organisms. White muscle is generally preferred for stable isotope analysis of fishes. However, obtaining white muscle tissue typically requires lethal take or invasive sampling techniques, which are undesirable for small-bodied species or those of conservation concern. We assessed the use of fish fin as a nonlethal alternative to muscle tissue for stable isotope analysis of four small-bodied fishes native to the upper Red River drainage of Texas and Oklahoma, USA: plains minnow Hybognathus placitus , prairie chub Macrhybopsis australis , Red River shiner Alburnops bairdi , and Red River pupfish Cyprinodon rubrofluviatilis . Fin isotope values were strong predictors of both δ 15 N and δ 13 C muscle isotope values (ANCOVA: δ 15 N: F 1,451 = 5312.09, P < 0.001; δ 13 C: F 1,451 = 7864.39, P < 0.001), although isotopic composition varied among species for δ 13 C ( F 3,451 = 4.29, P < 0.01). Species-specific regression models indicated positive linear relationships between fin and muscle isotope values (δ 15 N: P < 0.001, R 2 ≥ 0.80; δ 13 C: P < 0.001, R 2 ≥ 0.83) that did not vary significantly with body size or age of individuals. We suggest minimum total length thresholds for least destructive fin clipping at 70 mm, 62 mm, and 48 mm for plains minnow, prairie chub, and Red River pupfish, respectively. Nonlethal fin clipping may not be viable for Red River shiner within the size range reported here as multiple fins were required for routine analysis. Overall, we conclude that fin tissue may be used for δ 15 N and δ 13 C assessments to mitigate lethal take of imperiled, small-bodied fishes.

Oklahoma, Texas↗

USGS2015

Wide-ranging phylogeographic structure of invasive red lionfish in the Western Atlantic and Greater Caribbean

The red lionfish ( Pterois volitans ) is an invasive predatory marine fish that has rapidly expanded its presence in the Western Hemisphere. We collected 214 invasive red lionfish samples from nine countries and territories, including seven unpublished locations. To more comprehensively evaluate connectivity, we compiled our d-loop sequence data with 846 published sequences, resulting in 1,060 samples from 14 locations. We found low nucleotide diversity ( π = 0.003) and moderate haplotype diversity ( h = 0.59). Using haplotype population pairwise Φ ST tests, we analyzed possible phylogeographic breaks that were previously proposed based on other reef organisms. We found support for the Bahamas/Turks/Caicos versus Caribbean break ( Φ ST = 0.12) but not for the Northwestern Caribbean, Eastern Caribbean, or US East Coast versus Bahamas breaks. The Northern Region had higher variation and more haplotypes, supporting introductions of at least five haplotypes to the region. Our wide-ranging samples showed that a lower-frequency haplotype in the Northern Region dominated the Southern Region and suggested multiple introductions, possibly to the south. We tested multiple scenarios of phylogeographic structure with analyses of molecular variance and found support for a Northern and Southern Region split at the Bahamas/Turks/Caicos versus Caribbean break (percentage of variation among regions = 8.49 %). We found that Puerto Rico clustered with the Southern Region more strongly than with the Northern Region, as opposed to previous reports. We also found the rare haplotype H03 for the first time in the southern Caribbean (Panama), indicating that either secondary releases occurred or that the low-frequency haplotypes have had time to disperse to extreme southern Caribbean locations.

Marine Biology↗

USGS2015

Book review: Restoring paradise: Rethinking and rebuilding nature in Hawaii

The native ecosystems of Hawai‘i have been severely degraded by the introduction of herbivorous mammals and a myriad of invasive plant species. Left unmanaged, most natural areas would continue along a trajectory towards domination by nonnative species; however, several projects have undertaken the daunting task of ecological restoration, four of which are the subject of Restoring Paradise by Robert Cabin: Hakalau Forest National Wildlife Refuge; Hawai‘i Volcanoes National Park; the Auwahi dryland forest, Maui and Limahuli Garden and Preserve, Kaua‘i. After an introductory section discussing the setting and factors that have contributed to so much of the degradation and extinction of Hawai‘i’s native biota, Cabin outlines two different views of restoration in two central sections of the book: ad hoc, trial-and-error approaches versus the careful application of science to direct restoration. The time-tested methods of fence construction, ungulate removal, weed control, and replanting native species with the help of numerous volunteers and community support are presented in marked contrast to inconsistent applications of science in guiding restoration, and illustrated by some of the author’s unsuccessful research. The book is largely presented as a non-technical first-person account of travels and meetings with key personalities driving restoration projects. The philosophies of restoration practitioners are embedded in passages from interviews. Setbacks, obstacles, logistical constraints, and successes are narrated in between as Cabin revisits each of the restoration sites. The utility of science in restoration is frequently questioned by the author and sometimes abandoned by practitioners in favour of a ‘let-nature-take-its-course’ approach. Review info: Restoring Paradise: Rethinking and Rebuilding Nature in Hawaii . By Robert J. Cabin, 2013. ISBN: 978-0822836931, 236 pp.

Pacific Conservation Biology↗

USGS2026

A regional simulation modeling framework for evaluating invasive annual grass management across the sagebrush biome

Invasive annual grasses (IAG) continue to spread within the sagebrush biome of the western United States, degrading plant communities and wildlife habitat, decreasing forage for ranching livelihoods, and heightening wildfire risk. Effective management of IAGs requires action and long-term strategic planning across the sagebrush biome, but the cumulative effects of IAG treatments over time and space are not well understood, especially over broad extents defined for strategies like the Sagebrush Conservation Design. We developed a simulation model and sampling framework that allow local-scale actions to be ‘scaled up’ to evaluate large-scale regional and biome-wide management strategy outcomes. We worked with natural resource managers and experts to co-develop a spatially explicit state-and-transition simulation model of IAG dynamics in sagebrush landscapes that can be used to evaluate alternative management strategies. We evaluated our framework by contrasting two baseline scenarios in terms of their long-term effects on the sagebrush biome. We show that focusing management efforts on moderate to high IAG cover was effective at reducing full conversion to IAGs but failed to prevent widespread establishment of IAGs in core sagebrush areas, exposing them to increased risk of wildfire and wildlife habitat degradation. The results of our model help quantify the extent of the problem that IAGs pose to sagebrush ecosystems given current knowledge and management efforts. Our framework provides a platform to explore alternative management strategy outcomes and can help managers develop informed conservation plans with realistic expectations for return on investment of resources committed to sagebrush landscapes.

Arizona, California, Colorado, Idaho, Montana, Nev↗

USGS2021

The scope and severity of white-nose syndrome on hibernating bats in North America

Assessing the scope and severity of threats is necessary for evaluating impacts on populations to inform conservation planning. Quantitative threat assessment often requires monitoring programs that provide reliable data over relevant spatial and temporal scales, yet such programs can be difficult to justify until there is an apparent stressor. Leveraging efforts of wildlife management agencies to record winter counts of hibernating bats, we collated data for 5 species from over 200 sites across 27 U.S. states and 2 Canadian provinces from 1995 to 2018 to determine the impact of white-nose syndrome (WNS), a deadly disease of hibernating bats. We estimated declines of winter counts of bat colonies at sites where the invasive fungus that causes WNS ( Pseudogymnoascus destructans ) had been detected to assess the threat impact of WNS. Three species undergoing species status assessment by the U.S. Fish and Wildlife Service ( Myotis septentrionalis , Myotis lucifugus , and Perimyotis subflavus ) declined by more than 90%, which warrants classifying the severity of the WNS threat as extreme based on criteria used by NatureServe. The scope of the WNS threat as defined by NatureServe criteria was large (36% of Myotis lucifugus range) to pervasive (79% of Myotis septentrionalis range) for these species. Declines for 2 other species ( Myotis sodalis and Eptesicus fuscus ) were less severe but still qualified as moderate to serious based on NatureServe criteria. Data-sharing across jurisdictions provided a comprehensive evaluation of scope and severity of the threat of WNS and indicated regional differences that can inform response efforts at international, national, and state or provincial jurisdictions. We assessed the threat impact of an emerging infectious disease by uniting monitoring efforts across jurisdictional boundaries and demonstrated the importance of coordinated monitoring programs, such as the North American Bat Monitoring Program (NABat), for data-driven conservation assessments and planning.

Conservation Biology↗

USGS2015

A typology of time-scale mismatches and behavioral interventions to diagnose and solve conservation problems

Ecological systems often operate on time scales significantly longer or shorter than the time scales typical of human decision making, which causes substantial difficulty for conservation and management in socioecological systems. For example, invasive species may move faster than humans can diagnose problems and initiate solutions, and climate systems may exhibit long-term inertia and short-term fluctuations that obscure learning about the efficacy of management efforts in many ecological systems. We adopted a management-decision framework that distinguishes decision makers within public institutions from individual actors within the social system, calls attention to the ways socioecological systems respond to decision makers’ actions, and notes institutional learning that accrues from observing these responses. We used this framework, along with insights from bedeviling conservation problems, to create a typology that identifies problematic time-scale mismatches occurring between individual decision makers in public institutions and between individual actors in the social or ecological system. We also considered solutions that involve modifying human perception and behavior at the individual level as a means of resolving these problematic mismatches. The potential solutions are derived from the behavioral economics and psychology literature on temporal challenges in decision making, such as the human tendency to discount future outcomes at irrationally high rates. These solutions range from framing environmental decisions to enhance the salience of long-term consequences, to using structured decision processes that make time scales of actions and consequences more explicit, to structural solutions aimed at altering the consequences of short-sighted behavior to make it less appealing. Additional application of these tools and long-term evaluation measures that assess not just behavioral changes but also associated changes in ecological systems are needed.

Conservation Biology↗

USGS2012

Global change effects on Bromus tectorum L. (Poaceae) at its high-elevation range margin

Global change is likely to affect invasive species distribution, especially at range margins. In the eastern Sierra Nevada, California, USA, the invasive annual grass, Bromus tectorum , is patchily distributed and its impacts have been minimal compared with other areas of the Intermountain West. We used a series of in situ field manipulations to determine how B. tectorum might respond to changing climatic conditions and increased nitrogen deposition at the high-elevation edge of its invaded range. Over 3 years, we used snow fences to simulate changes in snowpack, irrigation to simulate increased frequency and magnitude of springtime precipitation, and added nitrogen (N) at three levels (0, 5, and 10 g m -2 ) to natural patches of B. tectorum growing under the two dominant shrubs, Artemisia tridentata and Purshia tridentata , and in intershrub spaces (INTR). We found that B. tectorum seedling density in April was lower following deeper snowpack possibly due to delayed emergence, yet there was no change in spikelet production or biomass accumulation at the time of harvest. Additional spring rain events increased B. tectorum biomass and spikelet production in INTR plots only. Plants were primarily limited by water in 2009, but colimited by N and water in 2011, possibly due to differences in antecedent moisture conditions at the time of treatments. The threshold at which N had an effect varied with magnitude of water additions. Frequency of rain events was more influential than magnitude in driving B. tectorum growth and fecundity responses. Our results suggest that predicted shifts from snow to rain could facilitate expansion of B. tectorum at high elevation depending on timing of rain events and level of N deposition. We found evidence for P-limitation at this site and an increase in P-availability with N additions, suggesting that stoichiometric relationships may also influence B. tectorum spread.

California↗

USGS2022

Impoundment increases methane emissions in Phragmites-invaded coastal wetlands

Saline tidal wetlands are important sites of carbon sequestration and produce negligible methane (CH 4 ) emissions due to regular inundation with sulfate-rich seawater. Yet, widespread management of coastal hydrology has restricted tidal exchange in vast areas of coastal wetlands. These ecosystems often undergo impoundment and freshening, which in turn cause vegetation shifts like invasion by Phragmites , that affect ecosystem carbon balance. Understanding controls and scaling of carbon exchange in these understudied ecosystems is critical for informing climate consequences of blue carbon restoration and/or management interventions. Here, we (1) examine how carbon fluxes vary across a salinity gradient (4–25 psu) in impounded and natural, tidally unrestricted Phragmites wetlands using static chambers and (2) probe drivers of carbon fluxes within an impounded coastal wetland using eddy covariance at the Herring River in Wellfleet, MA, United States. Freshening across the salinity gradient led to a 50-fold increase in CH 4 emissions, but effects on carbon dioxide (CO 2 ) were less pronounced with uptake generally enhanced in the fresher, impounded sites. The impounded wetland experienced little variation in water-table depth or salinity during the growing season and was a strong CO 2 sink of −352 g CO 2 -C m −2 year −1 offset by CH 4 emission of 11.4 g CH 4 -C m −2 year −1 . Growing season CH 4 flux was driven primarily by temperature. Methane flux exhibited a diurnal cycle with a night-time minimum that was not reflected in opaque chamber measurements. Therefore, we suggest accounting for the diurnal cycle of CH 4 in Phragmites , for example by applying a scaling factor developed here of ~0.6 to mid-day chamber measurements. Taken together, these results suggest that although freshened, impounded wetlands can be strong carbon sinks, enhanced CH 4 emission with freshening reduces net radiative balance. Restoration of tidal flow to impounded ecosystems could limit CH 4 production and enhance their climate regulating benefits.

Massachusetts↗

USGS2020

Testing environmental DNA from wolf snow tracks for species, sex, and individual identification

Monitoring elusive, relatively low-density, large predators, such as the grey wolf (Canis lupus), has often been accomplished by live-capture and radiocollaring. Increasingly, non-invasive methods are considered best practice whenever it is possible to use them. Recently, environmental DNA (eDNA) deposited in snow tracks was demonstrated as useful for identifying lynx (Lynx canadensis), fisher (Pekania pennanti), wolverine (Gulo gulo), sika deer (Cervus nippon), red fox (Vulpes vulpes), and the Japanese marten (Martes melampus) to species level using mitochondrial DNA (mtDNA) markers. We tested whether eDNA from fresh wolf snow tracks collected in the Superior National Forest, Minnesota, USA during winter 2019 could be used to identify species, sex, and individual. Seven of the 8 snow track samples were successfully identified to “wolf-dog” species using mtDNA, with alleles amplifying in 5 of the samples at 1 or both of loci u250 and FH2096 in the allele range for wolves for this population. None yielded enough high-quality DNA to obtain genotypes to determine individual or sex. We recommend additional field trials to determine the minimum number of tracks required per individual to obtain sufficient, high-quality eDNA, as well as collecting associated urine or blood (from estrus) when possible. If individual wolves could be identified and sexed by the eDNA in their snow tracks, researchers should be able to determine population and family or group metrics with greater precision and less effort than typically required when conducting winter scat or hair-based genetic field studies of low density, elusive carnivores. Furthermore, this method would have applications to other areas of research and management, such as hunting quota determinations, validation of field methods and, in particular regards to wolves and other predators, livestock depredation issues. Overall, this technique holds significant future promise as field and laboratory methods are further refined for greater precision and optimized regarding the varying collection, filtration, and extraction protocols for different species in various environments.

Minnesota↗

USGS2020

Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River Fall Chinook Salmon ESU: January 2019 - December 2019

The portion of the Snake River fall Chinook salmon Oncorhynchus tshawytscha evolutionary significant unit (ESU) that spawns upstream of Lower Granite Dam transitioned from low to high abundance during 19922019 in association with U.S. Endangered Species Act recovery efforts and other federally mandated actions. This annual report focuses on (1) numeric and habitat use responses by natural- and hatchery-origin spawners, (2) phenotypic and numeric responses by natural-origin juveniles, and (3) use of a small unmanned aerial system (sUAS) to search for fall Chinook salmon redds and carcasses. Spawners have located and used most of the available spawning habitat and that habitat is gradually approaching redd capacity. Timing of spawning and fry emergence have been relatively stable, but effects of density dependence are evident in juvenile life stages. Apparent abundance of juvenile fall Chinook salmon has increased and we noted the following responses: parr dispersal from riverine rearing habitat into Lower Granite Reservoir has become earlier; growth rate (g/d) and dispersal size of parr declined; and passage timing of smolts from the two Snake River reaches has become earlier and downstream movement rate faster. These findings coupled with stock-recruitment analyses presented in this report provide evidence for density-dependence in the Snake River reaches and in Lower Granite Reservoir that was influenced by the expansion of the recovery program. The long-term goal is to use this information in a comprehensive modeling effort to conduct action-effectiveness and uncertainty research and to inform Fish Population, Hydrosystem, Harvest, Hatchery, and Predation and Invasive Species Management Research, Monitoring, and Evaluation (RM&E) progams. In 2019, the U.S. Geological Survey (USGS) shifted survey efforts in the Snake River toward deepwater redd searches and fish collection for parentage-based tagging (PBT) analyses because all unmanned aerial system (UAS) activities were suspended by the Department of the Interior two weeks into the spawning season. We counted 81 deepwater redds at 17 of the 29 sites surveyed. Redd depths averaged 3.6 m. We collected a total of 123 live fall Chinook salmon from 16 unique geographic locations that spanned 55 river kilometers. Forty-six fish were recovered at Eureka Bar (rkm 307.1) and Kirby Creek (rkm 352.0), which accounted for 37% of all collected fish in 2019. Most (73 fish) post-spawned salmon were collected from early to mid-November just after peak spawning. A summary of 2019 PBT results can be found in Appendix A.1. In 2019, we PIT tagged subyearling fall Chinook salmon in both the Snake and Clearwater rivers. In the Snake River, we tagged 410 fish with 8-mm tags, 666 fish with 9-mm tags, and 1,082 fish 12-mm tags. During seining, our recapture rate of previously tagged fish was slightly higher in the lower reach at 11.4% than in the upper reach at 10.6%. In an effort to represent more of the population through tagging, we tagged fish as small as 45 mm with 8-mm tags at one site in the upper reach. This allowed us to increase the number of fish tagged in that reach by 17.7%. An additional 10.6% of collected fish could have been tagged in the lower reach had we used 8-mm tags in that reach. In the Clearwater River, we tagged 2,451 subyearlings and recaptured 260 (10.6%) fish in the river and 66 fish (48 tagged by USGS, 18 tagged by the Nez Perce Tribe) at Lower Granite Dam during October to provide information for growth estimation. Within riverine habitats, growth in both length and mass were higher for fish tagged with 8-mm tags than with 9- and 12-mm tags. Estimated growth in length and mass of subyearlings was higher in Lower Granite Reservoir than in riverine habitats. We adapted existing statistical models used to estimate abundance of steelhead and spring/summer Chinook salmon for fall Chinook salmon passing Lower Granite Dam. Run reconstruction efforts to date at Lower Granite Dam for Snake River fall Chinook salmon have provided estimates of the number of returning adults but with no measure of uncertainty about the estimates. The objective of this study was to estimate the abundance, with uncertainty, of marked (coded-wire tagged CWT or adipose clipped) and unmarked fall Chinook salmon past Lower Granite Dam for return years 20032018. Estimating uncertainty is important for informing the state-space life cycle model (Chapter 5), which incorporates both observation and process uncertainty into parameter estimates. The coefficient of variation (CV) for log- abundance was 1.0% or less in all years, whereas the CV for abundance averaged 4.2% and ranged from 1.4% to 10.4% among years. Over the past five years, we have been developing a two-stage state-space life-cycle model for naturally produced fall Chinook salmon in the Snake River basin. Initial efforts focused on generating juvenile and adult abundance estimates, with estimates of uncertainty, for informing the life-cycle model. In this report we 1) describe the statistical life-cycle model and improvements made since our last report to the Independent Scientific Advisory Board (ISAB), 2) estimate the effects of covariates on key demographic parameters, and 3) use the fitted life- cycle model to simulate population trajectories under hydrosystem actions proposed for the NOAA 2020 Biological Opinion (hereafter, the Proposed Action). Major recent advancements to the model include revised juvenile abundance estimates, the ability to estimate smolt-to-adult return rates (SAR) separately for subyearling and yearling juvenile fall Chinook salmon, and improvements in the observation model for estimating age, sex, and outmigration structure in adult returns. We examined the effect of numerous environmental, hydrosystem, and ocean covariates on key demographic parameters but only a few covariates were significant. For the adult-to-juvenile transition, we found the maximum weekly river flows during the winter egg- incubation period had a significant negative effect on the juvenile outmigrant abundance from that brood year. For subyearling outmigrants, percent spill during the summer had a significant positive effect on SAR and the mean winter PDO (Pacific Decadal Oscillation) had a significant negative effect on SAR. For yearling outmigrants, NPGO (North Pacific Gyre Oscillation) had a significant positive effect on SAR. We used the fitted model to simulate population trajectories under the Proposed Action, and the median 10-year geometric mean abundance was 8,222 female spawners (interquartile range: 2,592 26,714). Overall, the probability of quasi- extinction (probability of falling below 50 female spawners for 4 consecutive years) was low, with only 1.6% of all simulations having a quasi-extinction probability >0.95. Although quasi-extinction probability was low, we did not assess the additional effect of climate change, which would be expected to increase quasi-extinction probability.

Idaho, Oregon, Washington↗

USGS2024

Physics to fish—Understanding the factors that create and sustain native fish habitat in the San Francisco Estuary

Executive Summary The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of Reclamation to provide scientific support for the management of Reclamation’s CVP project. Major habitat restoration efforts and a new water-diversion point are planned to benefit delta smelt ( Hypomesus transpacificus ) and other species of concern while ensuring the reliability of water supply. In addition, various flow actions and management activities have been identified as possible methods to increase populations of delta smelt and salmonid ( Oncorhynchus spp.) runs of concern. The overarching goal of this cooperative project was to provide Reclamation with the scientific information needed to evaluate the efficacy of ongoing and future adaptive management actions and to improve the scientific basis for more flexible CVP operations that would achieve water-supply reliability and fish protection. The research and monitoring described in this report comprises the period 2015–19 and focuses on management issues related to native fish species of concern, especially delta smelt. Conserving the delta smelt population while providing a reliable water supply is a primary management and policy issue in California. Our approach for this cooperative project is based on the “physics to fish” concept, the idea that high-quality habitat is generated and sustained by the interaction between physical processes and the landscape. These interactions create a template for chemical and biological processes that can change across a variety of spatial and temporal scales. Following this concept, this project (hereafter referred to as “the physics to fish project”) included monitoring and studies of water flows, sediments, water quality, and invertebrate and fish dynamics across a range of spatial and temporal scales and in regions relevant to resource managers tasked with managing water supplies and ecosystem health in the San Francisco Estuary. The intent of this approach was to document the habitat conditions, important processes, and interactions among them that create high-quality habitat for native fishes so that the likely effects of future management actions (for example, habitat restoration) can be objectively assessed at the local (site-specific), regional (within subregions of the estuary), and landscape (across the entire estuary and beyond) scales. Hydrodynamically, the upper estuary (landward of Carquinez Strait) is characterized by a fixed volume of tidally exchanged water (for example, tidal prism) that interacts with the existing channel network and bathymetry to create regions with differing hydrodynamics. Our results indicate that careful study of construction or reoperation of existing infrastructure to perform management actions can help (1) improve the accuracy of hydrodynamic models; (2) further understanding of ecological effects; and (3) enhance abilities to predict ecological outcomes. At the local scale, we developed a new concept called the Lagrangian to Eulerian (LE) ratio that can be used as a tool for understanding the importance of various hydrodynamic processes in specific channels or channel networks and for forecasting transport dynamics. Channels with LE ratios<1 in a channel network or in a dead-end slough are hydrodynamically able to develop an exchange zone between two parcels of water that may have different chemical and physical properties. In a dead-end channel, there is a landward region with long residence time (no-exchange zone) and a seaward region with short residence time (high-exchange zone) that are well mixed with seaward waters. At the transition (exchange zone) between the high and no-exchange regions, a gradient will form in water-quality constituents that differ in concentration between the landward and seaward waters. Turbidity affects fish habitat and has declined through time in the San Francisco Estuary. Average turbidity across the Sacramento–San Joaquin Delta (hereafter referred to as “the Delta”) is dependent on annual hydrology. In dry years, the region around Cache Slough (known regionally as the “Cache Slough Complex”) in the northern Delta is generally more turbid than Suisun Bay and the lower Sacramento River. When the Yolo By-Pass (known regionally as “Yolo Bypass”), a large flood bypass that runs parallel to the Sacramento River in the northern Delta, is not flooding and river flows are lower, sediment is usually transported into the Cache Slough Complex because flood tides dominate ebb tides, resulting in transport of suspended sediment from seaward areas of the upper estuary into the Cache Slough Complex. These hydrodynamic conditions also favor the formation of turbidity maximums (TMs) in the Cache Slough Complex. The TMs are areas of higher suspended-sediment concentration, providing higher-turbidity habitat favored by some fishes, including delta smelt, and they can also concentrate other constituents, including phytoplankton and organic carbon that can be important in food webs. Pelagic primary production by phytoplankton is the basis for Delta food webs supporting pelagic fishes such as delta smelt; however, phytoplankton abundance in the Delta has declined during recent decades. We examined how nutrients, hydrodynamics, and other factors affect phytoplankton blooms. Based on our results, we developed three new concepts of phytoplankton bloom formation in the Delta, each associated with a distinct set of hydrologic conditions. First, productivity cascades highlighted how local processes can contribute to phytoplankton blooms observed at the regional scale. Second, we observed phytoplankton blooms in the upper San Francisco Estuary that were associated with transport out of Yolo By-Pass (transport blooms). Third, we also documented a series of phytoplankton blooms that were in the confluence area at the landward edge of Suisun Bay. The conditions leading to creation of confluence phytoplankton blooms are not yet understood, but the confluence region connects the Cache Slough Complex with Suisun Marsh. Therefore, blooms in this area have the potential to spread to large areas of the Delta. At the landscape scale, the distribution of the invasive clams ( Potamocorbula amurensis and Corbicula fluminea , hereafter referred to as “ Corbicula ”) is driven by salinity. At smaller spatial scales, the distribution of either species is sensitive to multiple factors affecting survival and reproduction, complicating efforts to predict distribution and abundance without considering local-scale conditions across the area of interest. In the Cache Slough Complex, the area landward of the exchange zone in regions with LE ratio<1 were characterized by low abundances of Corbicula probably because recruits from seaward areas are not transported past the exchange zone and because there are no landward tributaries with adult Corbicula to provide an upstream source of recruits. Corbicula biomass was highest near or downstream from the exchange zone consistent with Corbicula grazing on phytoplankton produced in the exchange zone or transported from the no-exchange zone. The severity of Corbicula grazing could be reduced by manipulating the hydrodynamic characteristics of waterways; however, the beneficial and harmful effects on the organisms meant to benefit from increased phytoplankton production, including zooplankton and fish species of concern, should be thoroughly examined before manipulating hydrodynamic characteristics. The distribution of fishes at the landscape scale is generally driven by the position of the salinity field in the estuary. The physics to fish project compared distributions of fishes at Ryer Island, a tidal wetland in Suisun Bay and a region of variable salinity, with fish distributions at the Cache Slough Complex, a freshwater region. At Ryer Island, there was an absence of freshwater invasive species and an abundance of native species, such as Sacramento splittail ( Pogonichthys macrolepidotus ), tule perch ( Hysterocarpus traskii ), and Sacramento pikeminnow ( Ptychocheilus grandis ). The native species were almost exclusively captured in wetland and nearshore shallow-water habitat regardless of water-quality conditions. In the Cache Slough Complex, our regional scale objective was to elucidate how hydrodynamic-physical habitat interactions drive fish-community structure. Our studies showed that dendritic channel systems were better able to support native species, while intertidal habitats supported those species best able to exploit the transient character of the habitat. Habitats upstream from the exchange zone were especially important in supporting high numbers of native fishes relative to within or downstream from the exchange zone. Many of the native species were associated with tidal marsh in the no-exchange zone. More pelagic-oriented, mobile species, such as Striped Bass ( Morone saxatilis ), threadfin shad ( Dorosoma petenense ), and Sacramento pikeminnow, were more affected by water-quality conditions, such as turbidity. The physics to fish concept developed in this project provides a framework for designing individual projects and for considering the cumulative effects of multiple projects in a region, using the LE ratio as a guiding metric. The physics to fish concept may also provide a suitable framework for coordinating management actions. Tidal wetlands can function in several ways in the hydrodynamic framework. Relatively small tidal wetlands with short channel networks and with LE ratios>1 are not able to maintain a landward no-exchange zone or an exchange zone. This likely means that any contributions to pelagic food webs would be limited to resources derived from wetland vegetation, which can include dissolved and particulate organic matter (detritus) and populations of consumers that can increase in abundance based on those resources. The fate of the contributed production from these channels depends on the characteristics of the receiving waters seaward of the tidal wetland. If these channels join a large system such as Suisun Bay, then any contribution is likely to be rapidly dispersed in the larger volume; however, the channel junction might provide a focal point for consumers, such as fishes, to congregate and feed on material leaving the wetland on ebb tides before it is dispersed in the larger volume. Fishes might also access these resources by entering the wetland. The physics to fish project has established a foundation and several new concepts for understanding how habitat restoration can benefit native fish populations at the local and regional levels. Many of the ideas regarding habitat restoration and channel modifications outlined in this report could help guide management actions that could improve conditions for native fishes at little or no water cost beyond water already dedicated to other management actions. A complete list of products originating from this work is provided in appendix 1.

California↗