Re-Oaking North Bay: A strategy for restoring native oak ecosystems, focusing on Napa and Sonoma valleys

San Francisco Estuary Institute (SFEI) | July 7th, 2020

Oaks are iconic trees in California, the defining feature of savannas and woodlands in many parts of the state. For millennia, these majestic trees have provided the e

Oaks are iconic trees in California, the defining feature of savannas and woodlands in many parts of the state. For millennia, these majestic trees have provided the ecological foundation upon which thousands of other organisms depend. Their cultural significance is equally profound: they are of central importance to diverse indigenous groups, and are prized for the many benefits they provide California residents. Vast expanses of oak savanna historically occupied the rich alluvial soils of Napa and Sonoma valleys. The immense and long-lived valley oak (Quercus lobata) dominated these savannas, accounting for more than 65% of trees (Dawson 2008, Grossinger et al. 2012). Early observers described the valleys as “studded with groups of oaks” (Marryat 1850), and extolled the “magnificent oaks” that were “the glory of the landscape scenery” (Smith and Elliott 1878). Black oak (Q. kelloggii), coast live oak (Q. agrifolia), and other oak species were present in smaller numbers on the valley floors and were more abundant in the hillsides (Dawson 2008, Grossinger et al. 2012). Over the past two centuries, however, much of this oak savanna has been cleared to make way for orchards, vineyards, and towns. In Napa Valley, the number of mature trees has declined from an estimated 45,000 in the early 1800s to less than 1,000 today (Grossinger et al. 2012). Valley oak habitat has been particularly affected by clearing and fragmentation: in many areas of the state, loss of valley oak woodland exceeds 90% (Kelly et al. 2005, Whipple et al. 2011). Documentation of this loss, and recognition of the value of oaks for both people and nature, has led to a growing desire to restore this unique ecosystem and bring back many of the benefits that oaks provide. Despite the significant changes the North Bay landscape has experienced since European settlement, there are opportunities to restore oaks in settings as diverse as backyards, parks, streets, farms, vineyards, and creeksides.

Re-Oaking Silicon Valley: Building Vibrant Cities with Nature

San Francisco Estuary Institute (SFEI) | August 1st, 2017

In this report, we investigate how integrating components of oak woodlands into developed landscapes — “re-oaking” — can provide an array of valuable functions fo

In this report, we investigate how integrating components of oak woodlands into developed landscapes — “re-oaking” — can provide an array of valuable functions for both wildlife and people. Re-oaking can increase the biodiversity and ecological resilience of urban ecosystems, improve critical urban forest functions such as shade and carbon storage, and enhance the capacity of cities to adapt to a changing climate. We focus on Silicon Valley, where oak woodland replacement by agriculture and urbanization tells a story that has occurred in many other cities in California. We highlight how the history and ecology of the Silicon Valley landscape can be used as a guide to plan more ecologically resilient cities in the Bay Area, within the region and elsewhere in California. We see re-oaking as part of, and not a substitute for, the important and broader oak woodland conservation efforts taking place throughout the state.  

Reconciling fish and farms: Methods for managing California rice fields as salmon habitat

PLOS | February 24th, 2021

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the pa

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the past century. Recently, through cooperative agreements with diverse stakeholders, winter-flooded agricultural rice fields in California’s Central Valley have emerged as ecologically functioning floodplain rearing habitat for juvenile Chinook Salmon. From 2013 to 2016, we conducted a series of experiments examining methods to enhance habitat benefits for fall-run Chinook Salmon reared on winter-flooded rice fields in the Yolo Bypass, a modified floodplain managed for flood control, agriculture, and wildlife habitat in the Sacramento River Valley of California. Investigations included studying the effect of 1) post-harvest field substrate; 2) depth refugia; 3) duration of field drainage; and 4) duration of rearing occupancy on in-situ diet, growth and survival of juvenile salmon. Post-harvest substrate treatment had only a small effect on the lower trophic food web and an insignificant effect on growth rates or survival of rearing hatchery-origin, fall-run Chinook Salmon. Similarly, depth refugia, created by trenches dug to various depths, also had an insignificant effect on survival. Rapid field drainage yielded significantly higher survival compared to drainage methods drawn out over longer periods. A mortality of approximately one third was observed in the first week after fish were released in the floodplain. This initial mortality event was followed by high, stable survival rates for the remainder of the 6-week duration of floodplain rearing study. Across years, in-field survival ranged 7.4–61.6% and increased over the course of the experiments. Despite coinciding with the most extreme drought in California’s recorded history, which elevated water temperatures and reduced the regional extent of adjacent flooded habitats which concentrated avian predators, the adaptive research framework enabled incremental improvements in design to increase survival. Zooplankton (fish food) in the winter-flooded rice fields were 53-150x more abundant than those sampled concurrently in the adjacent Sacramento River channel. Correspondingly, observed somatic growth rates of juvenile hatchery-sourced fall-run Chinook Salmon stocked in rice fields were two to five times greater than concurrently and previously observed growth rates in the adjacent Sacramento River. The abundance of food resources and exceptionally high growth rates observed.

Recovery Plan for Sacramento-San Joaquin Delta native fishes

U.S. Fish and Wildlife Service (FWS) | November 26th, 1996

Eight fish species are included in the Sacramento-San Joaquin Delta Native Fishes Recovery Plan. The delta smelt is listed as a threatened species. The Sacramento splitta

Eight fish species are included in the Sacramento-San Joaquin Delta Native Fishes Recovery Plan. The delta smelt is listed as a threatened species. The Sacramento splittail (splittail) was proposed as a threatened species on January 6, 1994. This recovery plan will recommend restoration criteria for the splittail that would be appropriate recovery criteria should the species be listed. Longfin smelt, green sturgeon, spring-run, late fall-run, and San Joaquin fall-run chinook salmon are species of concern for which restoration criteria are recommended. Information is also included on Sacramento perch, a species believed to be extirpated from the Delta at this time. Habitat Requirements and Limiting Factors: The eight species included in this recovery plan depend on the Sacramento-San Joaquin Delta for a significant segment of their life history. Threats to the Delta ecosystem and these species include loss of habitat due to increased freshwater exports resulting in increased salinity, loss of shallow-water habitat due to dredging, diking and filling, introduced aquatic species that have disrupted the food chain, and entrainment (movement offish by currents produced by diversions) in State, Federal and private water diversion. State and Federal water projects have also changed the pattern and timing of flows through the Delta. The salmon races are affected by sport and commercial harvest as well as by interactions with hatchery stocks. Recovery and Restoration Objective: Delisting of delta smelt. Restoration of splittail, longfin smelt, green sturgeon, spring-run, late fall-run, San Joaquin fall-run chinook salmon, and Sacramento perch. Recovery and Restoration Criteria: Recovery criteria are quantifiable and species specific and can be used to (1) monitor effectiveness of recovery actions, (2) determine when a species has recovered to a secure level (stabilized), and (3) determine when a species qualifies for delisting. In many cases, criteria are based on two independent measures: population abundance and geographic distribution. For each species a historic base period was established using available data to characterize abundance and distribution during a pre-decline period. The time period over which abundance and distribution criteria must be met was set at five generations. For five of the eight species there is an additional requirement of meeting the criteria through a minimum number of years of stressful environmental conditions. Action Needed: 1. Enhance and restore aquatic and wetland habitat in the Sacramento-San Joaquin River estuary. 2. Reduce effects of commercial and recreational harvest. 3. Reduce effects of introduced aquatic species on Delta native fishes. 4. Change and improve enforcement ofregulatory mechanisms. 5. Conduct monitoring and research on fish biology and management requirements. 6. Assess recovery management actions and re-assess prioritization of actions. 7. Increase public awareness of importance of Delta native fishes.

Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California

U.S. Fish and Wildlife Service (FWS) | September 23rd, 2013

The Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California features five endangered species: two endangered animals, California clapper rail (Rallus

The Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California features five endangered species: two endangered animals, California clapper rail (Rallus longirostris obsoletus) and salt marsh harvest mouse (Reithrodontomys raviventris) and three endangered plants, Cirsium hydrophilum var. hydrophilum (Suisun thistle), Chloropyron molle ssp. molle (soft bird’s-beak), and Suaeda californica (California sea-blite). The biology of these species is at the core of the recovery plan, but the goal of this effort is the comprehensive restoration and management of tidal marsh1 ecosystems. This recovery plan is an expansion and revision of The California Clapper Rail and Salt Marsh Harvest Mouse Recovery Plan (U.S. Fish and Wildlife Service 1984). The historic distribution of the California clapper rail encompasses major tidal marshes between Humboldt Bay and Morro Bay, defining the approximate geographic scope of this recovery plan. In addition to the California clapper rail and the salt marsh harvest mouse, the plan also covers three focal listed plant species that were listed as federally endangered in the 1990s and the northernmost population of an additional plant species. Two of the species, Cirsium hydrophilum var. hydrophilum and Chloropyron molle ssp. molle (this species’ former name is Cordylanthus mollis ssp. mollis which is how it appears on the List of Threatened and Endangered Species, but we use the currently accepted name here), are restricted to the northern reaches of the San Francisco Bay Estuary. The other endangered tidal marsh plant, Suaeda californica, historically occurred in both San Francisco Bay and Morro Bay but, except for three reintroductions to San Francisco Bay, is now restricted to Morro Bay. Another federally listed plant, Chloropyron maritimum ssp. maritimum (salt marsh bird’s-beak; formerly Cordylanthus maritimus ssp. maritimus), has its northern range limit in Morro Bay. Morro Bay was omitted from the Salt Marsh Bird’s-beak Recovery Plan (U.S. Fish and Wildlife Service 1985a) because the taxonomic interpretation at the time classified this population in another subspecies that is not federally listed. Current taxonomic interpretation considers the Morro Bay population as Chloropyron maritimum ssp. maritimum. It is included in this recovery plan due to its co-location with Suaeda californica in Morro Bay. Though recovery strategies and actions are provided for the Morro Bay population of C. maritimum ssp. maritimum, recovery criteria are not, therefore, the species should not be considered covered by the recovery portion of the document. In addition, this recovery plan addresses 11 species or subspecies of concern. These include the salt marsh wandering shrew (Sorex vagrans halicoetes), Suisun shrew (Sorex ornatus sinuosus), San Pablo vole (Microtus californicus sanpabloensis), California black rail (Laterallus jamaicensis coturniculus), three song sparrow subspecies of the San Francisco Bay Estuary (Alameda song sparrow [Melospiza melodia ssp. pusillula], Suisun song sparrow [M.m. maxillaris] and San Pablo song sparrow [M.m. samuelis]), saltmarsh common yellowthroat (Geothlypis trichas sinuosa), old man tiger beetle (Cicindela senilis senilis), Lathryrus jepsonii ssp. jepsonii (delta tule pea), and Spartina foliosa (Pacific cordgrass). These species occur in a variety of tidal marsh habitats where they are limited by the requirements of moisture, salinity, topography, soil types, and climatic conditions. Adjacent uplands and ecotone areas are also crucial habitats for many of these species. Primary threats to all the listed species include historical and current habitat loss and fragmentation due to urban development, agriculture, and diking related to duck hunting; altered hydrology and salinity; non-native invasive species; inadequate regulatory mechanisms; disturbance; contamination; risk of extinction due to small population size; and the most central threat, sea level rise due to climate change.

Reference Guide to On-Farm Groundwater Recharge on Annual Cropland | Recommendations for Creating Waterbird Habitat Benefits

Nature Conservancy | May 1st, 2019

With the Sustainable Groundwater Management Act (SGMA) requiring basins to balance water budgets and manage groundwater sustainably, there is an opportunity to demonstr

With the Sustainable Groundwater Management Act (SGMA) requiring basins to balance water budgets and manage groundwater sustainably, there is an opportunity to demonstrate groundwater recharge with benefits to birds and people. A multiple-benefit approach brings together water managers, farmers, agencies and conservation groups to stabilize groundwater in a manner that provides greater water reliability for farms and communities while protecting ecosystems, including migratory bird habitat.

Reforming Watershed Restoration: Science in Need of Application and Applications in Need of Science (The H.T. Odum Synthesis Essay)

Estuaries and Coasts (Springer) | December 23rd, 2008

Coastal and inland waters are continuing to decline in many parts of the world despite major efforts made to restore them. This is due in part to the inadequate role that

Coastal and inland waters are continuing to decline in many parts of the world despite major efforts made to restore them. This is due in part to the inadequate role that ecological science has played in shaping restoration efforts. A significant amount of fundamental ecological knowledge dealing with issues such as system dynamics, state changes, context-dependency of ecological response, and diversity is both under-used by managers and practitioners and under-developed by ecologists for use in real-world applications. Some of the science that is being ‘used’ has not been adequately tested. Thus, restoration ecology as a science and ecological restoration as a practice are in need of reform. I identify five ways in which our ecological knowledge should be influencing restoration to a far greater extent than at present including a need to: shift the focus to restoration of process and identification of the limiting factors instead of structures and single species, add ecological insurance to all projects, identify a probabilistic range of possible outcomes instead of a reference condition, expand the spatial scale of efforts, and apply hierarchical approaches to prioritization. Prominent examples of restoration methods or approaches that are commonly used despite little evidence to support their efficacy are highlighted such as the use of only structural enhancements to restore biodiversity. There are also major gaps in scientific knowledge that are of immediate need to policy makers, managers, and restoration practitioners including: predictive frameworks to guide the restoration of ecological processes, identification of social-ecological feedbacks that constrain ecosystem recovery and data to support decisions of where and how to implement restoration projects to achieve the largest gains. I encourage ecologists to respond to the demand for their scientific input so that restoration can shift from an engineering-driven process to a more sustainable enterprise that fully integrates ecological processes and social science methods.

Relationship between wetland condition, stress, and buffer

San Francisco Estuary Institute (SFEI) | April 25th, 2016

Relationship between wetland size and CRAM condition scores for depressional wetlands

San Francisco Estuary Institute (SFEI) | March 28th, 2016

Resilient landscape vision for Lower Walnut Creek

San Francisco Estuary Institute (SFEI) | November 30th, 2016

Lower Walnut Creek (Contra Costa County, CA) and its surrounding landscape have undergone considerable land reclamation and development since the mid-nineteenth century.

Lower Walnut Creek (Contra Costa County, CA) and its surrounding landscape have undergone considerable land reclamation and development since the mid-nineteenth century. In 1965, the lower 22 miles of Walnut Creek and the lower reaches of major tributaries were converted to flood control channels to protect the surrounding developed land. In the recent past, sediment was periodically removed from the lower Walnut Creek Flood Control Channel to provide flow capacity and necessary flood protection. Due to the wildlife impacts and costs associated with this practice, the Contra Costa County Flood Control and Water Conservation District (District) is now seeking a new channel management approach that works with natural processes and benefits people and wildlife in a cost-effective manner. Flood Control 2.0 project scientists and a Regional Science Advisory Team (RSAT) worked with the District to develop a long-term management Vision for lower Walnut Creek that could result in a multi-benefit landscape that restores lost habitat and is resilient under a changing climate. Development of the Vision began with technical analyses focused on understanding past and present landscape functioning and the changes to key processes and landscape features over the past 150 to 200 years. The key findings from these analyses include the following: • Landscape change – During the mid-19th century, lower Walnut Creek was surrounded by a continuous expanse of tidal wetlands occupying approximately 5,000 acres. Perennial freshwater marsh, willow thicket, and alkali meadow formed a large non-tidal wetland complex that adjoined the tidal marsh on its southern end. Over the past century and a half, the non-tidal wetland complex has been lost completely and the tidal wetland area has decreased by 40%. The remaining marsh areas are highly fragmented and cut-off from Walnut Creek by engineered levees. The loss of tidal wetland area has resulted in a substantial decrease in tidal prism and contributed to current in-channel sediment accumulation issues. Around the mouth of Walnut Creek, sediment accumulation has caused the position of the shoreline to expand into the Bay by up to half a mile. • Sediment accumulation – Since 1965, approximately 1.4M cubic yards of sediment have been removed from lower Walnut Creek, with approximately 70% coming from the tidal zone downstream of head of tide (i.e., the inland extent of tidal inundation at mean higher high water). Repeat channel cross-section surveys indicate that the channel quickly fills in with sediment following dredging events (due in large part to decreased tidal prism and associated channel scour capacity) and that the channel bed elevation is currently at or near “quasi-equilibrium.” A channel sediment budget for 1965-2007 indicates that approximately 80% of the watershed-derived sediment made it through lower Walnut Creek and out to the Bay, while the remaining 20% was likely deposited directly following channel construction and subsequent dredging events.