2007 Progress Report: Quantifying Stream Ecosystem Resilence To Identify Thresholds For Salmon Recovery

EPA Grant Number: R832439
Title: Quantifying Stream Ecosystem Resilence To Identify Thresholds For Salmon Recovery
Investigators: Merenlender, Adina , Kondolf, Matt , Moyle, Peter , Resh, Vincent
Institution: University of California - Berkeley
EPA Project Officer: Packard, Benjamin H
Project Period: July 1, 2006 through June 30, 2007 (Extended to August 31, 2008)
Project Period Covered by this Report: July 1, 2006 through June 30,2007
Project Amount: $299,922
RFA: Exploratory Research: Understanding Ecological Thresholds In Aquatic Systems Through Retrospective Analysis (2004) RFA Text |  Recipients Lists
Research Category: Aquatic Ecosystems , Ecosystems , Water


Research Questions Proposed

The overarching goal of this research is to increase our understanding of stream resilience and identify flow thresholds beyond which changes in macroinvertebrate community structure and decline in salmonid survivorship may result. To do this we proposed to use retrospective data to develop models based on the relationship among physical and biological variables that interact on different temporal and spatial scales in California’s North Coast mediterranean-climate watersheds.

Our research will provide the preliminary evaluations necessary for identifying how and where ecosystems could be recovered by reducing the stress human systems place on stream flow; and where restoration practices are likely to achieve desired results. Working with stakeholders, we are using this information to help develop best management guidelines so that vineyard managers can minimize the impacts of pumping stream water during the dry season. Since increasing water storage during the winter is often the only alternative to removing stream water during the dry season, we are also examining the potential consequences of appropriating additional winter storage on winter flows that can impact the ability for salmonids to move up to their spawning grounds.

Objective(s) of the Research Project

The distinct wet and dry seasons found in mediterranean-climate regions such as northern coastal California results in stream flow receding to approach or reach intermittency through spring and summer. The dry season can put stress on macroinvertebrates and native anadromous salmonids that use freshwater streams as habitat for their juvenile life cycle stages. Intensive agriculture in these areas requires water during the warm growing season. The cumulative effects of removing water for agricultural use during the dry season can result in stream levels dropping below critical ecological thresholds, thus increasing the probability of salmonid and macroinvertebrate mortality. To quantify the human impacts on the natural hydrologic regime and identify resilience thresholds we proposed the following methods: (1) creating models of natural flow regime on a daily-scale by using historical stream flow and rainfall data; (2) creating spatially explicit estimates of water demand in each stream in the study region over time; (3) identifying reaches where stream flow may be adversely affected by human water extraction; and (4) exploring the potential impacts that spring and summer stream flow dynamics have had on stream biota, evaluated using long-term fish and macroinvertebrate monitoring data. The data available for quantifying the variables described above are not perfect, but sufficient data do exist for estimating when human demand may lower resilience thresholds, leading to alternative states of biotic interactions in small coastal California streams.

We are working to identify streamflow thresholds that, when crossed, lead to changes in macroinvertebrate community structure and salmonid persistence/survivorship. Aquatic communities in our study region must withstand the drought conditions that occur each summer (wherein flows typically approach or reach intermittence) to persist in these environs; but particularly harsh conditions driven by prolonged drought or water removal for agricultural and other uses may cause re-structuring of ecosystems to an alternative regime. These alternate regimes may manifest themselves as a different macroinvertebrate community than would typically be expected, or the absence of anadromous salmonids in a particular reach or drainage.

Ecosystem Services that are being addressed are:

  • Fresh water
  • Water regulation
  • Cultural heritage values
  • Recreation and ecotourism
  • Biodiversity
  • Endangered species recovery

Progress Summary:

During the past two years of this research, we have made progress on all four tasks listed above for several upstream tributaries in North Coast California. We are studying stream ecosystems in tributaries to the Russian River and Putah Creek in northern coastal California. These streams provide habitat for a complex and diverse macroinvertebrate community throughout the drainage network; and anadromous salmonids use the Russian River tributaries for spawning in winter and juvenile rearing in summer. A persistent low-flow period from late spring until early fall results from the absence of precipitation between May and October; rainfall is highly variable across space and between years. Streams also represent an intersection of human-ecosystem interactions: wine grape growers in the region use these streams as a source for water needs during the growing season, which may amplify or accelerate the summer drought conditions.

Study location and its spatial extent

Our studies have focused on two particular areas in coastal California. Macroinvertebrate and fish data were collected in Hunting and Knoxville Creeks in Napa and Lake Counties; and salmonid data were collected in 10 Russian River tributaries in Sonoma County. See map of California with study sites in red and blue below. Also see two study site maps.

Two California study sites

Hunting and Knoxville map

Russian River sites map

Time period being investigated

Macroinvertebrate data span 20 years (from 1982 to 2002); and salmonid data span ten years (from 1994 to 2003). Biotic community data were not augmented, but streamflow data were modeled for the Russian River tributaries to fit the period of salmonid data based on historical precipitation and streamflow data collected from 1960 to 1980.

Natural and human stressors being investigated

We are investigating the effects of low streamflow during the summer dry season on aquatic macroinvertebrates and anadromous salmonids. Partciular low flow thresholds may be imposed by natural drivers such as prolonged or particularly intense drought; but low streamflow may also be amplified by diversion from streams to meet demands for viticulture. Wine grape growers in the Russian River basin use surface water as a source for spring frost protection and summer irrigation and heat protection, and increased demand for water from small streams may threaten particularly valuable habitat for salmonid spawning and rearing throughout the region. Some of these water demands are constant from one year to the next (such as water for irrigation needs), while others vary with weather conditions (such as water for frost protection, needed only on cold mornings after grape buds have emerged).

Hydrologic alterations caused by surface water abstraction vary based on timing and mechanisms; sudden reductions in streamflow from instream diversions especially during the spring and summer may cause flow to be much less or cease prematurely relative to a natural flow recession. The magnitude of flow alteration is also related to streamflow at a given time and the magnitude of water demand; both of these factors vary from one study site to the next.

Explicit definition of the system variables being investigated

Fast variables

  • Macroinvertebrate community composition: the characteristics of the macroinvertebrate community that tend to be organized in a typically lentic or a typically lotic aquatic environment.
  • Salmonid survivorship: the ratio of juvenile anadromous salmonids present at the end of the summer to those present at the beginning.
  • Surface water diversion: water diverted from streams can cause sudden changes in streamflow, which can propagate downstream. Changes in streamflow may cause ecological surprise, causing rapid mortality among some organisms that cannot adapt to new conditions. Other organisms may be affected long-term by reduced resources caused by changes in streamflow.

Slower variables

  • Natural streamflow recession: streamflow recedes throughout spring and summer, until rains begin again in late fall and early winter. Streamflow recession occurs gradually, but the magnitude of flow at various times in the year may vary from one year to the next based on magnitude and distribution of precipitation during the preceding winter.
  • Vineyard development: the magnitude of vineyard development may also affect instream diversion: the greater or more dense vineyard development in catchments, the more water will likely be needed for various uses.
  • Alternative water use mechanisms: certain practices, such as storage of water in winter, can offset water demand during the summer months. Such practices may alleviate the pressures that grape growers place on small streams during the summer dry season.

Analytical method being developed for identifying thresholds

Non-metric multidimensional scaling ordination was used to examine to examine temporal patterns in community composition of macroinvertebrates and the influence of flow on these patterns (using Spearman rank correlation). To determine the influence of flow on fish populations and relative abundance at each site in Napa and Lake Counties, we examined the data for temporal trends; if a significant temporal trend was found, the data were detrended using linear regression. Detrended population data were then correlated with flow, precipitation, and habitat data using Spearman’s rank correlation. Stepwise multiple regression with forward selection was used to determine which combination of physical habitat variables that best explained year-to-year fluctuations in fish abundances such that all variables included were significant at a = 0.05. Changes in size distributions for roach and green sunfish were examined to explain observed fish population trends. Furthermore, we examined the relationship between fish and macroinvertebrate communities using a Mantel test.

Multivariable regression is being used to examine potential empirical thresholds for effects of low flow periods on salmonid survivorship. We started with linear regression to report level of contribution that habitat quality index has on outcomes in addition to flow. Now we are using a fixed effects regression model to account for site effects at each pool that have not been adequately measured and explore low flow threshold.

Outcome Variables

─ recruitment

─ survivorship

Explanatory Variables

─ number of low flow days based on modeled flow

─ habitat quality

─ land use cover

─ stream

Stream flow for most Russian River sites is modeled using a statistical model of stream flow as a function of rainfall for the day, as well as rainfall over previous antecedent periods using a multiple regression analysis. Antecedent periods include rainfall over the previous 3 days (illustrating the extent to which flow may be affected by a storm), the previous 14 days (illustrating the influence of rainfall over a biweekly scale), or the previous 90 days (showing the potential effects of seasonal trends in rainfall). Simple flow-scaling techniques are also employed to estimate flow at sites along the same stream.

Sensitivity analysis will be used to examine model behavior.

We will compare our predicted stream flows to periodic measurements of stream flows at each of the site during the course of the proposed study to further test our modeled stream flow, recognizing that land use conversions that have occurred since historical stream flow records were collected could have altered the previous relationship.

Discussion of threshold effects

Our research in Napa/Lake County showed one stable alternative state where after 6 years of drought one site is now dominated by a non-native fish whose establishment appears to be aided by the dominance of an invasive riparian plant that has changed the flow regime. This altered habitat state was highly resilient to even dramatic increases in flow that resulted in a steadily decline of native fish. These habitat changes also resulted in strong directional change in macroinvertebrate community structure towards taxa that are more tolerant of lentic and sandy conditions. Furthermore, a positive feedback between flow and habitat conditions was created, where flow is reduced because of high density of aquatic macrophytes, which in turn favors the continued presence of these macrophytes. This flood-resistant habitat may represent an alternative stable state that resulted from the drought disturbance. We belive that a press disturbance altered the physical and biological habitat of fish and macroinvertebrates, and this altered state has proven resistant (over the course of many years) to the “restoration” of winter floods.

The prolonged drought eliminated suitable native fish habitat at another site entirely. At this site, California roach were not found for 13 years (6 years of prolonged drought and 7 years post-drought). Prolonged drought reduced available habitat size such that they were not large enough to support fish; however, roach were observed at a site 1 km downstream with deeper pools. Macroinvertebrates were present at this site for the duration of the study period, which provided evidence that the drought resulted in directional change in community structure followed by recovery many years after the end of drought. The recovery of roach populations was likely facilitated by the downstream source of colonists, and the habitat downstream of this site likely provides refuge from the summer dry period at this ephemeral site. In general, the macroinvertebrate communities demonstrated a reversible regime shifts between wet and dry communities.

Our preliminary results from anadromous salmonid data also indicate a positive relationship between higher streamflow and the survivorship of salmonids through the summer dry season. Habitat, land use, location in the watershed, location in the basin also influence recruitment and survivorship to some extent. We are currently investigating low flow threshold metrics to evaluate potential thresholds. Also, tradeoff analysis is underway to examine the environmental and economic impacts of storing winter rainfall vs. pumping in the dry season to meet the demand for water from agriculture. This analysis will allow for an empirical examination of storage thresholds beyond which winter flows required for salmon bypass may be impacted.

Reversibility of threshold exceedance / shift

In most cases the macroinvertebvrated and fish communities reverted back to wet community types after the drought in Napa/Lake Counties ended. However, in one case non-native fish species remain dominant and appear to represent an irreversible alternate state.

Our statistical analysis of juvenile salmonid survivorship and low-flow conditions have not yet resulted in determination of thresholds resulting in a reversed system: survivorship is correlated with streamflow, but no thresholds leading to an alternate state (i.e., absence of salmonids) have been detected in our data set. This may in part be due to the limited extent of our data: our retrospective data set only includes salmonid populations at a few locations. Other reaches in the Russian River drainage network have higher amounts of vineyard development, and thus have greater water demand for frost protection, heat protection, and irrigation. We anticipate a more complete statistical analysis and further investigation of thresholds associated with water management will help elucidate our understanding of hyteresis in this system.

Interesting or surprising findings that have emerged to date

  • Recovery from drought was rapid for macroinvertebrates at all sites; however community shifts were evident at the first-order sites using non-metric multidimensional scaling.
  • All three native fish species exhibited a lag in responding to changes in flow (1-2 years), but no lag was observed for the non-native green sunfish.
  • During the drought, numerical dominance shifted from the native California roach to the non-native green sunfish and in one case this appears to be an alternative stable-state where future large flow events may not be sufficient to recover a dominance of native fish.
  • The concordance we observed between fish and macroinvertebrates (Mantel test) is most likely due to the fact that the prolonged drought suppressed recovery of both assemblages.
  • Substantial inter-annual variation in recruitment and survivorship emphasizes the need for long-term population data.
  • Although site location and habitat variables are significant factors controlling the distribution of juvenile steelhead, the decline in survivorship with decreasing summer flows indicate that water quantity may be an important limiting factor. (Figure 8)
  • Investigations of the best metric to evaluate flow thresholds is underway using fixed effects regression models.
  • In recognition of the growing regional demand on water resources, these findings suggest that protections of tributary flows during the dry season are critical to salmon recovery efforts in the Russian River watershed.
  • So far, we have demonstrated the effect of reservoirs early in the rainy season immediately downstream of the reservoirs, but the cumulative effects of reservoirs in the watershed has a small effect on flows farther downstream and after several storms have passed.
  • This model allows us to place reservoirs in a specific context of space, thus considering upstream flow contributions, other reservoirs in the drainage network, and their impacts at any point downstream
  • We can change the conditions of flow, for example, among normal-type flow years, dry-type years, or wet-type years to consider variable rainfall patterns.
  • We can add new reservoirs, to asses their cumulative impact, and change reservoir conditions and management strategies. This makes our model especially useful for region-wide water planning and restoration.

Application for resource management

The importance of spring and summer flows to anadromous salmonids has important implications for water management in the California wine country. Best management practices for vineyards has thus far focused on reducing fine sediment inputs to limit impacts on salmonid populations; though fine sediment inputs may indeed play a role in limiting persistence of salmonids in coastal watersheds, our research supports the argument that streamflow in the dry season may be limiting salmonid recovery. Because the dry season corresponds with the period when wine grape growers need water for crop protection and irrigation, demand for surface water may exceed flow throughout the growing season.

We are currently exploring potential mechanisms for grape growers to acquire water for use through the growing season during periods of greater water availability. The high flows that occur during winter may be large enough to meet all environmental needs and also allow water users to store winter discharge for use during summer; but whether a particular abstraction may impair environmental flows requires careful consideration the abstraction methods in appropriate spatial and temporal contexts. Possible mechanisms for winter storage include diversion at appropriate times into individual offstream reservoirs; diversion into collective regional offstream reservoirs; and construction of reservoirs on swales and small drainages in far headwaters

Given the established importance of preserving spring and summer flows for salmonid persistence, we are currently constructing a geographic information system-based model to evaluate the potential for alternative water abstraction methods, especially small winter storage reservoirs, on streamflow necessary for various environmental needs. Of particular concern to California Dept. of Fish and Game and NOAA fisheries is ensuring that stream flows are sufficient to allow for salmonids to move up stream during the winter. Our preliminary results have examined the impacts of currently existing reservoirs on streamflow at the onset of the winter rainy season. Our GIS model indicates that the majority of the upland drainage network is unimpaired by the several hundred small reservoirs that currently exist in the study area; and that, with careful planning, additional reservoirs may also be constructed to meet current and future water needs with similar low levels of hydrologic impact.

Interactions with potential clients to date, or anticipated in the future

We are currently collaborating with a stakeholder group land owners, urban water managers, resource agency staff, and the Sonoma County Water Agency to make more precise linkages between water management practices and hydrologic impacts in our study region. The field and survey data we anticipate collecting with assistance of the Salmon Coalition will help us to further explore the potential costs and benefits of altering water management practices to remove pressures from periods of need to periods of availability. There is also interest by the State Water Resources Control Board for a decision-support system to evaluate cumulative watershed effects of small water storage projects on winter salmon bypass to allow them to make decisions on hundreds of appropriative rights request which are currently stalled due to uncertainty about these effects.

Quality Assurance

In the analysis of spatial data, the process of preparing data for use involves many steps such as conversions between spatial data models (vector, raster) and reprojections (putting multiple maps into the same model of the earth's surface). Each of these necessary steps involves potential for the introduction of positional error and the recombination of many data sets each with its own error may lead to exponential growth in error. Care is being taken in the preparation of all data sets involved and when data from independent sources do not align we track down any mistakes in data conversion and correct them. Summary statistics and spot comparisons of many of our datasets are being undertaken by our team members as we continue the research and quality assurance will be documented after the models are fully developed.

Key Personnel

We provided support to two post docs and two graduate students during this year as well as receive assistance with GIS programming from a staff programmer at the Hopland Research and Extension Center.

Future Activities:

Our future efforts will focus on merging existing biological data describing salmonid populations with stream hydrology and expressions of surface water demand, both in our primary study area and throughout the region. The hydrology components described above will be adjusted to predict stream flow in the primary study region over the ten-year period during which salmonid survivorship surveys were conducted; and offer more detailed descriptions of how human water demand influences stream hydrology through the wine grape growing season. We will also adjust the expressions of water demand to distinguish among study sites within the same drainage network (present estimates are for entire catchments). These steps will be essential for determing how salmonid populations are affected by small differences in the natural flow regime and influences of human water demand through the growing season.

We also will refine and expand our evaluation of the impacts of small study reservoirs over temporal and spatial scales. The influence of small reservoirs is limited to the period before which reservoirs fill to capacity and begin to spill into the creek below; we will conduct analyses using historical stream flow data to determine when during the winter rainy season reservoirs fill and begin to contribute to downstream flows. We will also expand our study to evaluate the impacts of small reservoirs on winter flow throughout the Russian River basin, allowing us to identify those regions where winter flows are most likely impaired, and those that are largely unaffected by small reservoirs. These analyses can serve as the foundation to direct hydrologic restoration by directing where existing water needs can be met by shifting demand from summer to winter.

Budget report

In June, 2007 we had spent $47,361 on salaries, $9,542 on benefits and other compensation, $14,895 on supplies and GIS analysis, and $2,747 on domestic travel.  We request a no-cost extension for an additional year to allow more graduate student participation in the research and this additional time is critical for us to refine our models, work with stakeholders, and improve resulting decision-support tools to better apply our findings.  In the end, the requested additional time will greatly increase the impact of this research effort.   

Journal Articles on this Report : 3 Displayed | Download in RIS Format

Other project views: All 10 publications 5 publications in selected types All 5 journal articles
Type Citation Project Document Sources
Journal Article Beche LA, Resh VH. Short-term climatic trends affect the temporal variability of macroinvertebrates in California 'Mediterranean' streams. Freshwater Biology 2007;52(12):2317-2339. R832439 (2007)
R832439 (2008)
R832439 (Final)
  • Abstract: Wiley Online-Abstract
  • Journal Article Beche LA, Resh VH. Biological traits of benthic macroinvertebrates in California mediterranean-climate streams:long-term annual variability and trait diversity patterns. Fundamental and Applied Limnology/Archiv fur Hydrobiologie 2007;169(1):1-23. R832439 (2007)
    R832439 (2008)
    R832439 (Final)
  • Abstract: IngentaConnect-Abstract
  • Other:
  • Journal Article Deitch MJ, Kondolf GM, Merenlender AM. Hydrologic impacts of small-scale instream diversions for frost and heat protection in the California wine country. River Research and Applications 2009;25(2):118-134. R832439 (2007)
    R832439 (2008)
    R832439 (Final)
  • Full-text: University of California-PDF
  • Abstract: Wiley Online-Abstract
  • Supplemental Keywords:

    environmental flow, ecological resilience, anadromous salmonids, threshold, surface water abstraction, inter-annual variability, benthic macroinvertebrate, water management, nonlinear ecosystem dynamics, aquatic ecology, coupled human and natural systems, cumulative watershed effects, RFA, Scientific Discipline, Ecosystem Protection/Environmental Exposure & Risk, Aquatic Ecosystems & Estuarine Research, Aquatic Ecosystem, Environmental Monitoring, Ecological Risk Assessment, Ecology and Ecosystems, anthropogenic stress, estuarine research, species interaction, ecological thresholds, salmon recovery, anthropogenic impact, ecosystem indicators, modeling ecosystem change, stream habitat, aquatic ecosystems, water quality, ecosystem stress, riverine ecosystems, trophic interactions, aquatic ecosystem restoration, ecosystem response

    Relevant Websites:

    Merenlender Lab Exit
    Russian River Interactive Information System Exit

    Progress and Final Reports:

    Original Abstract
  • 2008 Progress Report
  • Final Report