The purpose of this August 2013 Terraqua contract amendment (CCR-30643) is to:
- Support additional macroinvertebrate sample processing by Rhithron Associates in association with 2013 benthic and drift macroinvertebrate analysis efforts.  Invertebrate drift sampling collects invertebrates drifting in the water column where they are vulnerable to salmonids as a food resource.  ISEMP research has shown direct relationships between salmonid food consumption, growth rates and invertebrate drift samples, which are collected at the site level under the CHaMP protocol. In 2011 and 2012 samples from each participating CHAMP watershed were shipped to an invertebrate processing lab for identification and sorting according to a non-standard protocol provided by CHaMP.  A single invertebrate processing lab was chosen to sort and process the samples to maintain standardization and consistency across watersheds.  In 2013, to further investigate drift macroinvertebrate and fish growth relationships as well as evaluate the utility of benthic macroinvertebrate samples, Terraqua will subcontract with Rhithron Associates, Inc. of Missoula, MT for processing and identification of up to a total of 350 macroinvertebrate (combination of drift and benthic) samples collected by CHaMP in watersheds at sites where ISEMP fish capture/growth data are also available, e.g., Entiat, Lemhi, Asotin. Rhithron Associates will process up to 350 macroinvertebrate samples from watersheds with colocated CHaMP-ISEMP data in 2013.  Delivery of samples will be staggered throughout the field season to enable processing of all the samples by November 1, 2013.  Processing of CHaMP stream macroinvertebrate samples will require the following procedures:

1. Sample sorting – Separation of organisms from accompanying organic and inorganic materials retained by drift nets and substrate material during sample collection.  

2. Identification and size-class determination – Macroinvertebrates in samples will be categorized according to environment (terrestrial or aquatic), life-stage (pupa, larva, adult) and identified to a coarse taxonomic level (family or genus).  In addition, macroinvertebrates will be binned into size-classes based on their total body length.  

3. Biomass determination – The biomass (mg dry weight) of sample partitions will be measured after being placed in a drying oven until samples have reached a constant weight.

4. Protocol documentation – Assist CHaMP collaborators in development of a macroinvertebrate sample processing protocol that documents each aspect of laboratory processing procedures.
To accomplish this task $16,500 is being added to the existing contract.

The purpose of this May 2013 Terraqua contract amendment (CCR-30065) is to deobligate $165,000 not required in 2013 for variability studies and reassign these funds through three CCRs (CCR-29036, Sitka Technology Group; CCR-30089, Eco Logical Research; and CCR-30066, Quantitative Consultants, Inc.) to support additional CHaMP project development tasks that were identified in 2012 and early 2013, and continue efforts to improve and refine CHaMP during the third year of pilot program implementation.  Specific May 2013 amendment tasks are as follows:

Sitka amendment (CCR-29036):
- Add new work element K (Import and Display Indicators): This work element will enhance the CHaMP Monitoring data system to support the display of habitat indicators at the scale of watersheds, sub-basins, and interior Columbia River Basin. (Add $33,968 to the contract value for Work Element K)

ELR contract amendment (CCR-30089):
- Additional CHaMP project coordination related to development tasks (Work Element B)
- Development of 2013 macroinvertebrate protocol and related coordination and field implementation (2 crew for flow and macroinvertebrate data collection to refine protocol and support drift and hydraulic model development), and development of spatially explicit AUX data and metrics (Work Elements C and G)
- Addition of work to support RBT development/coordination (Work Element H), data reduction and NREI model refinement (Work Element L), and statistical tool refinement, e.g. correlation of drift and growth, model and metric refinements (Work Element M)
- Add $79.766 to the overall contract value.

QCI contract amendment (CCR-30066):
- Add an additional CHaMP crew person to assist in collection of invertebrate and hydrologic flow data in CHaMP Lemhi surveys as part of an effort to improve the macroinvertebrate sampling protocol and further the development and validation of drift and hydraulic models (WE J - CHaMP 1h(1): Conduct CHaMP surveys in the Lemhi River; Additional funding for WE J = $12,666)
- Add additional deliverables to the ESSA Subcontract associated with CHaMP RBT completion.  The SOW deliverables are detailed in the attached document.  No change in the SOW scope is required.  Additional work was determined by the CHaMP RBT Working group in February 2013 (WE K - CHaMP 1.4(1): River Bathymetry Toolkit (RBT) Development; Additional funding for WE K = $8,600)
- Add new work element (WE L - Habitat Suitability Index Modeling) to fund QCI scientists to assist CHaMP cooperators and staff in the development of Habitat Suitability Indices that can be applied to CHaMP Digital Elevation Models and associated instream habitat metrics as they relate to fish populations.  It focuses on development of metrics, analytical methods, field collection techniques, and GIS tools implemented by the River Bathymetric Toolkit (RBT).  (Additional funding for WE L = $30,000)




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This contract is in support of a BiOp Fast track II project.

In support of habitat restoration, rehabilitation and conservation action performance assessments and adaptive management requirements of the 2008 Federal Columbia River Power System Biological Opinion (FCRPS BiOp), the Bonneville Power Administration is working with NOAA and other regional fish management agencies to monitor status and trends of fish habitat for each major population group (MPG) in the Pacific Northwest identified through the Endangered Species Act (ESA).   Status monitoring provides information on the quantity and quality of current habitat and thus maximizes spatial coverage with a given number of sample sites.  Trend monitoring is used to detect changes in habitat through time and thus requires repeat samples at given sites.  Minimizing sampling and measurement error is crucial in order to differentiate this variability from natural variability though time and space.  

In order to compare information across multiple MPGs, BPA is adopting a standardized fish habitat monitoring protocol, the Columbia Habitat Monitoring Program (CHaMP) for the Columbia River Basin monitoring programs.  CHaMP is a Columbia River basin-wide habitat status and trends monitoring program built around a single habitat monitoring protocol with a program-wide approach to data collection and management which meets FCRPS Action Agency (2010) programmatic prescriptions for habitat monitoring.    CHaMP will help BPA meet the requirements of the 2008 FCRPS BiOp and RPA 56.3.  This program will provide information on the status/trends in habitat conditions, and will support habitat restoration, rehabilitation and conservation actions, performance assessments, and the adaptive management requirements of the 2008 FCRPS BiOp.  In addition, the CHaMP meets RPA 56.3, RPA 57, and RPA 3 by characterizing stream and fish responses to watershed restoration and/or management actions in at least one population within each steelhead and Chinook MPG which have, or will have, fish in-fish out monitoring (identified in RPA 50.6).  The watersheds originally identified for CHaMP include: Hood River, Wind River, Toppenish, Klickitat, Fifteen Mile, Lower Mainstem JD, North Fork JD, Upper Mainstem JD, Middle Fork JD, South Fork JD, Umatilla, Upper Grande Ronde, Catherine Ck, Imnaha, Lolo Ck, Tucannon, Asotin, SF Salmon, Big Ck, Lemhi, Pahsimeroi, Wenatchee, Entiat, Methow, and Okanogan.  These watersheds were chosen to maximize the contrast in current habitat conditions and also represent a temporal gradient of expected change in condition through planned habitat actions.  CHaMP was implemented  in the first year of implementation FY11, in a subset of these subbasins, which are referred to as the pilot watersheds and include: Lower Mainstem JD, North Fork JD, Upper Mainstem JD, Middle Fork JD, South Fork JD, Upper Grande Ronde, Catherine Ck, Tucannon, SF Salmon, Lemhi, Wenatchee, Entiat, and Methow, In FY13, CHaMP will be implemented in these same pilot watersheds.  Coordination and support of CHaMP deliverables associated with additional watersheds beyond those included in the list of pilot watersheds are outside the scope and budget of this contract.

CHaMP collaborators will be supported by cross-project data management, stewardship and analysis staff, annual pre- and post-season meetings, annual field protocol and data management tool implementation training sessions.  

(1)             Roles
CHaMP staff - refers to individuals under contract with BPA through the following list of contractors (e.g. TQ, QCI, SFR, Sitka) and includes Chris Jordan (NOAA) who is principle investigator of Project #2011-006.  Collaborators/Collaborating Agencies:  Refers to those contractors implementing CHaMP status/trend monitoring under Project #2011-006. First-Time Collaborators - Refers to collaborators whose first year of sampling is 2013.  Returning Collaborators - Refers to collaborators whose first year of sampling was 2011 or 2012.

Program Elements

(2) Sampling Design
A Generalized Random-Tessellation Sampling (GRTS) survey design was recommended by Crawford and Rumsey (2009) for monitoring habitat status and trend in the Columbia River Basin.  The GRTS design was initially developed under the EPA’s Environmental Monitoring and Assessment Program and is a probabilistic sampling design that has been shown to be advantageous for generating habitat condition parameters with known statistical characteristics.  The CHaMP monitoring design follows a  GRTS design with a 3 year rotating 1-to-1 split panel structure to distribute sampling effort in space and time, and has management tools for sampling design.  Implementing a GRTS survey design correctly is critical to producing a final dataset with known statistical characteristics requiring the implementation of strict procedures during the site evaluation and selection process.  A GRTS Site Selection Protocol and Tool will be provided to each collaborator to support field crews with efficiently completing the process while strictly enforcing design requirements.  

(3) Field Sampling
Habitat field sampling will follow the Bouwes et al. (2011) protocol that will be modified in 2012 in response to Pilot-year "lessons-learned" and that was developed after a review of fish habitat requirements, interactions of processes that influence fish habitat, the spatial scales for the context of these interactions, and current monitoring programs.  The protocol has the greatest probability of being comparable to other protocols and most relevant to salmonids and has been designed to be applied across varying spatial contexts depending on the logistical constrains of the sites.  In areas where GPS signals can be obtained, along with aerial photos, habitat units within reaches can be superimposed onto aerial photos with a map grade GPS.  In situations, where a GPS signal is not obtainable, units can be referenced to aerial photos and supplemented with on the ground measurements.  All approaches use a GPS map-grade data logger and thus do not require new gear for differing spatial contexts across related approaches.  

(i) Standardized Crew Training: Sampling and Data Capture Tool
Standardized field crew training in the recommended methods will be provided/required of all CHaMP field crews.  This standardized approach will promote crew efficiency and improved standardization across the region.  In addition to agency-specific safety and other training, CHaMP staff will provide training to support cooperating agencies that implement the recommended habitat protocol.

(ii) QA/QC crews to do repeat sampling across all participating watersheds
Repeated sampling of habitat monitoring sites within the same sampling season has proven to be an important component of GRTS-based, watershed-scale habitat monitoring.  Repeat sampling assists with 1) quality assurance/quality control, 2) the assessment of crew variability as a component of variation, and 3) providing improvements to temporal variability recognition (i.e., trend detection).  Furthermore, repeat sampling will be important to CHaMP's research goals of testing the performance of the recommended protocols across the Columbia Basin.  To achieve these objectives, CHaMP will conduct repeat sampling visits for all watersheds in this program at 10 percent of all sampling sites during the low-flow index period.

(4) Data Management
For a monitoring program at the scale of the Columbia River Basin to be successful a robust data management system must be in place before initiating data collection.  Monitoring habitat in the CHaMP watersheds will generate a massive volume of data.  A system of data processing, storage, analysis, reporting, and distribution is available to meet the needs of a large-scale monitoring program, such as (a) documenting monitoring objectives, study design and intended analysis; (b) summarizing how, when, and where the monitoring data were collected, (c) supporting a range of analytical methods, such as hypothesis testing, time series analysis, structural equation modeling, and GIS support; and (d) adapting to changing requirements in the future.  The data system (see www.CHaMPMonitoring.org) includes a centralized data warehouse and web-based data discovery tool; data exchange and loading procedures; a database schema that defines data storage format; metadata tools; data capture, validation, and summary tools; quality control and assurance procedures; and data stewards who support the system.

(i) Field Data Capture Tools: Hand Held Loggers
Field crews will need applications to support data capture, review, summarization, and reporting and a suite of handheld and desktop tools to support both habitat and fish monitoring is available.  These tools have XML-based mechanisms to synchronize data.  This workflow includes documenting metadata about project and statistical design, entering survey event information and observations, performing quality assurance procedures, deriving metrics, and submitting data for archiving.

(ii) GIS Data Management and Geoprocessing
The large spatial scales that the CHaMP will cover means that assimilating and managing spatial datasets in GIS, accounting for the geomorphic context of sampling, and performing watershed or subbasin-scale analyses are important data features within these programs.  GIS data management support, coordination, and basic processing for monitoring programs that require data management guidance or processing assistance is available and development of geospatial models, the use of remote sensing technologies to collect continuous GIS datasets, such as LIDAR and aerial photos, and integrating field-based tabular data within a geospatial context is ongoing.  

(iii) Data Storage and Retrieval
The CHaMP will have multiple groups collecting data and it will be critical to have data accessible and available for use by all groups within the program.  The CHaMP data management system serves as a long-term storage facility for monitoring datasets including metadata and features online interfaces for searching, viewing, and downloading datasets and documents associated with the coordinated monitoring program.

(5) Reporting
In such a large and geographically dispersed program such as CHaMP it is important to have an annual review of the data collection events so that any issues experienced or lessons learned over the field season can be addressed in a timely manner and with each collaborators' input.  To that end,  collaborators will submit a summary of their field season to the CHaMP Lead Coordinator who will collate and summarize the data collected, logistics of implementation and lessons learned from each field season into the RME and BiOp reports.  This report will be used to inform full implementation in 2014, including any adjustments that may be appropriate on the design or scope of the project.

(6) Post-season Workshop
A post-season workshop will be held to address the questions and comments posed by the ISRP and the Council pertaining to CHaMP and to review the FY13 season, look at the data, discuss the protocol, review the draft logistics/RME and BiOp reports, and plan the next season. Topics covered could include a programmatic overview of CHaMP, an overview of the study design and objectives, review of the protocol and data management tools, and analytical approaches.