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EMP’s benthic monitoring program began in May 1975, with either one or three replicate sample grabs taken at each site visit. From 1975 through 1979 the program collected three replicate samples biannually from 18 to 35 stations, for a total of 48 stations over the period. In reviewing the data collected between 1975 and 1979, EMP scientists determined semi-annual monitoring was insufficient to track long term ecological changes in the SFE as mandated by Water Right Decision 1485. In 1980, EMP revised its benthic monitoring and began a monthly sampling program at nine stations.

EMP revised the benthic monitoring program again in 1995. Upon review of data collected from 1980 to 1990, EMP scientists recommended that across-channel sampling be reduced to a single station per location in the Delta to widen the geographic coverage of the program. The revised program began in 1996, increasing the number of sites sampled each month from nine to ten and increasing the number of replicates per station from three to four. Detailed information about location, number and characteristics of the historical sites can be found in IEP Technical Report 12 (Markmann, 1986) and IEP Technical Report 38 (Hymanson, et al., 1994).

Results from a programmatic review of the EMP in 2001-2002 led to fundamental and comprehensive re-consideration of the benthic monitoring. Reviewers recommended a temporary reduction in sampling frequency to free up EMP resources to conduct the more spatially intense sampling without requiring additional resources. Reduced monthly monitoring began in October 2003 and sampling was conducted quarterly (in October, January, April, July) at each station until October 2005, when monthly sampling resumed. Stations have been monitored monthly since this time.

Instances of missing data are compiled in the "DWR benthic monitoring, missing data" table.

References:

Hymanson, Z., Mayer, D., & Steinbeck, J. 1994. Long-Term Trends in Benthos Abundance and Persistence in the Upper Sacramento-San Joaquin Estuary. Technical Report no. 38, Interagency Ecological Program Sacramento, California.

Markman, C. 1986. Benthic Monitoring in the Sacramento-San Joaquin Delta - Results from 1975 through 1981. Technical Report no. 12, Interagency Ecological Program Sacramento, California.

Field collection

All samples of benthic invertebrates are collected using Ponar dredge deployed by boat using a hydraulic winch. The dredge samples an area of roughly 0.052 square meters of the estuary’s bottom. The depth of sediment penetrated by the dredge depends on the composition of the sediment and the dredge itself. Under the current sampling program, four replicate grabs are collected at each site. The contents of the dredge are brought to the surface and placed in a large plastic bucket. Water is then added to the sample to create a slurry. The contents of each grab sample bucket are rinsed into a Standard No. 30 stainless steel mesh screen (0.595 mm openings). Each sample is carefully washed with a fine spray to remove as much non-living substrate as possible without damaging the organisms within. All material remaining on the screen after washing is preserved for laboratory analysis in a solution of ~20% formaldehyde containing Rose Bengal dye and buffered with sodium tetraborate. The benthic macroinvertebrate sampling methodology used in this program is described in Standard Methods for the Examination of Water and Wastewater (see pages 10-60 through 10-74.)

References:

Franson, M. A. H., Eaton, A. D., Greenberg, A. E., Clesceri, L. S., Water Environment Federation., American Water Works Association., American Public Health Association. (1998). Standard methods for the examination of water and wastewater. 20th ed. Washington, DC: American Public Health Association.

Lab Processing

At the laboratory, the volume of settleable substrate in each sample jar is estimated and recorded. The formalin fixative is decanted and the sample is thoroughly washed on a 30-mesh (0.6 mm) screen. The composition of the substrate is estimated and recorded noting the relative percentages of peat, sand, mica, organic detritus, and other materials. Organisms are picked by hand from the substrate using an illuminated three diopter magnifier. These are preserved in 70% ethyl alcohol for subsequent identification. A stereoscopic dissecting microscope (70-120x) is used to identify most organisms. Taxonomic features too small for accurate identification under the dissecting scope are visualized under a compound microscope after permanently mounting the organism on a slide.

If more than four hours of picking is required, and a sample contains many homogenously distributed organisms but few species, a one-fourth subsample is chosen at random. The subsample is picked and the results are multiplied by four to represent the total sample. The remainder of the sample is inspected to make sure no other taxa were overlooked. Laboratory identification and enumeration of macro-benthic organisms in each sample is performed under contract by Logical Zoology (under direction of Sarah Pearson), West Sacramento, California. Analysis by Logical Zoology started in 2022; previously, taxonomy was performed by Wayne Fields of Hydrozoology, Inc. from 1975-2022.

Data processing

Data for the main dataset ("DWR Benthic data 1975-2023", or any later versions) is minimally processed. Raw counts of organisms found in each replicate grab sample are reported as they come from the taxonomist. QC is performed to make sure that the data entry matches the input from the taxonomist, and zeros for all other organisms in the species list are added during data entry and processing.

Data for the CPUE dataset ("DWR Benthic CPUE data 1975-2023", or later versions) differs in three main ways from the main dataset to make its analysis more tractable for non-experts. First, the data is converted from count data to organisms/m2 (organisms/m2 = raw count of organisms per grab / (0.052 m2/ grab)). Second, the data for each of the four (or three, in earlier years) replicate grab samples is averaged together. Finally, the species that were not found at a site visit (count and CPUE =0) are removed from the dataset. Since there are usually ~10x more zeros than species present, this condenses the dataset very efficiently, and the zeros are easily added back in by pivoting the data to a wide format.

Data on site visits ("DWR benthic monitoring site visits, 1975-2023") and number of grabs ("DWR benthic monitoring grab totals, 1975-2023") list the annual totals of site visits and replicate grabs taken at each site through EMP's benthic monitoring history. This is provided as a convenience for the data user trying to understand the changes in location varying levels of monitoring effort through the long period of record.

Data for the list of missing data ("DWR benthic monitoring, missing data") was compiled by reviewing the data record of site visits and grab totals. Data was counted as missing all grabs on a given date if the site had been sampled at dates both earlier and later than the date in question; many of the early "missing" dates may not be truly missing, since the sampling design from 1975-mid 1979 was still being settled. Data was counted as missing some grab samples when the total taken at a site x date was smaller than the number taken at other sites in in that month.

Data for the species list ("DWR benthic monitoring, organism keylist") is the list of all species that have been found or were expected to be found during any EMP benthic monitoring, including special studies not included in this data entity. It is updated whenever new species are found and is provided as a convenient reference for data users.

Data for the station list ("DWR benthic monitoring sites, active and historic site locations", or later versions) is the list of all sites that have been visited during EMP monitoring and is provided as a convenience for data users.