Eyes on the Eel

Eyes on the Eel: Synoptic summer surveys of food web biomass  in the South Fork and Mainstem Eel River

This is a period of rapid and critical change for the Eel River ecosystem.  Many groups are keeping their eyes on the Eel watershed, and we are grateful for their vigilance and their partnership.  Here is what the Berkeley-based Eyes on the Eel group is doing:

We survey selected tributaries and mainstem reaches near their confluences within the S. Fork and mainstem Eel basins to document changes in key species and groups of organisms that make up the summer food web in these channels.  We’re interested in what the food webs look like during three periods of summer baseflow:  mid-June, when production of algae, invertebrates, and growth of fish is typically peaking;  July, when temperatures are warmest; and September, when discharge is lowest.

Our data could address a number of questions, but we are initially interested in testing hypotheses about “patterns of trophic level biomass” (the biomass of organisms in various feeding groups at different levels in food webs: basal (primary producer, mostly algae), intermediate (consumers, mostly aquatic invertebrates), and top (predators, mostly fish). Previous work at the Angelo Reserve suggested that year-to-year variation in food webs, particularly the peak abundance of attached algae, depends on whether or not scouring floods occurred during the previous winter.  The dominant type of algae–i.e., the prevalence of nutritious diatoms versus potentially toxic cyanobacteria–depends on how much summer flows drop and temperatures warm.  Different patterns of trophic level biomass are also expected in sunlit mainstem channels versus darker tributaries. Clearly, there will be changes over the summer season as well.  Will patterns we’ve seen within the Angelo Reserve in the upper South Fork, where the river drains 116-160 km2, apply more broadly across the 9,540 km2 Eel River.

Hypothesis I:  Effect of annual hydrology. During the summer low flow season, we think the algal-based food web of the Eel River can assemble into one of three alternative states (Power et al. 2008, 2014, 2015*hotlink to papers*). In Salmon state, rock substrates and streamers of the macroalga Cladophora glomerata become covered with nutritious diatoms, which in turn support many edible prey, including primary consumers (invertebrates and tadpoles that eat living or dead plant tissue). Diatom energy, nutrients, and lipids (including PUFAs) are transferred up the food chain to support rearing juvenile salmonids and other predators. Salmon state generally occurs after winters when one or more bankfull floods scour out grazing insects that grow large enough to escape gape-limited predators the next summer.  These armored, predator-resistant but slow-growing grazers include stone-cased caddisflies:  (Dicosmoecus in mainstems, and Glossosoma and Neophylax in both mainstems and tributaries).  Dicosmoecus state characterizes summer food webs that follow winters when scouring winter floods have not occurred. In Dicosmoecus state, large macroalgal blooms do not proliferate because these large grazers are very abundant the following summer, and graze down the algae before it can grow long streamers.  Algal energy and nutrients is sequestered in the body of large armored (or sessile) grazers that aren’t vulnerable to juvenile salmonids, so they don’t grow as well.  Fig. 2. In recent years, a third summer food web state, Cyanobacteria state, has emerged. Potentially neurotoxic cyanobacteria (Anabaena or its relatives) can proliferate if summer base flows grow critically low, so that sunny mainstems warm and backwaters or side pools stagnate. Blankets of cyanobacteria can overgrow the edible diatom epiphytes and their green macroalgal hosts, forming what Keith Bouma-Gregson calls “spires”. Bouma-Gregson et al., 2017  Other neurotoxic cyanobacteria (Phormidium spp, Bouma-Gregson et al. in prep) have been observed attached to rocks in mainstem riffles where flows remain relatively strong.

These three proposed food web “states” are simplified hypotheses, and in need of constant test and better understanding.  We need to learn more about the environmental conditions that steer the river food web towards one state or another to forecast summer food web structure in the Eel and manage flows and land cover for food webs that support salmonids.

Hypothesis II: Downstream changes in food web controls.  Food web assembly is controlled less by energy loading and more by disturbance regime as one moves downstream into habitats with increasing sunlight and bedload mobility (decreasing substrate stability (Finlay et al. 2010; Power, Kupferberg, Cooper and Deas, 2015 ).

Hypothesis III: Changes below critical flow thresholds. Summertime water extraction can potentially tip the Eel food web from salmon-supporting to cyanobacterialy degraded states (Bauer et al. 2015; Carah et al., 2015, Power et al. 2015).


We selected four tributary mainstem confluences, one in the mainstem Eel at Jordan Creek, and three in the South Fork.  Fig. 3. We have some infrequently monitored transects  ~100 m upstream from the Fernbridge, near the Eel estuary. We have monitored now in 2015, 2016, and 2017 (but started in July in 2015).

With a team of 10-12, we can complete a site (one mainstem and its tributary) in one day, so each complete survey takes 4 days in our June, July or September sampling effort.

Initial set up–site benchmarks and mapping:

At a given site (mainstem-tributary confluence), we choose four ‘hydraulic units’ (a riffle and its receiving pool on upstream and downstream reaches of the tributary, and above and below the confluence on the mainstem) are benchmarked on the first visit.  For each riffle-pool, permanent x-stream transects (both sides marked with small nails and tags in trees or rock) are benchmarked, one across the upstream (riffle), and two across the pool. Fig. 4. *methods shot, shelley shot*  (Later, when time allows, we locate our transects on Google Earth for later preparation of sketch maps of substrate facies,  and to link them to bathymetric LiDar Data from the Eel River Critical Zone Observatory, available to the public on Open Topography. In addition, sketches of microhabitat flow estimates in broad intervals (see Appendix A) and overhead (forest, canyon wall) canopy cover (with cameras or spherical densiometer measurements) will be added as overlays on these maps. Laminated copies will be made and used during subsequent surveys so that important changes (e.g. in big wood, algal cover, etc.) can be documented (on transparent film laid over each laminated map).)

Surveys of biota and seasonal environmental conditions:

Snorkeling counts of large fish.

This is done first so that large vertebrates will be minimally disturbed.  Two snorkelers (wet suits needed) swim slowly from downtream to upstream through pools, counting and estimating lengths of the various species of fish they see.  Other large vertebrates (turtles, lamprey, otters, etc.) are also noted.

Bankside counts of small fish and large invertebrates.

After snorkelers have passed through a reach, bankside observers take positions on left and right sides of rivers (left and right determined when looking downstream).  They choose shallow sites with sufficient visibility, and sit quietly for at least 5 minutes (giving fish a chance to recover from the disturbance of human movement).  During this time, each observer picks landmarks on the stream bed that delimit the area to be observed.    Time of day is noted on the data sheet.  When bankside counts begin, the observer scans this area for a timed 3 minute interval, writing down for each visual scan the number, species, and estimated sizes of the fish seen.  Numbers of water striders, crayfish, newts, and other large animals are also recorded for each scan sample. About 5 scans can be done per 3 minute interval.  After completing five successive 3-minute intervals, the raw data sheets are collected by the data Czarina (or Czar).  Later, either the maximum number or the average number of individuals of given species and size classes will be used to estimate abundances of smaller (often yoy) fishes and larger invertebrates in this river margin habitat.

Transects for documenting physical conditions and macroalgal/macrophyte abundance (Appendix A).

After fish counts, we string a meter tape from nail to nail across the each of the three benchmarked x-stream transects.

At ~ 12 or more evenly-spaced fixed points along the meter tape, we record: stream depth (cm), substrate texture (estimated by eye according to the Wentworth scale, see Appendix A), stream surface velocity in broad categories that can be estimated by eye, Appendix A), and record attached algae:  dominant and subdominant taxa, their modal height, % cover in 5 broad intervals, and if possible, algal condition in 5 categories (details in Appendix A).  We also note here deposited litter or detritus; conspicuous macrobiota, and notes on other important observations at the point along the transect.

Epibenthic Invertebrates on cobbles

Five cobbles are sampled along each transect–we choose cobbles that range from 60-120 mm median diameter, trying for grapefruit-sized stones.  We use ~25 cm wide 1-mm mesh aquarium nets to sample epifaunal invertebrates on coarse (large-pebble-small boulder) substrates, placing the net downstream from the stone, quickly and carefully rolling the stone into the net, lifting so as to minimize loss of invertebrates, then carefully brushing off all attached fauna into a white tray of water streamside. (similar to Peggy’ Wilzbach’s rapid assessment method).  Bankside, seated next to a partner who records data, we first estimate the area of cobble sampled by measuring its major and minor axes (of the habitable area when rock was on the bed) and noting its shape (oval, rectangle, or triangle).  These lengths will later be used to estimate habitable area.  We then count numbers (and estimated lengths of everything 1 mm or larger) of invertebrates, keeping track of taxa at least to order, often to family, and sometimes to genus and species (see Appendix C for identification guide).   Some invertebrates are measured within their cases, and this is noted.  We have length-weight regressions for both invertebrate bodies, and invertebrate cases (the latter of course have much greater variation).  Data on invertebrates are later entered into a controlled-vocabulary data base.


Appendix A. Transect survey methods (MEP)

I repeatedly survey permanent cross-stream transects (“x-scns”) to follow changes in algae, environmental conditions, and associated organisms over time, documenting seasonal and interannual variation. Transects are benchmarked at both ends with nails in trees or bedrock—these can be labeled with aluminum tree tags (Forestry Supply) and should be carefully located with hand-drawn maps, GPS, triangulation (measure distance to spot from two other conspicuous landmarks), etc. Benchmarks should be on ‘permanent’ structures (e.g. large trunks) high enough so that high as well as low flows can be documented (just above bank full is ideal, higher than that and it’s hard to read the tape while walking the streambed). On each survey, stretch a meter tape tightly between the nails. Nail to nail distance should vary less than 1 cm over repeated surveys. Take enough points to obtain about 15-20 measurements for each x-scn. At 0.5 m or 1.0 m intervals along each transect:

  1. note distance along the meter tape (X-strm (m))
  2. measure water depth (cm) (a ski pole marked in decimeters is good, doesn’t flex in high flow, and saves you from falls)
  3. measure velocity with a current meter, or estimate surface current velocity (cm s-1) by timing floating objects across your measurement point1
  4. note dominant and subdominant substrate particle sizes2
  5. using a diving mask or plexiglass view box, note the dominant and subdominant macroscopic algal taxa within an estimated 10 cm x 10 cm area around each sampling point3
  6. record the modal height (cm) of attached filaments or the length from point of attachment of strands of algae floating over the site on the water surface, if these obscured view of the bed.
  7. characterize algal density (% cover) 4
  8. if possible (for Cladophora, zygnematales, perhaps Nostoc) characterize algal condition5
  9. note conspicuous animals within the same 100 cm2 observation area, bearing in mind that some will be attracted to you (minnows) and others will be hiding (mayflies) 6.

Key–Codes and categories used:

Flow velocity (cm s-1)
0 (silt settles vertically)

Wentworth Particle size (median diameter, mm)
<<< 2 mm, not gritty = silt, mud M
< 2, gritty = sand S
2-8 = small gravel Gs
8-16 = large gravel Gl
16-32 = small pebbles Ps
32-64 = large pebbles Pl
64-256 = cobbles C
> 256 but discrete = boulder Bld
continuous = bedrock Br

  1. Algal (etc.) codes

Clad Cladophora (note color as green G, yellow Y or Rust R)

Moug, Spg Mougeotia or Spirogyra (need to distinguish under scope)

Zyg Zygnema (more chatreuse than Spg or Moug, earlier in season)

diat sk diatom skin (gold, orange or yellow-brown) on rocks

bg sk dark or grey skin (often Phormidium, Tolypothrix or Scytonema)

Nos b Nostoc balls

Nos e Nostoc ears (colonized by Cricotopus midge larvae)

Riv Rivularia black freckles to larger circular spots or blotches

Anab deep turquoise Anabaena, loosely epiphytic on Clado

Phor Phormidium—dark brown epilithic cyanobacteria turf in riffle flow

Sedge dominant bunched graminoid along active channel is Carex nudata

Moss Fontinalis is long moss, other riverine mosses are mats < 3 cm high

Terr lvs Terrestrial leaf litter

  1. Algal density (~ % cover)
  1. a few filaments
  2.  < 10% basal cover
  3. 10-50% basal cover
  4. 50-99% cover
  5. can’t see substrate through growth
  1. Algal condition (can’t assess for many taxa)
  1. nearly detritus
  2. senescent, discolored, fragile and falling apart
  3. discolored but less fragile
  4. slightly discolored, but robust
  5. vibrantly healthy
  1. commonly observed Fauna (optional)

Diptera (flies)

tufts (retreats of midge, Pseudochironomus) woven into Cladophora (long woven infested Clado streamers look like dreadlocks)

tube midges-small light colored tubes attached to rocks

Lepidoptera (moths)

Pet – Petrophila, aquatic moth larvae, live under transparent retreats attached to boulders as larva, these retreats condensed to small (~1.5 x .75 cm2) white pupal cases in stage before moth emerges.

Ephemeroptera (Mayflies)

Hept – heptageniids

Baet – baetids (Baetis, Centroptilum)

Ephem –ephemerellids

Siph – siphlonurids

Leps –Leptophlebiiids

Trichoptera (Caddisflies):

Dicos – Dicosmoecus gilvipes-saddle shaped head aperture framed with two ‘saddlepack’ stones

Oncos – Oncosmoecus, similar to Dicosmoeucus, circular head aperture

Tin – Tinodes tube dwelling caddis, like spaghetti

Leuco rice grain size sessile caddis

Gum – Gumaga, slender curved sand cases

Neo – Neophylax, stone cylindrical case

Glosso – Glossosoma, turtle shell stone case


Rams horns – Helisoma

Physella spp


Ferrissia — fw limpets



R roach

Stl steelhead- Onchorhynchus mykiss

Coho-coho, Onchorhynchus

Stk stickleback

PM pike minnow

GSfish green sunfish-Lepomis cyanellus

Bass – large mouth or black bass-Micropterus

Bullh-Black bullheads—Ictalurus nebulosus


Pacific pond Turtle—

Rough skinned newt

Giant Pacific salamander

Foothills yellow-legged frog


Pacific tree frog

Glossary of terms