NSF BIOCOMPLEXITY PHYSICAL/BIOLOGICAL METADATA 2005
GEOMORPHIC SURVEYING PROTOCOL
Andrew Pike
POOL SELECTION
At each node, we surveyed between one and five pools; one at the crossing itself,
and the others divided equally upstream and downstream of the crossing. The number of
pools sampled at each node was determined by both the availability of pools, and the
number of pools utilized for human recreation. The reason for sampling multiple pools is
to represent the range of pool morphology present at a site, as well as correlate to the pool
locations where human and biological sampling occurred.
In this dataset, geomorphic data for only one representative pool at each node site
is presented. At recreation sites, the representative pool is the one with the presumed
greatest human recreation. At non-recreation sites, the pool at or nearest to the bridge was
chosen.
GEOMORPHIC SURVEYING
Within a given pool, a cross-section was measured at a uniform section that best
represented the average characteristics of the pool. At each cross-section, relative
distance and elevation were measured at evenly spaced intervals from bank to bank using
a Sokkia Total Station Laser Theodolite (Set 530). Cross-sections extended into the
adjacent woody vegetation and away from the edge of the active (bankfull) channel,
which was determined by the edge of woody vegetation and high flow features (fine
sediment lines). Both baseflow (wetted channel at summer low flows) and active channel
widths, average channel depths, and active channel cross-sectional areas were calculated
for each-cross section. Slope was similarly calculated by surveying elevation points at
equally spaced intervals along the profile of the river, intending to capture the average
characteristics and slope breaks of the reach.
Grain size in the active channel was estimated using a modified Wolman Pebble
Count method (Wolman, 1954). The size of 100 clasts, selected randomly by pacing
across the width of the stream at survey sites, were measured and visually classified into
the following 7 size categories: Bedrock, Megaboulder (>2000mm), Boulder (2562000mm), Cobble (64-256mm), Gravel (2-64mm), Sand (.063-2mm), and Fines
(silt/clay, 0.001–0.063 mm).
A high-resolution GIS analysis was performed to derive physical site
characteristics for each node site. The analysis incorporates GIS spatial analytical tools to
estimate a variety of landscape factors, such as elevation, drainage area, slope, flow
direction, accumulated runoff, both downstream and upstream distances, and channel
energetics. A 10m DEM (digital elevation model) was digitally derived from the USGS
topographic quadrangle map, available at http://biocomplexity.cnr.colostate.edu/data.htm. Flow
direction and flow accumulation algorithms were used in ESRI ArcGIS to calculate least
resistant paths between adjacent cells to determine downstream flow direction and the
accumulation of contributing cells.
BIOLOGICAL SAMPLING PROTOCOL
Katie Hein
At each river-road node, the biological team sampled fish and shrimp upstream and
downstream from the road with a variety of methods. Below, we describe the details of
the study design for each method.
POOL SELECTION
At each node, we sampled one to four pools: the pools immediately up and downstream
from the road, and a second pool up and downstream from the road within 325 m of the
road crossing. If the pool extended below the road crossing, we sampled the entire thing.
At low elevations where brackish water reached the road crossing, we only sampled
upstream from the road.
BIOLOGICAL SAMPLING
1. Snorkeling: Two people snorkeled one transect each along the length of the pool
simultaneously. Each snorkeler held a 1 m long stick in front of and
perpendicular to his/her body to demarcate the sampling area. He/she identified
and counted the number of each fish species seen while swimming upstream. We
only snorkeled when turbidity was low, where sewer water was not entering the
stream, and in pools deep enough to swim (> 1 m).
2. Trapping: We used three types of traps to sample all pools at all sites. Wire mesh
gee minnow traps (0.635 cm mesh, 22.9 cm diameter, 44.5 cm long) with a 3.5
cm diameter opening, gee minnow traps with a 5 cm diameter opening, and large
cylindrical traps (1.4 X 2.6 cm mesh, 35 cm diameter, 65 cm long) with a 13 cm
diameter opening. In small pools (< 30 m2), we set 1 of each type of trap, and we
set 3 of each type of minnow trap and 2 large traps in medium pools (30-200 m2).
In large pools (> 200 m2), we set 5 of each type of minnow trap and 2 large traps.
Each trap was baited with 22 g of cat food and set over night. The traps with
larger openings captured large Macrobrachium sp., Agonostomus monticola,
Anguilla rostrata, Eleotris pisonis, Epilobocera sinuatifrons, Gobiomorous
dormitor, and Sicydium plumieri, whereas minnow traps with a small opening
effectively captured Atya sp., Xiphocaris elongata, Anguilla rostrata, and juvenile
Macrobrachium sp.
A few Eleotris pisonis, Epilobocera sinuatifrons,
Gobiomorous dormitor, Poecilia vivipara, and Sycidium plumieri were also
captured in minnow traps with a small opening. Each individual was identified to
species, but juvenile Macrobrachium could not be identified to species.
3. Electrofishing: One person used a backpack shocker to stun and net fish, and a
second person helped to net fish in each pool and/or associated riffle. The
electrofishing team moved upstream, sweeping from one side of the pool to the
other until they reached the upper bound of the pool. The team also shocked
riffles adjacent to the pools trapped and snorkeled. When the pools were too large
to electrofish effectively (> 215 m2, > 1.3 m deep), the team only electrofished the
riffles.
** The total number of freshwater fish species found at a site could include (latin,
English, Spanish names):
a. Agonostomus monticola, mountain mullet, dajao
b. Anguilla rostrata, American eel, anguila
c. Awaos tajasica, river goby, saga or ciaga
d. Eleotris pisonis, spinycheek sleeper, moron
e. Gobiomorus dormitor, bigmouth sleeper, guavina
f. Poecilia sp.(vivipara?), guppy, sardinita
g. Sicydium plumieri, sirajo goby, olivo or chupa piedras or setí or tri-tri
All species were native except Poecilia sp. We did not include estuarine fish in our
calculations of the total number of fish present at a site.
** The total number of decapod species found at a site could include (latin, English,
Spanish names):
h. Atya innocous, shrimp, gata or guábara or chágara
i. Atya lanipes, sinous-faced shrimp, guábara
j. Atya scabra, serrei shrimp, jonga
k. Epilobocera sinuatifrons, river crab, buruquena
l. Macrobrachium acanthurus, ?, silgao
m. Macrobrachium carcinus, giant-hand shrimp, bocú
n. Macrobrachium crenulatum, pubescent-hand shrimp, camaron
o. Macrobrachium faustinum, pubescent-hand shrimp, camaron
p. Macrobrachium heterochirus, teeth-faced shrimp, leopardo
q. Xiphocaris elongata, glass or long-faced shrimp, salpiche or chiripi or
chillo
All species were native.
** Rows by species give the presence or absence of a particular species at each site (0
indicates absence and 1 indicates presence).
BRIDGE SCOUR ASSESSMENT PROTOCOL
Kirk Sherrill
A quantitative and qualitative local bridge scour and physical connectivity survey was
performed at 24 RRC sites. The bridge scour survey was adopted from Johnson et al.
1999, slight modifications where made including the addition of two scour indicator
variables: channel bed material and presence of a blow hole or scour pool. Channel bed
material significantly determines how susceptible a site is to stream channel erosion, thus
this criteria was added. Secondly blow holes and scour pools often result from deposition
of streambed material flowing through undersized pipe culverts, which in turn can yield
creation of a vertical barrier (Baker and Votapka 1990). Four of Johnson’s et al. (1999)
variables where omitted as they where deemed inappropriate for the streams understudy,
these included bed material consolidation and armoring, shear stress ratio, bridge/culvert
distance from meander impact point, and percent channel constriction stability. Surveys
where preformed over four days from August 8/9/05 thru 8/12/05, during what could be
considered low flow conditions.
Eleven indicator variables of stream bed stability around the RRC sites were evaluated
along with other relevant observations including presence of vertical barriers, stream
reach type, RRC type, culvert slope, length and height. Each variable was measured
using a scale from 1-12, where a rating of 1 implies a site with excellent stability (little to
no erosion) and conversely a rating of 12 would imply poor stability (highly degraded,
much erosion potential). For the 9 variables used in Johnson et al.’s (1999) survey the
same variable rating criteria was used to assign appropriate ratings. Rating criteria used
for the channel bed material and blow hole/scour pool variables is shown in Table 1.
Weights where assigned to each variable based upon what is believed to be the influence
each respective variable has on the overall amount of alteration of sedimentation and
hydrologic flow or scour around RRC. Taking the scores for each variable and
multiplying by the assigned weight and adding the scores together yield the overall scour
rating by site (Table 3).
Works Cited:
Baker C.O. and Votapka. 1990. Fish Passage Through Culverts. U.S. Department of
Transportation FHWA-FL-90-006.
Johnson P.A., Gleason G.L., and Hey R.D. (1999). “Rapid Assessment of Channel
Stability in Vicinity of Road Crossing”. Journal of Hydraulic Engineering
ROW DESCRIPTIONS
Site Characteristics
1. GPS Coordinate N – Coordinate (deg-min-sec) of road crossing
2. GPS Coordinate W – Coordinate (deg-min-sec) of road crossing
3. Elevation (m) – Elevation of stream at road crossing, derived from the 10m DEM.
4. Road – 1 is a major 4-lane highway, 2 is a 2-lane highway, 3 is a paved road, 4 is
an unpaved road, and 5 is a trail
5. Stream – stream size from small ( m wide) to medium ( m wide) to large ( m
wide)
6. Human – level of human use from 0 visitors to high use
7. Watershed – watershed of the site’s location
8. Distance to Ocean (m) - Distance to the river mouth (ocean), derived from the
flow direction grid.
9. Distance from Headwaters (m) - Distance to the headwater source, derived from
the flow direction grid.
10. Drainage Area (km2) – Contributing basin area, derived by summing contributing
upstream cells.
11. Avg. Canopy Cover (%) – Average closed canopy percentage at a site; average
was taken for measurements from two pools at each site using a spherical
densiometer.
12. GIS Slope (%) – Slope, in percent gradient, derived from the nearest 10m
contours on a USGS 1:24000 quadrangle map.
13. Field Slope (%) - Slope, in percent gradient, calculated from the surveyed water
surface slope along the length of a characteristic reach at each site.
14. Weighted Upstream Elevation [WAE] (m) – Mean elevation of contributing basin
area, derived from the 10m DEM.
15. Rainfall (mm/yr) – Mean annual rainfall at site. Derived from regression equation
(Garcia-Martino et al., 1996): Mean Annual Rainfall = 2300 + 3.80*Elev.(m) .0016 Elev.2(m)
16. No Rain Days – Mean number of days per year with no rain. Derived from
regression equation (Garcia-Martino et al., 1996): No Rain Days = 133.30 0.09*Elev.(m)
17. Mean Annual Discharge (m3/sec) - Product of runoff (mm/yr), time coefficient
(yr/sec), and drainage area (m2). Runoff values derived from regression equation
(Garcia-Martino et al., 1996): runoff (mm/yr) = 3.22* WAE(m) + 816.16
18. Avg. Unit Stream Power (W/m) – Stream Power per unit bed area: ρ * S * Q,
where: ρ = specific weight of water (= 9810 N/m3), Q = mean annual discharge
(m3/s), S = slope (m/m)
19. GeoPotential Energy Flux (J/yr) – Potential energy of the annual water mass
discharged at a given site: mgh/t = ρ * h * Qyr, where: ρ = specific weight of water
(= 9810 N/m3), h = elevation (m), Qyr = total annual discharge (m3/yr)
Geomorphology
20. Pool ID – ID and location of pool: D = downstream, U = upstream, Bridge =
below/at bridge
21. Pool Comment – Small description of pool characteristics, for aid in identification
22. Distance to Bridge (m) – Pool distance upstream or downstream from bridge
23. Width (m) – Distance from water edge to water edge
24. Hydraulic Radius (m) – Average depth, calculated as the ratio of cross-sectional
area(m2) : wetted perimeter(m)
25. Max Depth (m) – Maximum depth along the cross-section
26. X-Sectional Area (m2) – Cross-sectional area of channel perpendicular to flow
27. Ratio, Width:Depth – Ratio of width to mean depth
28. Width (m) – Distance from woody vegetation edge to woody vegetation edge
29. Hydraulic Radius (m) – Average depth, calculated as the ratio of cross-sectional
area(m2) : wetted perimeter(m)
30. Max Depth (m) – Maximum depth along the cross-section, from active channel
height
31. X-Sectional Area (m2) – Cross-sectional area of channel perpendicular to flow
32. Ratio, Width:Depth – Ratio of width to mean depth
33. Deepest point (m) – Depth of deepest point in the pool relative to baseflow water
surface
34. C.V. Depth – Coefficient of variation (standard deviation / mean) of 5 equally
spaced depth measurements across the length of the pool (front to back)
35. Pool Length (m) – Length of the pool from front to back with boundaries defined
by slope breaks and/or velocity increases.
36. Surface Area (m2) – Surface area of the pool at baseflow discharge, calculated as
the product of pool length and pool width, assuming a rectangular geometry
37. Pool Volume (m3) – Volume of the pool at baseflow discharge, calculated as the
product of pool length and pool x-sectional area, assuming the x-sectional area is
relatively constant throughout the length of the pool
38. Median Grain Size d50 (mm) – Median grain size of non-bedrock bed material
sampled using a modified Wolman pebble count
39. Max Grain Size (mm) – Maximum grain size of non-bedrock bed material
sampled using a modified Wolman pebble count
40. Bedrock (%) – Percentage of bedrock from Wolman pebble count
41. Megaboulder (%) – Percentage of megaboulder sized (>2000mm) bed material
from Wolman pebble count
42. Boulder (%) – Percentage of boulder sized (256-2000mm) bed material from
Wolman pebble count
43. Cobble (%) – Percentage of cobble sized (64-256mm) bed material from Wolman
pebble count
44. Gravel (%) – Percentage of gravel sized (2-64mm) bed material from Wolman
pebble count
45. Sand (%) – Percentage of sand sized (.063-2mm) bed material from Wolman
pebble count
46. Fines (%) – Percentage of silt/clay sized (.001-.063mm) bed material from
Wolman pebble count
Biology
47. Number of fishes - Total number of fish species found in pools and/or their
associated riffles at a site. All species were native except Poecilia sp. The
species found are (latin, English, Spanish names):
a. Agonostomus monticola, mountain mullet, dajao
b. Anguilla rostrata, American eel, anguila
c. Awaos tajasica, river goby, saga or ciaga
d. Eleotris pisonis, spinycheek sleeper, moron
e. Gobiomorus dormitor, bigmouth sleeper, guavina
f. Poecilia sp.(vivipara?), guppy, sardinita
g. Sicydium plumieri, sirajo goby, olivo or chupa piedras or setí or tri-tri
48. Number of decapods - Total number of decapod species found in pools and/or
their associated riffles at a site. All species were native. The species found are
(latin, English, Spanish names):
a. Atya innocous, shrimp, gata or guábara or chágara
b. Atya lanipes, sinous-faced shrimp, guábara
c. Atya scabra, serrei shrimp, jonga
d. Epilobocera sinuatifrons, river crab, buruquena
e. Macrobrachium acanthurus, ?, silgao
f. Macrobrachium carcinus, giant-hand shrimp, bocú
g. Macrobrachium crenulatum, pubescent-hand shrimp, camaron
h. Macrobrachium faustinum, pubescent-hand shrimp, camaron
i. Macrobrachium heterochirus, teeth-faced shrimp, leopardo
j. Xiphocaris elongata, glass or long-faced shrimp, salpiche or chiripi or
chillo
49 - 66. Presence (1) or absence (0) of listed taxa, combined for all traps and all pools
at each node
Bridge Scour
67. Reach Type – Classification of reach type into 6 Categories: Waterfall, Cascade,
Step-Pool, Plane-Bed, Riffle, Pool.
68. Road Crossing Type – Physical structure of road crossing: Bridge, Foot Bridge,
Culvert (Box/Circular). Number of culvert openings is indicated.
69. Soil Texture – Rating (1-12) of soil texture coherence.
70. Bank Slope – Rating (1-12) of bank slope/stability
71. Bank Vegetation – Rating (1-12) of bank vegetative cover
72. Bank Cutting – Rating (1-12) of amount of bank cutting
73. Mass Wasting – Rating (1-12) of evidence of mass wasting
74. Channel Bar Development – Rating (1-12) of degree of channel bar development
75. Debris Jam Potential – Rating (1-12) of potential for debris jam
76. Obstructions – Rating (1-12) of amount and size of flow obstructions
77. Bed Material – Rating (1-12) of size and mobility of bed material
78. High Flow Angle – Rating (1-12) of high flow angle of approach to bridge
79. Blowhole/Scour Presence – Rating (1-12) of observed scour by presence of a
blowhole and/or scour pool
80. Scour Score – Raw weighted scour score
81. Scour Rating – Rating (Excellent, Good, Fair, Poor) as a function of scour score
provided by Johnson et al. 1999
82. Relative Rating – Rating (Excellent, Good, Fair, Poor) as a function of scour
score amended to apply to study streams
83. Biological Connectivity Score – Rating (1-12) of the potential biological
connectivity at a site as a function of the vertical barrier created by the road crossing
Table 2: Indicator variables measured in scour survey, φ indicator variables which were added for this
study. (Env) is a variable controlled by broad environmental variables, and (R/C) is a variable controlled
by local road crossing structure characteristics.
Indicator
Variable
Bank Soil Texture
and Coherence
(Env)
Average Bank
Slope Angle
(Pfankuch 1978)
(Env)
Vegetative Bank
Protection
(Pfankuch 1978)
(Env and R/C)
Rating
Excellent (1-3)
Good (4-6)
Fair (7-9)
Poor (10-12)
Clay and silty clay;
cohesive
Clay loam to sandy
clay loam
Sandy clay to sandy loam
Loamy sand to sand;
noncohesive
< 20% average
30 to 40% average
30 to 50% average
>60% average
Dense understory
and overstory
Mostly dense
understory and
overstory some areas
with only understory
Mixture of Dense
understory and overstory,
with moderate patches only
understory or no vegetation
Little to no dense
understory and overstory,
large patches only
understory or no
vegetation
Bank Cutting
(Pfankuch 1978)
(Env and R/C)
Little or none
evident, eroded
banks are infrequent,
short and
predominately <
15cm high
Some intermittent
along channel out
curves and prominate
constrictions. Cuts
are mostly < 30cm
high
Significant and Frequent.
Cuts 30-60cm high, root
mat overhangs
Almost continuous cuts
some >60cm high.
Undercutting, sod-root
overhangs, side failures
Mass Wasting or
Bank Failure
(Pfankuch 1978)
(Env)
No or little evidence
of potential for
Evidence of
infrequent and/or
very small slumps.
Evidence of mass
wasting is mostly
revegeated
Evidence of frequent or
significant occurrences of
mass wasting, with
potential for increased
wasting during high water
flow
Frequent mass wasting
easily detectable due to
presence of bank failures,
undercuttings, and bank
slumping, often
unvegetated
Amount of Bar
Development
(Lagasse et al.
1995)
(Env and R/C)
None or bars are
mature and
vegetated, mostly
coarse gravel or
cobble and narrow
relative to channel
width
Debris and potential
for debris
accumulation is
minimal
Bars are present,
mostly unvegetated,
coarse gravel to
cobble
Bars are present, not
vegetated, evidence of
recent deposition, bar
width < 1/2 stream width
Large unvegetated bars,
bar width > 1/2 stream
width
Minimal debris
present. Debris jam
potential is only for
small jams
Noticeable accumulation
of all sized debris present.
Potential for a moderate
sized jam downstream
Moderate to large
accumulation of all size
debri. Debris jam
potential is high.
None
Some flow
obstruction causing
flow alteration, with
minimal impact on
sediment
Moderately frequent
obstructions, causing some
erosion of channel
Frequent obstructions
yielding unstable
hydraulics and continual
sediment movement within
channel
Vegetative and
Rock Debris Jam
Potential
(Pfankuch 1978)
(R/C)
Obstructions,
Presence of Flow
Deflection
(Pfankuch 1978)
(R/C)