Mississippi Valley Division Engineer Research and Development Center

Comparison of Benthic Fish 

Assemblages along 

Revetted and Natural Banks 

in the Lower Mississippi 

River: A 30-Year Perspective

MRG&P Report No. 29 • January 2020

Mississippi River Geomorphology and 

Potamology Program 

MRG&P Report No. 29 

January 2020 

Comparison of Benthic Fish Assemblages along 

Revetted and Natural Banks in the Lower 

Mississippi River: A 30-Year Perspective

K. Jack Killgore and Steven G. George

Environmental Laboratory

US Army Engineer Research and Development Center

3909 Halls Ferry Road

Vicksburg, MS 39180-6199

Final report 

Approved for public release; distribution is unlimited. 

Prepared for US Army Corps of Engineers

Mississippi Valley Division

Vicksburg, MS 39180

Under WAT 2019-3478
MRG&P Report No. 29 ii

Abstract

Benthic fish assemblages were compared in 2016-2017 among three 

different bank types in the Lower Mississippi River (LMR) using hoopnets: 

Articulated Concrete Mattress (ACM) along main channel banks, natural 

banks along main channel, and natural banks in a secondary channel. 

Species richness was highest in secondary channels (21 species), followed 

by ACM (20 species), and natural banks (16 species). However, abundance 

of dominant species (i.e., Flathead Catfish, Blue Catfish, Freshwater Drum, 

and Buffalo) differed seasonally. Blue Catfish were more abundant along 

natural banks and secondary channels during the summer. Flathead 

Catfish abundance peaked during the summer in the secondary channels 

but were also abundant along ACM year-round. Freshwater Drum 

abundance was highest along natural banks in the winter and ACM in the 

spring. Juvenile Buffalo utilized secondary channels in the winter 

indicating the importance of these habitats for over-wintering fishes. 

Comparison of the native benthic fish assemblage between 1985 and 

2016-17 revealed minimal differences in species composition and 

abundance indicating long-term stability and resilience of LMR fishes. An 

exception was the prevalence of Asian Carp (Silver and Bighead), which 

were two to three times higher than any native species. 
MRG&P Report No. 29 iii

Contents

Abstract .......................................................................................................................................................... ii

Figures and Tables........................................................................................................................................iv

Preface.............................................................................................................................................................v

1 Introduction............................................................................................................................................1

Background .............................................................................................................................. 1

Objectives ................................................................................................................................. 3

Approach................................................................................................................................... 3

2 Methods..................................................................................................................................................4

3 Data Analyses........................................................................................................................................6

4 Results ....................................................................................................................................................8

Physical habitat ........................................................................................................................ 8

Fish community – Bank relationships...................................................................................10

Decadal comparison ..............................................................................................................18

5 Summary and Recommendations ...................................................................................................20

References ...................................................................................................................................................23

Unit Conversion Factors ............................................................................................................................25

Report Documentation Page
MRG&P Report No. 29 iv

Figures and Tables

Figures

Figure 1. Mat Sinking Unit operating on the Mississippi River; inset of ACM grooves..........................2

Figure 2. Sampling locations on the Mississippi River..............................................................................4

Figure 3. Hydrograph during the 2016-17 sampling period. Red dots indicate sampling 

events (source: Rivergages.com). ................................................................................................................9

Figure 4. Comparison of mean CPUE (overnight sets of hoopnets) of fish in the LMR 

between 1985 (n=10 each habitat) and 2016-2017 (n=15 for ACM and n=14 for Natural 

Banks)............................................................................................................................................................19

Tables

Table 1. Summary of water quality variables measured in the Island 82 reach, LMR, from 

December 2016 to November 2017. ..........................................................................................................8

Table 2. Summary of physical habitat variables measured at each hoopnet in the Island 

82 reach, LMR, from December 2016 to November 2017......................................................................9

Table 3. Number of individuals collected during the 2016-17 study by hoopnet size and 

habitat. Species are arranged in phylogenetic order...............................................................................11

Table 4. Pairwise PERMANOVA by habitat type of the 4th root transformed resemblance 

matrix (Bray-Curtis Similarity) of all fish species collected by 3 and 4 ft hoopnets in the 

LMR................................................................................................................................................................13

Table 5. Mean CPUE ± 1 standard deviation of fish species collected by 3 ft hoopnets in 

the LMR during 2016 and 2017. Values with letters in the column are significantly 

(p<0.05) different among seasons within a habitat based on a mixed model ANOVA......................14

Table 6. Mean CPUE ± 1 standard deviation of fish species collected by 4 ft hoopnets in 

the LMR during 2016 and 2017. Values with letters in the column are significantly 

(p<0.05) different among seasons within a habitat based on a mixed model ANOVA......................15

Table 7. Mean CPUE ± 1 standard deviation of Asian Carp collected by 4 ft hoopnets in

the LMR during 2016 and 2017. Values with letters in the column are significantly 

(p<0.05) different among seasons within a habitat based on a mixed model ANOVA......................16

Table 8. Mean length (millimeter) of fish species collected in the LMR, 2016-2107. All 

values are total length except Shovelnose Sturgeon (fork length) and Paddlefish (eye-tofork length). ...................................................................................................................................................17
MRG&P Report No. 29 v 

Preface

The research documented in this report was conducted as part of the 

Mississippi River Geomorphology and Potamology (MRG&P) Program, 

under WAT 2019-3478. The MRG&P Program is part of the Mississippi 

River and Tributaries Project and is managed by the U.S. Army Corps of 

Engineers (USACE), Mississippi Valley Division (MVD), and districts. At 

the time of publication of this report, the MRG&P Program Director was 

Dr. James W. Lewis. The MVD Commander was MG R. Mark Toy. The 

MVD Director of Programs was Mr. James A. Bodron.

The work was performed by the Aquatic Ecology and Invasive Species 

Branch of the Ecosystem Evaluation and Engineering Division, U.S. 

Army Engineer Research and Development Center, Environmental 

Laboratory (ERDC-EL). At the time of publication of this report, 

Mr. Alan Katzenmeyer was Branch Chief; Mr. Mark Farr was Division 

Chief; and Dr. Al Confrancesco was the Technical Director for ERDC-EL. 

The Deputy Director of ERDC-EL was Dr. Jack Davis, and the Director 

was Dr. Ilker Adiguzel.

Mr. Bill Lancaster (JAYA and ERDC-EL) assisted in hoopnet collections. 

Ms. Amanda Oliver (GSI and ERDC-EL) produced the map. This technical 

report was reviewed by Dr. Jan Jeffrey Hoover and Dr. Catherine Murphy, 

ERDC-EL, and Dr. James Lewis, MVD. 

The Commander of ERDC was COL Teresa A. Schlosser, and the Director 

was Dr. David W. Pittman.
MRG&P Report No. 29 1 

1 Introduction

Background 

The Lower Mississippi River (LMR) meanders within the confines of the 

mainline levee system for almost 1,000 miles to the Gulf of Mexico 

creating two major types of riverbank habitat. The concave side of the 

meander loop typically has high velocities forming steep (30 degrees to 

almost vertical), erosional banks consisting of consolidated clays and silts 

(Baker et al. 1988). The convex side is depositional due to lower water 

velocities forming large, primarily sand pointbars. The river straightens 

between meander loops as the thalweg crosses the channel with both types 

of bank habitats present along its course. 

The erosional nature of concave banks leads to channel instability that 

could impact minimum commercial navigation depth and undermine 

nearby levees. Therefore, the Mississippi River and Tributaries (MR&T) 

Project authorized the construction of almost 1,000 miles of revetment to 

stabilize river banks (Benjamin et al. 2016). Banklines are cleared of trees 

and woody debris, graded to a lower slope (<30 degrees), riprap is placed 

near the top bank, and Articulated Concrete Mattress (ACM) is laid from 

the top bank to the edge of the channel up to water depths of 120 feet (ft) 

(Baker et al. 1988). Articulated Concrete Mattress is formed by linking 

concrete blocks with corrosion resistant wires into units and deployed 

from a vessel known as the Mat Sinking Unit, a vessel uniquely designed 

for this purpose (Figure 1 – Mat Sinking Unit). Each block is 4 ft long, 18 

inches (in.) wide, and 3 in. thick and each linked unit is 25 ft long by 4 ft 

wide (Pokrefke 2012). Horizontal grooves are formed in each concrete 

block to increase the surface area for macroinvertebrate attachment 

(Baker et al. 1988). 
MRG&P Report No. 29 2 

Figure 1. Mat Sinking Unit operating on the Mississippi River; inset of ACM grooves. 

The conversion of natural steep banks to ACM has ecological 

consequences. The aquatic invertebrate fauna shifted from burrowing 

mayflies (i.e., Pentagenia vittiqera and Tortopus incertus) to net-spinning 

caddisflies (primarily Hydropsyche orris) (Baker et al. 1988). The effect 

on fish foraging is unknown. In addition, the loss of trees and woody 

debris from bank clearing and stabilization, as well as snag removal 

operations in the early to mid-1900s, reduced instream habitat complexity 

and substrates for macroinvertebrate colonization. The benefits of woody 

debris on habitat quality and aquatic biodiversity are well established in 

the literature (Wondzell and Bisson 2003). 

ACM does provide a supplemental hard substrate sometimes used by 

gravel-spawning riverine fishes. Pallid Sturgeon were documented with 

sonic telemetry spawning over revetted banks in the Missouri River 

(DeLonay et al. 2016). ACM tends to buckle over time, creating 

depositional areas that increase substrate heterogeneity in high-velocity 

habitats, and forms crevices used as velocity refugia by rheophilic fishes 

and macroinvertebrates. Periphyton has been observed covering ACM in 

shallow, lower-velocity habitats, which based on previous studies, is 

grazed upon by small invertebrates, fishes, and other aquatic animals and 

contributes considerably to the productivity of aquatic ecosystems, natural 

or human-made (Azim 2009).
MRG&P Report No. 29 3 

Objectives 

Physical, chemical, and biological surveys were made along three revetted 

and two natural banks in the LMR during the summer and fall of 1985 

(Baker et al. 1988). This was the first ecological study of riverbanks along 

the LMR. The present study was initiated to compare benthic fish 

assemblages among riverbank habitats over a 30-year time period (1985 

and 2016-17). The same collecting gear (i.e., 3 ft diameter hoopnet) was 

used in both studies. The 2016-17 study also included 4 ft diameter 

hoopnets to target larger benthic fish and evaluate the relative abundance 

of Asian Carp (Hypophthalmichthys sp.) in the collections. In addition, 

the 2016-17 study sampled secondary channel river banks because of their 

importance to the LMR Conservation Plan (Killgore et al. 2014) and 

Biological Opinion (USFWS 2013) as key habitats for the three endangered 

species in the LMR: Pallid Sturgeon, Fat Pocketbook Mussel, and Interior 

Least Tern. 

Approach 

The approach is presented in Chapter 2 Methods.
MRG&P Report No. 29 4 

2 Methods

Sampling with hoopnets occurred along the Island 82 reach in the LMR 

from River Mile 542 to 547 (Figure 2). The ACM and natural bank sites 

were positioned along the concave side of the main channel. The lower 

reach of Island 82 chute was sampled as the secondary channel site. The 

three sites were sampled two to three times seasonally from December 

2016 to November 2017. 

Figure 2. Sampling locations on the Mississippi River. 
MRG&P Report No. 29 5 

Hoopnets were constructed of fiberglass hoops and tarred nylon netting 

using 5/16 in. braided polypropylene. Two sizes of hoopnets were used 

targeting a wide range of benthic species: 3 ft diameter opening, seven 

hoops, 10 ft long, 1 in. square mesh; 4 ft diameter opening, seven hoops, 13 

ft long, 3 in. mesh. The former was used by Baker et al. (1988) in the 

original hoopnet study of LMR bank habitats. The latter are typically used 

by commercial fisherman in the LMR. All hoopnets were placed close to 

the bank to minimize confounding influences of water depth, water 

velocity, and distance from shore. Unbaited nets were deployed during the 

afternoons and retrieved the following morning, with an average (±1 

standard deviation) soak time of 20 ± 0.9 hours. Fish were identified in 

the field, total length measured, and released. 

Physical habitat measurements were taken at each hoopnet to characterize 

the fluvial environment associated with benthic fish assemblages. Depth 

was recorded with a transom-mounted depth finder; surface water velocity 

was recorded with a Marsh-McBirney Flo-Mate, Model 2000; distance 

from shore was measured with Bushnell® laser rangefinder (Pro1600), 

and each hoopnet was georeferenced using a hand-held Garmin GPSMAP 

64st (datum WGS 84). Water quality parameters were measured on the 

surface with a YSI Pro DSS once per trip near the center of each site and 

included dissolved oxygen (milligrams per liter), pH, conductivity 

(microsiemens per centimeter), water temperature (C°) and turbidity 

(Nephelometric Turbidity Unit). 
MRG&P Report No. 29 6 

3 Data Analyses

Relative abundance (catch per unit effort [CPUE]) was compared among 

the three riverbank types, and the 3 ft hoopnet collections in 1985 were 

compared with those from 2016-17. CPUE is defined as number of 

individuals per species or species guild caught per hoopnet night. 

Different-size hoopnets were analyzed separately because size of fish 

entering the net and retention were dependent on mesh size and hoop 

diameter. Abundance data were 4th-root transformed to down-weight 

highly abundant taxa while still taking into account rare species, and a 

dummy variable (n=1) was added to each sample to mathematically adjust 

for sparsity within the data table (Goodsell and Connell 2002). A 

resemblance matrix of transformed species abundances was created by 

computing Bray-Curtis similarity indices for each assemblage comparison 

(Clarke and Gorley 2015). Differences in community composition among 

sites were tested on the resemblance matrix using a one-factor (fixed effect 

= habitat type) permutational multivariate analysis of variance 

(PERMANOVA) performed using PRIMER software, version 7 (PRIMERe, QUEST Research Ltd.). This test estimates, through permutation, a 

Pseudo-F statistic analogous to the univariate F-statistic and an associated 

p value (Clarke et al. 2014). The test statistic of PERMANOVA indicates 

the significance value among the three different habitats. Similarity 

percentages were calculated (SIMPER, 80% cutoff for low contributions) 

on CPUE values to determine which species contributed to the similarity 

pattern depicted among groups (i.e., typifying species), as well as those 

species that contribute to the dissimilarity between groups (i.e., 

discriminating species). 

Differences in the abundance of individual species or taxonomic groups 

among habitats and seasons were analyzed using a mixed model analysis 

of variance (ANOVA) to account for repeated measures covariance 

structure because fixed stations were sampled over four seasons. Repeated 

sampling of the same sites violates the assumption of independence 

among observations. For this application, a mixed design partitioned the 

variation due to fixed sampling stations and the temporal autocorrelation 

that may occur among repeated measurements (Maceina et al. 1994). 

Sample size was partitioned by four seasons and nine sampling dates with 

five nets usually set in each habitat. In some instances, nets were lost or 

hung on debris. Mixed model calculated least squares means for nets per 
MRG&P Report No. 29 7 

date, then averaged the value by seasons to account for unbalanced data. 

Least squares means in the mixed model were compared among habitat, 

seasons, and the interaction between the two. Least squares means were 

used to account for skewness due to zero-inflated data. Prior to ANOVA, 

CPUE was log transformed (Log[x+1]) to stabilize variance and meet 

parametric assumptions. 
MRG&P Report No. 29 8 

4 Results

Physical habitat 

Sampling occurred on eight separate dates from December 2016 to 

November 2017 for the ACM and Natural Bank sites whereas the 

Secondary Channel site was sampled six times from February 2017 to 

November 2017. Water quality variables were comparable among sites 

(Table 1). Water temperature ranged from 5.5 to 30.8 °C across all four 

seasons. Dissolved oxygen measurements were always above 6 milligrams 

per liter (mg/L) and averaged near 9.0 mg/L. Mean turbidity was slightly 

higher in the Secondary Channel site, possibly due to an increase in 

primary productivity, with maximum values for all sites near 100 NTUs 

during high river stages. Winter and spring samples were taken during a 

mostly rising hydrograph while summer and autumn samples were taken 

on a mostly falling hydrograph (Figure 3). 

Table 1. Summary of water quality variables measured in the Island 82 reach, LMR, from 

December 2016 to November 2017. 

 

Habitat N 

Water 

Temperature 

°C 

Dissolved 

Oxygen 

mg/L 

Conductivity 

μS/cm pH 

Turbidity 

NTU 

ACM 8

Mean 15.5 9.7 443.3 7.7 39

Std Dev 8.7 2.1 43.7 0.5 25.6

Minimum 5.5 6.1 373 6.9 17.4

Maximum 30.5 12.7 512 8.6 107

Natural Bank 8

Mean 15.5 9.8 442.7 7.7 38.7

Std Dev 8.9 2.2 44.8 0.5 26.2

Minimum 5.5 6.1 373 6.9 14.2

Maximum 30.5 12.7 512 8.6 107

Secondary Channel 6

Mean 18.2 8.7 427.3 7.4 49.3

Std Dev 7.8 1.9 38.2 0.2 24.5

Minimum 8.1 6.1 369 6.9 14.2

Maximum 30.8 12.3 490 8.6 98.8
MRG&P Report No. 29 9 

Figure 3. Hydrograph during the 2016-17 sampling period. Red dots indicate sampling 

events (source: Rivergages.com). 

A total of 309 hoopnets were deployed and retrieved during the study 

comprised of 155 3 ft hoopnets and 154 4 ft hoopnets. The mean values of 

the five physical variables characterizing hoopnet habitat locations were 

comparable among sites (Table 2). Shoreline and submerged bank slope 

were slightly higher at the Natural Bank site; depth of net-sets averaged 

approximately 3.0 meters (m); distance to shore was approximately 4.0 m 

on average, and mean surface water velocity ranged from a low of 47 

centimeters per second (cm/s) at the Secondary Channel site to 69 cm/s at 

the ACM site. Maximum surface velocity recorded was 116 cm/s along ACM.

Table 2. Summary of physical habitat variables measured at each hoopnet in the Island 82 

reach, LMR, from December 2016 to November 2017. 

Habitat N 

Shoreline 

Slope 

Degrees 

Bottom 

Slope 

Degrees 

Depth 

Meters 

Distance 

to Shore 

Meters 

Velocity 

cm/sec 

ACM 100

Mean 44.5 37.8 2.7 3.6 69.2

Std Dev 11.4 10.9 1.2 2.4 22

Minimum 15 15 1.0 0.6 14

Maximum 75 75 7.8 15.5 116

Natural Bank 97

Mean 54.4 39 2.9 4.7 57.3

Std Dev 20.4 15.4 1.4 3.2 21

Minimum 15 5 1.0 0.9 2

Maximum 90 75 8.8 18.9 111
MRG&P Report No. 29 10

Habitat N 

Shoreline 

Slope 

Degrees 

Bottom 

Slope 

Degrees 

Depth 

Meters 

Distance 

to Shore 

Meters 

Velocity 

cm/sec 

Secondary Channel 112

Mean 44.7 38.1 3.7 4.2 48.6

Std Dev 27 16.2 1.9 3.8 25

Minimum 0 0 0.9 0.9 3

Maximum 93 60 8.9 22.3 114

Fish community – Bank relationships 

A total of 26 fish species was collected during the study with 3 and 4 ft 

hoopnets (Table 3). Only 18 species were collected in 4 ft hoopnets 

whereas 24 species were collected in 3 ft hoopnets. Paddlefish and Bighead 

Carp were not collected in 3 ft hoopnets; these large-bodied species likely 

avoided the smaller diameter and mesh of 3 ft hoopnets. The eight species 

not collected in 4 ft hoopnets were American Eel, Shortnose Gar, 

Longnose Gar, Goldeye, Mooneye, Longear Sunfish, White Crappie, and 

Sauger; larger mesh size probably allowed these smaller-bodied or tereteshaped species to escape.

Fish community structure differed significantly (Pseudo-F=1.852, 

p=0.045, 999 permutations) among the three habitat types using 3 ft 

hoopnets (Table 4). Pair-wise tests indicated that community structure 

was significantly different between the secondary channel and ACM 

(t=1.6907, p=0.013). Dissimilarity between these two habitats was due to 

greater number of species collected in the secondary channel but not 

found along ACM including Grass Carp, Longear Sunfish, Mooneye, 

Shovelnose Sturgeon, and Silver Carp (Table 3). Average faunal similarity 

percentages among the three habitats ranged 14.1% – 20.1%, indicating 

differences in overall species composition. However, the typifying or more 

common species collected in all three habitats comprising at least 50% of 

the abundance were Flathead Catfish, Blue Catfish, and Freshwater Drum. 
MRG&P Report No. 29 11

Table 3. Number of individuals collected during the 2016-17 study by hoopnet size and habitat. Species are arranged in phylogenetic order. 

 

Fish Taxon 

HN3 HN4 

 

ACM

Natural 

Bank

Secondary 

Channel ACM

Natural 

Bank

Secondary 

Channel Total

Scaphirhynchus platorynchus, Shovelnose Sturgeon 1 1 2

Polyodon spathula, Paddlefish 1 1

Lepisosteus osseus, Longnose Gar 2 3 2 7

Lepisosteus platostomus, Shortnose Gar 2 2 4

Hiodon alosoides, Goldeye 5 2 7

Hiodon tergisus, Mooneye 1 1

Anguilla rostrata, American Eel 1 1 2 4

Dorosoma cepedianum, Gizzard Shad 9 2 4 2 1 18

Ctenopharyngodon idella, Grass Carp 2 2 2 6

Cyprinus carpio, Common Carp 2 1 4 7

Hypophthalmichthys molitrix, Silver Carp 1 37 38 62 138

Hypophthalmicthys nobilis, Bighead Carp 2 3 9 14

Carpiodes carpio, River Carpsucker 1 2 11 3 5 22

Carpiodes velifer, Highfin Carpsucker 1 5 3 9

Cycleptus elongates, Blue Sucker 1 1 2 1 1 6

Ictiobus bubalus, Smallmouth Buffalo 4 2 10 19 17 34 86

Ictiobus cyprinellus, Bigmouth Buffalo 1 3 7 8 6 25
MRG&P Report No. 29 12

 

Fish Taxon 

HN3 HN4 

 

ACM

Natural 

Bank

Secondary 

Channel ACM

Natural 

Bank

Secondary 

Channel Total

Ictiobus niger, Black Buffalo 1 1 4 2 3 11

Ictalurus furcatus, Blue Catfish 4 14 14 1 6 2 41

Ictalurus punctatus, Channel Catfish 7 4 2 1 3 17

Pylodictis olivaris, Flathead Catfish 18 14 32 10 5 1 80

Morone chrysops, White Bass 4 1 3 5 8 21

Lepomis megalotis, Longear sunfish 1 1

Pomoxis annularis, White Crappie 1 1 2

Sander canadensis, Sauger 1 1

Aplodinotus grunniens, Freshwater Drum 9 8 14 14 4 10 59

Total Number 73 48 97 127 93 152 590
MRG&P Report No. 29 13

No significant differences in fish community structure among habitats 

were detected using 4 ft hoopnets (Pseudo-F=1.3416, p=0.176, 999 

permutations, Table 4). Average faunal similarity among the three habitats 

ranged 17.3% – 21.3%. Silver Carp were most abundant in 4 ft hoopnets, 

followed by buffalo (Smallmouth, Bigmouth, and Black) and Freshwater 

Drum. Abundance of other species was comparable among habitats. The 

primary difference between 3 and 4 ft hoopnet collections was lower 

species richness and the presence and high abundance (approximately 

20% of the total individuals) of Silver Carp in the larger hoopnets. 

Table 4. Pairwise PERMANOVA by habitat type of the 4th root transformed resemblance 

matrix (Bray-Curtis Similarity) of all fish species collected by 3 and 4 ft hoopnets in the LMR. 

3 ft Hoopnets 

Bank Habitats (Groups) T P (perm) Unique Permutations

Secondary Channel, ACM 1.6907 0.013 999

Secondary Channel, Natural Bank 1.0443 0.369 999

ACM, Natural Bank 1.2252 0.192 999

4 ft Hoopnets 

Secondary Channel, ACM 1.1972 0.231 999

Secondary Channel, Natural Bank 1.2528 0.156 998

ACM, Natural Bank 1.3266 0.147 998

Back-calculated least square means provided the model-adjusted median 

value, which is a more appropriate measure of central tendency for skewed 

data. However, zero-inflated data resulted in a median approximating zero 

in all cases, so mean CPUE was reported in the tables (Tables 5 and 6). 

Statistical significant difference (P<0.05) in CPUE among seasons and 

habitats was denoted in the tables based on results of the mixed model.

Blue catfish abundance in 3 ft hoopnets was significantly higher during the 

summer whereas there were no significant differences among habitats or 

the interaction between habitat and seasons. No significant differences 

were detected using 4 ft hoopnets. Flathead catfish abundance was 

significantly higher in the summer at ACM and secondary channel sites in 

3 ft hoopnets, and only during summer on ACM in 4 ft hoopnets. 

Smallmouth Buffalo abundance was significantly higher in secondary 

channels during the winter in 3 ft hoopnets. No significant difference 

among habitats and seasons occurred for Buffalo in 4 ft hoopnets 
MRG&P Report No. 29 14

indicating their ubiquitous distribution in the LMR. There were no 

significant differences among seasons and habitats for Freshwater Drum 

in 3 ft hoopnets. However, Freshwater Drum were significantly more 

abundant in 4 ft hoopnets in the spring at all three habitat types, and 

maximum abundance occurred along ACM. 

Table 5. Mean CPUE ± 1 standard deviation of fish species collected by 3 ft hoopnets in the LMR 

during 2016 and 2017. Values with letters in the column are significantly (p<0.05) different 

among seasons within a habitat based on a mixed model ANOVA. 

Habitat Season N Blue Catfish 

Flathead 

Catfish 

Smallmouth 

Buffalo 

Freshwater 

Drum 

ACM Fall 12 0 0 0.07 ± 0.26 0

Spring 10 0 0.40 ± 0.70 0.10 ± 0.32 0.40 ± 0.70

Summer 15 0.20 ± 0.41 0.93 ± 1.53x 0.20 ± 0.56 0.33 ± 0.49

Winter 10 0.10 ± 0.32 0 0.10 ± 0.32 0

Natural

Bank Fall 12 0.21 ± 0.58 0.07 ± 0.27 0.07 ± 0.27 0.21 ± 0.43

Spring 10 0.10 ± 0.32 0 0 0

Summer 14 0.40 ± 0.74 0.80 ± 1.61x 0 0.07 ± 0.26

Winter 10 0.20 ± 0.42 0.10 ± 0.32 0.10 ± 0.32 0.40 ± 0.52

Secondary

Channel Fall 12 0.25 ± 0.45 0.25 ± 0.62 0.08 ± 0.29 0.08 ± 0.29

Spring 20 0 0.30 ± 0.57 0 0.05 ± 0.22

Summer 20 0.45 ± 0.60 1.15 ± 1.35x 0 0.40 ± 0.68

Winter 10 0.20 ± 0.42 0 0.90 ± 1.37x 0.40 ± 1.26

 
MRG&P Report No. 29 15

Table 6. Mean CPUE ± 1 standard deviation of fish species collected by 4 ft hoopnets in the LMR 

during 2016 and 2017. Values with letters in the column are significantly (p<0.05) different 

among seasons within a habitat based on a mixed model ANOVA. 

Habitat Season N Blue Catfish Flathead Catfish Buffalo Freshwater Drum 

ACM Fall 11 0 0.13 ± 0.35 0.47 ± 0.52 0.20 ± 0.41

Spring 10 0 0.10 ± 0.32 0.60 ± 0.52 0.70 ± 0.82x

Summer 15 0.07 ± 0.26 0.46 ± 0.52x 0.53 ± 0.74 0.20 ± 0.41

Winter 10 0 0.00 0.90 ± 0.57 0.10 ± 0.32

Natural 

Bank Fall 12 0 0.08 ± 0.28 0.38 ± 0.65 0

Spring 10 0.20 ± 0.42 0.20 ± 0.63 0.80 ± 1.14 0.30 ± 0.67x

Summer 15 0.13 ± 0.52 0.13 ± 0.35 0.47 ± 0.92 0.07 ± 0.26

Winter 10 0 0 0.70 ± 0.95 0

Secondary 

Channel Fall 11 0.09 ± 0.3 0.09 ± 0.30 0.82 ± 0.98 0.18 ± 0.40

Spring 20 0.05 ± 0.22 0 1.00 ± 1.03 0.30 ± 0.57x

Summer 20 0 0 0.45 ± 0.69 0.10 ± 0.31

Winter 10 0 0 0.50 ± 0.71 0

Bighead Carp were collected only in 4 ft hoopnets, and except for one 

individual, all Silver Carp were collected in 4 ft hoopnets. Bighead Carp 

abundance was significantly higher in the summer, but no differences 

occurred among habitats (Table 7). Bighead Carp were not collected 

during winter and spring. The highest CPUE for any species occurred for 

Silver Carp during the spring along ACM. However, abundances among 

habitats were not significantly higher, but were significantly higher in 

summer and spring. Silver Carp were mostly absent during the fall and 

completely absent during the winter. 
MRG&P Report No. 29 16

Table 7. Mean CPUE ± 1 standard deviation of Asian Carp collected by 4 ft hoopnets in 

the LMR during 2016 and 2017. Values with letters in the column are significantly 

(p<0.05) different among seasons within a habitat based on a mixed model ANOVA. 

Habitat Season N Bighead Carp Silver Carp 

ACM Fall 15 0 0

Spring 10 0 2.10 ± 1.91x

Summer 15 0.13 ± 0.35 1.07 ± 1.44y

Winter 10 0 0

Natural Bank Fall 13 0 0.23 ± 0.44

Spring 10 0 0.8 ± 1.32

Summer 15 0.20 ± 0.56 1.53± 2.53x

Winter 10 0 0

Secondary Channel Fall 11 0 0

Spring 20 0.05 ± 0.22 1.15 ± 2.16x

Summer 20 0.40 ± 0.88 1.85 ± 2.68y

Winter 10 0 0

Mean lengths for each species were highest in 4 ft hoopnets given the 

larger hoop and mesh size (Table 8). Several notable observations were 

derived from the length table. Smaller (475 millimeter [mm]) bigmouth 

buffalo were collected in the secondary channel, and juvenile Blue Catfish, 

Freshwater Drum, and River Carpsucker were common along natural 

banks and occasionally ACM. The largest individuals of seven species were 

collected in the secondary channel including Bighead Carp (1060 mm), 

Buffalo (732-952 mm, depending on species), Blue Sucker (766 mm), and 

White Bass (491 mm). The largest Flathead Catfish (1095 mm) was 

collected along ACM during the summer. 
MRG&P Report No. 29 17

Table 8. Mean length (millimeter) of fish species collected in the LMR, 2016-2107. All values 

are total length except Shovelnose Sturgeon (fork length) and Paddlefish (eye-to-fork length). 

Species 

HN3 HN4 

N ACM 

Natural 

Bank 

Secondary 

Channel N ACM 

Natural 

Bank 

Secondary 

Channel 

American eel 4 671 593 621

Bighead carp 14 907 905 947

Bigmouth buffalo 4 519 475 21 539 567 616

Black buffalo 2 583 640 9 735 661 792

Blue catfish 29 197 264 329 6 627 427 424

Blue sucker 2 241 710 4 658 630 766

Channel catfish 11 501 393 6 601 716 107

Common Carp 2 586 5 794 617

Flathead catfish 64 566 570 528 16 826 697 742

Freshwater drum 31 379 263 443 28 486 499 499

Gizzard shad 11 202 330 7 421 419 170

Goldeye 4 211 208

Grass carp 2 944 4 958 889

Highfin carpsucker 1 289 5 339

Longear sunfish 1 123

Longnose gar 7 729 775 1052

Mooneye 1 134

Paddlefish 1 885

River carpsucker 3 141 333 16 436 475 386

Sauger 1 243

Shortnose gar 4 600 613

Shovelnose sturgeon 1 490 1 813

Silver carp 1 791 128 802 801 815

Smallmouth buffalo 10 545 428 519 70 513 504 525

White bass 8 336 345 338 10 428 391 308

White crappie 2 310 200
MRG&P Report No. 29 18

Decadal comparison 

The benthic fish assemblage in terms of numerically dominant species was 

similar between the two decades based on 3 ft hoopnet catches in summer 

and fall (4 ft hoopnets were not used in 1985). In the 1985 study, Flathead 

Catfish were most abundant (36% of total individuals), followed by Blue 

Catfish (28%) and Freshwater Drum (22%). In the 2016-17 study, the 

order of abundance was the same with slight differences in percentages: 

Flathead Catfish (31%), Blue Catfish (22%), and Freshwater Drum (10%). 

Species richness was different with a total of 12 species collected in 

2016-17 compared to 7 species in 1985. Species that were collected in 

2016-17 but not in 1985 were Longnose Gar, Smallmouth Buffalo, Blue 

Sucker, River Carpsucker, Goldeye, and White Bass. Only the Freshwater 

Eel was collected in the summer-fall of 1985 and not in 2016-17, although 

this species was collected in other seasons during the present study. Some 

discrepancies may have been due to different sample sizes (n=40 in 1985 

versus n=59 in 2016-17). 

Considering the most abundant species, Blue Catfish CPUE along ACM in 

1985 was almost double that of other habitats and decades (Figure 4). 

Conversely, Flathead Catfish CPUE was twice as high along ACM in 2017. 

Freshwater Drum abundance tended to decrease between 1985 and 

2016-17 and was lowest on natural banks. Gizzard shad were either absent 

or in low abundance along natural banks in both decades but were 

commonly collected along ACM. 

Asian Carp were rarely caught in the 1980s. Pugh and Schramm (1998) 

sampled the LMR with 4 ft hoopnets in August-December 1994 and caught 

only one Bighead Carp and no Silver Carp. Considering the high catch rate 

of Silver Carp in the 2016-17 study, population expansion of these invasive 

species occurred over the past 20 years. 
MRG&P Report No. 29 19

Figure 4. Comparison of mean CPUE (overnight sets of hoopnets) of fish in the LMR between 

1985 (n=10 each habitat) and 2016-2017 (n=15 for ACM and n=14 for Natural Banks). 
MRG&P Report No. 29 20

5 Summary and Recommendations

Bank stabilization is required for flood risk management and maintenance 

of river channels for commercial navigation. Eroding banks may impact 

nearby levees, result in unwanted adjustments in channel alignment, and 

lead to greater accretion of sediments requiring dredging or addition of 

other river training structures (Pokrefke 2012). Large rivers, such as the 

LMR, pose greater challenges because of the magnitude and duration of 

high water that erodes banks and threatens the infrastructure of the 

MR&T, which is the largest flood risk management and navigation project 

in US Army Corps of Engineers. The advent of ACM to stabilize banks was 

a significant step forward in river management because of its feasibility, 

measured in terms of cost effectiveness and its sustainability to withstand 

major fluctuations in river stages with reduced maintenance for the life of 

the project. The success of ACM is exemplified by its widespread use in the 

LMR, in which it encompasses almost 1,000 miles of river bank (Benjamin 

et al. 2016). However, conversion of natural banks to hardened structures 

has impacts to the aquatic fauna inhabiting these types of habitats. 

Benthic fish represent an important group of obligate riverine species that 

utilize different substrates and banklines as they search for food and move 

throughout the river system. It is assumed that their bottom-oriented 

behaviors make them sensitive to changes in substrates or river bank 

characteristics. However, the hoopnet study in 1985 by Baker et al. (1988) 

revealed minimal differences between revetted and natural banks. The 

follow up study in 2016-17 using the same type of hoopnets (3 ft diameter) 

had similar results in terms of the dominant species collected but differed 

in seasonal habitat associations.

Flathead Catfish are apex predators in the LMR and demonstrated an 

affinity to ACM during summer 2017. Blue Catfish, also apex predators, 

were rarely captured along ACM in 2016-17 and were mostly associated 

with natural banks and secondary channels, particularly young-of-year life 

stages. Conversely, Blue Catfish were abundant on ACM in the 1985 study, 

indicative of the generalist behaviors of large, predatory catfishes. Larger 

catfishes were captured along ACM where Gizzard Shad, their primary 

food resource (Eggleton and Schramm 2004), were relatively abundant. 

Although water velocities are generally higher along ACM, large catfishes 

and apparently Gizzard Shad co-occur at these locations providing 

foraging habitat for a large component of the fish assemblage. 
MRG&P Report No. 29 21

Secondary channels were not sampled during the 1985 study. In the 

present study, secondary channels were highly utilized by Buffalo and 

Freshwater Drum during the winter, and juveniles of Blue Catfish and 

Buffalo were more common in secondary channels and to a lesser degree, 

natural banks. These results indicate the importance of secondary 

channels as over-wintering areas to avoid stronger currents along ACM 

and natural banks in the main channel and for rearing habitat for juvenile 

life stages in spring and summer. Overall, species richness was highest in 

secondary channels (21 species) based on both sizes of hoopnets, 

compared to ACM (20 species) and natural banks (16 species). 

Similarity in species richness among the three bank habitats suggests that 

benthic fishes are widespread in the LMR. Most species are bottomoriented habitat generalists found along a variety of bank types and, based 

on the comparison with the 1985 data, the assemblage exhibits both 

stability in the dominant taxa (Catfishes, Buffaloes, and Freshwater Drum) 

and long-term resilience in the overall community structure (Ross et al. 

1985). Despite the extensive coverage of ACM in the LMR, the availability 

of diverse bank habitats, prevalence of connected secondary channels, and 

the annual connection of the channel with the remaining floodplain 

continue to support a diverse fish assemblage and may offset adverse 

impacts of revetted banks. 

With these characteristics and the results obtained during this study, 

benthic fishes may not be an ideal group to differentiate preferences or 

impacts of riverbank alterations. Additional studies are warranted to 

continue evaluating other components of the river bank environment 

including aquatic macroinvertebrates with characteristically limited 

aquatic dispersal abilities compared to fishes, as well as better defined 

habitat affinities. Diet studies linking foraging habitat with fish utilization 

will also provide a more complete understanding of the potential impacts 

of armoring river banks on aquatic resources. 

The prevalence of Asian Carp in the collections was anticipated, along with 

their overwhelming abundance during certain time periods. Asian carp 

were not collected during the 1985 study using 3 ft hoopnets. Only one 

Silver Carp was collected in 3 ft hoopnets during the 2016-17 study 

whereas 14 Bighead Carp and 138 Silver Carp were collected with 4 ft 

hoopnets. Asian Carp were introduced into the LMR basin in 1973 for 

control of algal blooms in aquaculture ponds (Starling 1993). Therefore, it 
MRG&P Report No. 29 22

is doubtful that Asian Carp occurred in the LMR at any measurable 

abundance in the 1980s, but the use of only 3 ft hoopnets prevents a direct 

comparison. Not only were Asian Carp collected in all three habitats 

during the 2016-17 study, they were the most abundant fishes in spring 

and summer likely associated with spawning movements. Bighead and 

Silver Carp exhibit protracted, incremental spawning in flowing water 

generally between April to July (Deters et al. 2013) and apparently move 

along the bankline before and during spawning movements where they are 

readily caught with hoopnets. Their influence on native benthic fishes is 

unknown, but Asian Carp likely will compete for food and space, which 

could impact the stability and resilience of obligate riverine species native 

to the LMR. 
MRG&P Report No. 29 23

References

Azim M. E. 2009. “Photosynthetic Periphyton and Surfaces.” Encyclopedia of Inland 

Waters. Edited by G. E. Likens, 184-191. Boston, MA: Elsevier Publishers. 

Baker, John A., Richard L. Kasul, C. Rex Bingham, Richard E. Coleman, C. H. 

Pennington, and Linda A. Winfield. 1988. An Ecological Investigation of 

Revetted and Natural Bank Habitats in the Lower Mississippi River. Lower 

Mississippi Environmental Program, Report 9. Vicksburg, MS: USACE 

Mississippi Valley Division. 

Benjamin, G. L., Angeline. J. Rodgers, and K. Jack Killgore. 2016. “Mississippi River 

Ecosystem Restoration: The Past Forty-Plus Years.” Edited by Y. Chen, D. C. 

Chapman, J. R. Jackson, D. Chen, Z. Li, K. J. Killgore, Q. Phelps, and M. A. 

Eggleton. Fisheries Resources, Environment, and Conservation in the 

Mississippi and Yangtze (Changjiang) River Basins, American Fisheries Society, 

Symposium 84, Bethesda, MD. 

Clarke K. R., and R. N. Gorley. 2015. PRIMER v7: User Manual/Tutorial. 7th ed. 

PRIMER-E. Plymouth, UK. 

DeLonay, A. J., K. A. Chojnacki, R. B. Jacobson, J. L. Albers, P. J. Braaten, E. A. Bulliner, 

C. M. Elliott, S. O. Erwin, D. B. Fuller, J. D. Haas, H. L. A. Ladd, G. E. Mestl, D. 

M. Papoulias, and M. L. Wildhaber. 2016. Ecological Requirements for Pallid 

Sturgeon Reproduction and Recruitment in the Missouri River—A Synthesis of 

Science, 2005 to 2012. Scientific Investigations Report 2015-5145.

http://dx.doi.org/10.3133/sir20155145

Deters, J. E., D. C. Chapman, and B. McElroy. 2013. “Location and Timing of Asian Carp 

Spawning in the Lower Missouri River.” Environmental Biology of Fishes 96(5): 

617–629. 

Eggleton, M. A., and H. L. Schramm. 2004. “Feeding Ecology and Energetic 

Relationships with Habitat of Blue Catfish, Ictalurus furcatus, and Flathead 

Catfish, Pylodictis olivaris, in the Lower Mississippi River, U.S.A.”

Environmental Biology of Fishes 70: 107-121. 

Goodsell, P. J., and S. D. Connell. 2002. “Can Habitat Loss Be Treated Independently of 

Habitat Configuration? Implications for Rare and Common Taxa in Fragmented 

Landscapes.” Marine Ecology Progress Series 239: 37-44.

Killgore, K. J., P. Hartfield, T. Slack, R. Fischer, D. Biedenharn, B. Kleiss, J. Hoover, and 

A. Harrison. 2014. Conservation Plan for the Interior Least Tern, Pallid 

Sturgeon, and Fat Pocketbook Mussel in the Lower Mississippi River 

(Endangered Species Act, Section 7(a)(1)). MRG&P Report No. 4. Vicksburg, 

MS: US Army Engineer Research and Development Center. 

Maceina, M. J., P. W. Bettoli, and D. R. DeVries. 1994. “Use of a Split-Plot Analysis of 

Variance Design for Repeated-Measures Fishery Data.” Fisheries 19: 14-20. 
MRG&P Report No. 29 24

Pokrefke, T. J. 2012. Inland Navigation Channel Training Works. Prepared by the Task 

Committee on Inland Navigation of the Waterways Committee of the Coasts, 

Oceans, Ports, and Rivers Institute of the American Society of Civil Engineers. 

ASCE Manuals and Reports on Engineering Practice No. 124. Reston, VA: 

American Society of Civil Engineers. 

Pugh, L. L., and H. L. Schramm. 1998. “Comparison of Electrofishing and Hoopnetting in 

Lotic Habitats of the Lower Mississippi River.” North American Journal of 

Fisheries Management 18(3): 649-656. 

Ross, S. T., W. J. Matthews, and A. A. Echelle. 1985. “Persistence of Stream Fish 

Assemblages: Effects of Environmental Change.” The American Naturalist 126 

(1): 22-40. 

Starling, F. L. 1993. “Control of Eutrophication by Silver Carp (Hypophthalmichthys 

molitrix) in the Tropical Paranoa (Brasilia, Brazil): A Mesocosm Experiment.”

Hydrobiologia 257: 143-152. 

USFWS (U.S. Fish and Wildlife Service). 2013. Biological Opinion: Channel 

Improvement Program, Mississippi River and Tributaries Project, Lower 

Mississippi River. Prepared by Mississippi Field Office, USFWS. Jackson, MS: 

USFWS. 

Wondzell, S. M., and P. A. Bisson. 2003. “Influence of Wood on Aquatic Biodiversity.”

The Ecology and Management of Wood in World Rivers. Edited by S. Gregory, 

K. Boyer, and A. Gurnell, 249-263. American Fisheries Society Symposium 37, 

Bethesda, MD. 
MRG&P Report No. 29 25

Unit Conversion Factors

Multiply By To Obtain

acres 4,046.873 square meters

degrees Fahrenheit (F-32)/1.8 degrees Celsius

fathoms 1.8288 meters

feet 0.3048 meters

hectares 1.0 E+04 square meters

horsepower (550 foot-pounds force per 

second)

745.6999 watts

inches 0.0254 meters

miles (nautical) 1,852 meters

miles (U.S. statute) 1,609.347 meters

yards 0.9144 meters
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4. TITLE AND SUBTITLE

Comparison of Benthic Fish Assemblages along Revetted and Natural Banks in the Lower 

Mississippi River: A 30-Year Perspective

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K. Jack Killgore and Steven G. George

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Environmental Laboratory

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3909 Halls Ferry Road

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MRG&P Report No. 29

9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES)

US Army Corps of Engineers

Mississippi Valley Division

Vicksburg, MS 39180

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USACE MVD

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WAT 2019-3478

14. ABSTRACT

Benthic fish assemblages were compared in 2016-2017 among three different bank types in the Lower Mississippi River (LMR) using 

hoopnets: Articulated Concrete Mattress (ACM) along main channel banks, natural banks along main channel, and natural banks in a 

secondary channel. Species richness was highest in secondary channels (21 species), followed by ACM (20 species), and natural banks 

(16 species). However, abundance of dominant species (i.e., Flathead Catfish, Blue Catfish, Freshwater Drum, and Buffalo) differed 

seasonally. Blue Catfish were more abundant along natural banks and secondary channels during the summer. Flathead Catfish 

abundance peaked during the summer in the secondary channels but were also abundant along ACM year-round. Freshwater Drum 

abundance was highest along natural banks in the winter and ACM in the spring. Juvenile Buffalo utilized secondary channels in the 

winter indicating the importance of these habitats for over-wintering fishes. Comparison of the native benthic fish assemblage between 

1985 and 2016 17 revealed minimal differences in species composition and abundance indicating long-term stability and resilience of 

LMR fishes. An exception was the prevalence of Asian Carp (Silver and Bighead), which were two to three times higher than any native 

species. 

15. SUBJECT TERMS 

Benthos—Mississippi River, Embankments, Fish populations—Mississippi River, Flood control, River engineering, Stream ecology

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