The effect of in-stream gravel extraction in a pre-alpine gravel-bed river on hyporheic invertebrate...

PRIMARY RESEARCH PAPER

The effect of in-stream gravel extraction in a pre-alpinegravel-bed river on hyporheic invertebrate community

Natasa Mori • Tatjana Simcic • Simon Lukancic •

Anton Brancelj

Received: 2 August 2009 / Revised: 10 August 2010 / Accepted: 21 August 2010 / Published online: 4 March 2011

� Springer Science+Business Media B.V. 2011

Abstract We investigated the effect of in-stream

gravel extraction in a pre-alpine gravel-bed river on

hyporheic invertebrate community, together with

changes in the hyporheic geomorphology, physico-

chemistry and biofilm activity. Hyporheic inverte-

brates were collected, together with environmental

data, on seven sampling occasions from June 2004 to

May 2005, at two river reaches—at the site of in-

stream gravel extraction and at a site 2.5 km

upstream. The hyporheic samples were taken from

the river bed and from the gravel bars extending

laterally from the stream channel. The invertebrate

community was dominated by insect larvae (occa-

sional hyporheos), followed by meiofauna (perma-

nent hyporheos). Stygobionts were present at low

species richness and in low densities. Gravel extrac-

tion from the stream channel led to changes in the

patterns of water exchange between surface and

subsurface and changes in the sediment composition

at the site. Immediate reductions in density and

taxonomic richness of invertebrates were observed,

together with changes in their community composi-

tion. The hyporheic invertebrate community in the

river recovered relatively fast (in 2.5 months) by

means of density and taxonomic richness, while by

means of community composition invertebrates

needed 5–7 months to recover. The impact of fine

sediments (\0.1 mm) on biofilm activity measured

through ETS activity and hyporheic invertebrate

density and taxonomic richness was strongly con-

firmed in this study.

Keywords Disturbance � In-stream gravel

extraction � Pre-alpine river � Hyporheic zone �Invertebrates � Biofilm

Introduction

Rivers and streams continuously transport and

deposit sediments of a range of granulation through-

out their length. These sediments are often exten-

sively managed or exploited, especially the gravel

(2–64 mm) and sand (0.063–2 mm) fractions. The

extraction of sediments directly from river channels

is usually carried out for commercial reasons (min-

ing), or for maintenance or remediation (Jensen &

Mogensen, 2000).

The consequences of in-stream gravel extraction

include alteration of geomorphological and hydro-

logical characteristics of the river channel and

Electronic supplementary material The online version ofthis article (doi:10.1007/s10750-011-0648-x) containssupplementary material, which is available to authorized users.

Handling editor: Robert Bailey

N. Mori (&) � T. Simcic � S. Lukancic � A. Brancelj

Department of Freshwater and Terrestrial Ecosystems

Research, National Institute of Biology, Vecna pot 111,

1001 Ljubljana, Slovenia

e-mail: [email protected]

123

Hydrobiologia (2011) 667:15–30

DOI 10.1007/s10750-011-0648-x

http://dx.doi.org/10.1007/s10750-011-0648-x

impacts on aquatic organisms and biogeochemical

processes in the sediments (Jensen & Mogensen,

2000). The impacts are usually referred to under the

general term of ‘mechanical pollution’ (Rivier &

Seguier, 1985). Extraction involves changes in chan-

nel morphology, river-bed elevation (i.e. reduction),

substrate composition and stability, deposit of in-

stream roughness elements (large woody debris,

boulders, etc.), depth, turbidity, sediment transport,

flow velocity and temperature (Jensen & Mogensen,

2000). In-stream sediment mining can disrupt the

balance between sediment supply and transporting

capacity, resulting in channel incision and river-bed

degradation (Kondolf, 1997). Degradation and ero-

sion can extend both upstream and downstream of an

individual extraction operation (Rivier & Seguier,

1985).

The complex and dynamic physical impacts of

gravel extraction influence the chemical and biolog-

ical elements of a riverine ecosystem. Such changes

result in changes in biodiversity and community

composition of microorganisms and invertebrates, as

well as of fish, macrophytes and riparian vegetation.

The scarce ecological studies have shown that river

bed (RB) incision impedes biofilm development and

activity in the sediment (as a result of changes in

vertical distribution of bacteria and biofilm activi-

ties), decreases the efficiency of oxygen consumption

and dissolved organic carbon mobilization in sedi-

ment (Barlocher & Murdoch, 1989), and decreases

nitrate production (Claret et al., 1998). Suspended

sediments can clog up the natural interstices in

substratum, which are of vital importance to certain

species of invertebrates and fish (Rivier & Seguier,

1985). Removal or reduction of existing habitats

leads to depletion of suitable spawning habitats for

fish and decreases benthic invertebrate abundance

and taxonomic richness (Pearson & Jones, 1975;

Rivier & Seguier, 1985; Brown et al., 1998; Kelly

et al., 2005).

Alluvial sediments, which extend vertically and

laterally from the river channel are recognized as a

hyporheic zone (Orghidan, 1959) and are an impor-

tant area of active exchange of water and dissolved

material between river and groundwater. From the

ecological point of view, the hyporheic zone consti-

tutes an ecotone between surface and groundwater

environments and between terrestrial and subterra-

nean aquatic systems on the banks of the river (Gibert

et al., 1990; Vervier et al., 1992). The hyporheic zone

acts as a mechanical, biological and chemical filter

(Vervier et al., 1992). The sediment particles impede

the flow of silt and particulate organic matter,

dissolved minerals and metals are precipitated and

trapped here and the microbial biofilm coating the

sediments takes up or transforms organic compounds

(Hancock, 2002). The hyporheic zone thus contrib-

utes significantly to the metabolism of stream

ecosystems (Grimm & Fisher, 1984), and the biolog-

ical self-purification capacity of the stream is

increased by the contribution of an intact and active

hyporheic zone (Pusch, 1996). Moreover, the porous

sediments in banks adjacent to rivers can act as

buffers to rising water levels and reduce, delay, or

even prevent the occurrence of flooding (Brunke &

Gonser, 1997).

The hyporheic zone is also a habitat for many

surface and groundwater dwelling invertebrates

(Gibert et al., 1994), a site of spawning and egg

incubation for some salmonid species (Geist &

Dauble, 1998), a site of wintering and reproduction

for some benthic fish species (Cobitidae) (Shimizu,

2002; Kawanishi et al., 2010), as well as a nursery

site for some insect taxa, such as Leuctridae and

Heptageniidae (Malard et al., 2003). The hyporheic

sediment pores can act as a refuge for invertebrates

during periods of drought (Williams, 1977), and can

be used by early instars of benthic insects as a refuge

against strong currents (shear stress) and extreme

temperatures, offering stable substrates during bed

load movement (Schwoerbel, 1964; Ward, 1992).

Ecological studies on gravel extraction impacts are

scarce. However, since gravel-bed rivers are often

heavily exposed to in-stream gravel extraction, and

the hyporheic zone plays an important role in-stream

metabolism, it is important to obtain more detailed

information on the consequences of that kind of

activity. The main objectives of our study were to

determine how in-stream gravel extraction affects

the geomorphology and patterns of hydrological

exchange in the hyporheic zone, the hyporheic water

chemistry, and the biofilm activity and structural and

functional biodiversity of the hyporheic invertebrate

community. We hypothesised that (a) down-welling

will increase due to channel incision, followed by

decrease of hydraulic conductivity due to fine sedi-

ment loading, (b) biofilm activity will decrease

following gravel extraction, and (c) invertebrate

16 Hydrobiologia (2011) 667:15–30

123

taxonomic richness and density will decrease signif-

icantly and community composition will change

following gravel extraction.

Materials and methods

Study area

The study was carried out in a downstream section of

the fourth order gravel-bed river Baca in western

Slovenia (SE Europe) (Fig. 1). Its catchment area is

about 145 km2, with geology of predominantly

limestone and dolomite, and a river length of about

25 km. The Baca River is a run-off fed stream, with

torrential nature, where discharge is primarily a

function of rainfall. The mean monthly discharges

over a 13-year period (1991–2004) ranged from

3.15 m3 s-1 (July/August) to 11.34 m3 s-1 (October/

November). Peak discharge reached 243 m3 s-1 in

the same period. Due to the high precipitation rates in

the area, steep relief, and erosion-prone rock in the

catchment, the Baca River is aggrading, with high

production of sand (0.0625–2 mm) and gravel

(2–64 mm).

Sample collection

Two sampling sites, located 2.5 km apart, were

selected: an upstream reference (Site 1 in Fig. 1)

and an impacted site (Site 2 in Fig. 1). Sampling was

carried out seven times from June 2004 to May 2005

Fig. 1 Maps of the study area (above) and sampling stations at reference and impacted sites (below). RB river bed, GB gravel bars

Hydrobiologia (2011) 667:15–30 17

123

(Fig. 2). The first sampling was conducted on 11 June

2004 (pre-disturbance data). Gravel extraction activ-

ities started on 23 October 2004 and finished on 28

October 2004, by which time an area of 10 9 100 m

was excavated to a depth of 3 m. The extraction was

followed by flood event due to heavy rain lasting

from 30 October to 2 November (peak discharge

44 m3 s-1). Post-disturbance sampling was carried

out 8, 15, 23, 77, 139 and 208 days after.

Six stations were installed along the 50 m long

reach at each site. Since hyporheic community is

highly variable within the stream sediments and

depends on the hydrological patterns occurring there,

three hyporheic samples were taken from depths

30–60 cm in the RB and three from depths 60–90 cm

in the gravel bars (GB) in order to adequately

represent the sampling sites (Downes et al., 2002).

Samples from RB and GB constitute observations

from two distinct habitat units in the hyporheic zone,

where habitats in RB are in better hydrological

connection with surface water in comparison with GB

(Fig. 1).

At each sampling station, 10 l mixture of water,

sediment and invertebrates was extracted using a

piston pump fixed on a mobile steel pipe (Ø45 mm)

with a perforated distal end (apertures of Ø10 mm in

a length of 30 cm) (Bou & Rouch, 1967). The method

is not strictly quantitative because faunal density and

diversity cannot be expressed per volume of hypor-

heic sediment. Nevertheless, comparisons between

samples of equal volume and equal depth are still

possible with caution (Malard et al., 2002b). The

mixture of water and sediment was gently elutriated

five times in order to separate invertebrates and

particulate organic matter from the sediment. A hand

net (mesh size 100 lm) was used to filter the water.

The sediment was stored and taken to the laboratory.

Part of this sediment was used as a coarse fraction for

further measurements of biofilm activity. Since the

biofilm in oligotrophic systems frequently disturbed

by flood is thin, the pumping and gentle elutriation of

sediments should not affect its structure. The portion

of the water filtered through the hand net was stored

in 1 l plastic bottles to give hyporheic water and, after

Fig. 2 Mean daily discharge (m3 s-1, grey columns) and

surface water temperatures (�C, black line) of the Baca River

during the study period. Arrows indicate the sampling dates

(preD pre-disturbance sampling, postD1-6 post-disturbance

sampling) and the period of gravel extraction

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settling, a fine sediment fraction (\0.1 mm) for

measurement of microbial activity. The samples were

refrigerated and taken to the laboratory where

measurements were conducted within 24 h. Another

sample of hyporheic water was stored in a plastic

bottle and taken to the laboratory for chemical

analyses. After collecting the biological samples,

oxygen (WTW Multiline P4, CellOx 325) and

conductivity (WTW Multiline P4, TetraCon 325)

were measured in the hyporheic water in the steel

pipes. Hydraulic head measurements in the RB were

conducted with a T-bar (Malard et al., 2002b).

Laboratory analyses

pH of water samples was measured using a WTW pH

540 GLP, with a TetraCon 325 probe. Nitrate and

sulphate were measured by ion chromatography

(Metrohm, 761 Compact IC; precision ±0.01 ppm).

Coarse sediments extracted from each sampling

station were dried and measured as volume per 10 l

of sample. The amount of fine sediment fraction

(\0.1 mm) in 1 l of water was measured after all

particles had settled in the bottle (after 24 h). The

amount of organic matter was estimated by loss on

ignition (Pusch & Schwoerbel, 1994). After removing

the invertebrates, the particulate organic matter

([0.1 mm) was dried (24 h, 105�C), weighed, burned

(2 h, 520�C) and weighed again. The difference in

weight gave the amount of organic matter in 10 l of

sample.

Electron transport system (ETS) activity was

measured in both surface and hyporheic water, in

the fine (\0.1 mm) and coarse ([0.1 mm) sediment

fractions (Packard, 1971; G.-Toth, 1999) in order to

estimate the microbial activity in the water, and on

the two sediment fractions. Water samples were

filtered through a 100 lm mesh to remove larger

particles, then through a membrane filter (pore size

0.2 lm; Millipore) which was used in analyses.

Water and solid samples were homogenized in 4 ml

final volume of ice-cold homogenization buffer,

using an ultrasonic homogenizer (Cole-Parmer) for

3 min at 40 W, then centrifuged for 4 min at 0�C at

8,5009g (2K15, Sigma). Homogenate incubation and

measurement of formazan production were per-

formed according to the procedure described in

Simcic & Brancelj (2003). ETS activity was mea-

sured as the rate of tetrazolium dye reduction, which

was converted to equivalents of oxygen utilized per

wet mass in a given time interval (ll O2

gWW-1 h-1) (Kenner & Ahmed, 1975).

Oxygen consumption, as a measurement of biofilm

activity, was estimated under laboratory conditions

using the closed bottle method (Lampert, 1984).

Ground glass stoppered bottles (160 ml) were filled

with water aerated in advance for 24 h. About 1 g

wet mass of sediment was added to each of three

bottles for oxygen consumption measurement, and

three bottles without sediment served as controls. All

bottles were closed and kept in the dark at 20�C.

After 48 h, the concentration of dissolved oxygen

was measured using a polarographic oxygen elec-

trode (OXI 96, WTW).

Invertebrates were counted and identified.

Taxa were assigned to the three ecological catego-

ries—permanent hyporheos, occasional hyporheos

(Williams, 1984), and stygobionts (Ginet & Decou,

1977; Botosaneanu, 1986). The classification is based

on their affinity for the hyporheic habitat. Permanent

hyporheos were classified as species that may be

present during all life stages, either in the hyporheic

or benthic habitat, but predominantly in the former.

Occasional hyporheos were classified as larvae of

aquatic insects that spend part of their aquatic-stage

in the surface environment (in addition to the obligate

aerial stage) and part in the hyporheic zone (early

stages). Stygobionts were considered as true ground-

water taxa, completing their entire life cycle in

subsurface water.

Data analyses

A three-way analysis of variance (ANOVA) was used

to test the influence of site, date and habitat type on

differences in physico-chemical characteristics, bio-

film activity and hyporheic invertebrate density and

diversity. A three-way ANOVA consists of seven

significance tests: a test for each of the three main

effects, a test for each of the three two-way interac-

tions and a test of the three-way interaction. Only

significant interactions are presented in the results.

Data were normalized by log10(x ? 1) (for environ-

mental data and invertebrate density) and bypðxþ

3=8Þ (for taxonomic richness) transformations. Cor-

relation between biofilm activity (ETS on fine

sediments) and fine sediment amounts was calculated

using Pearson’s correlation coefficient. Spearman’s

Hydrobiologia (2011) 667:15–30 19

123

rank correlation coefficient was used to search for

relationships between invertebrate diversity and den-

sity and the following environmental characteris-

tics—temperature, conductivity, oxygen, fine and

coarse sediment amounts, organic matter and meta-

bolic activity of biofilm. The analyses were per-

formed using SPSS for Windows, Version 17.0.

Principal component analysis (PCA) was used to

examine the variation in community composition

between reference and impacted sampling sites, pre-

disturbance and post-disturbance sampling occasions

and habitat types. Relationships between environ-

mental data (habitat type, sampling occasion—pre- or

post-disturbance, temperature, conductivity, oxygen,

nitrate, sulphate, fine and coarse sediment amounts,

organic matter contents, biofilm activity) and the

abundances of invertebrate taxa were explored using

canonical correspondence analysis (CCA) (ter Braak

& Prentice, 1988). An unrestricted random Monte

Carlo permutation test under null model was per-

formed to determine the statistical significance of

individual environmental variables. The PCA and

CCA analyses were conducted using the computer

program CANOCO version 4.5 (ter Braak & Smil-

auer, 2002). The invertebrate data were normalized

by log10(x ? 1) in PCA as well as in CCA analyses.

Results

Physical and chemical characteristics

of the hyporheic zone

Temperature, dissolved oxygen, pH, nitrate and sul-

phate concentrations in surface water and hyporheic

water from the RB and GB were similar indicating

good permeability of sediments in the hyporheic zone

and the short retention times of the water in the

sediments (Table 1). However, there was a significant

difference in conductivity between RB and GB and

seasonal variation in temperature, oxygen and con-

ductivity at both sites (Table 3).

Vertical hydrological exchange, sediment

composition and particulate organic matter

The hydraulic heads of the sampling stations were

close to or below zero, indicating a constant flow of

surface water into the RB sediments (Table 1). At the

impacted site, stronger down-welling occurred after

gravel extraction at all sampling stations (-4.8 ±

7.6 cm), the greatest increase being at sampling station

RB3 at the downstream end of the sampling area

(RB3; -30 cm). The mean volume of fine sediments

(\0.1 mm) extracted with the Bou-Rouch pump varied

from 13 to 493 ml 10 l-1 at reference site and from 33

to 180 ml 10 l-1 at impacted site, while the amounts of

coarse sediments ([0.1 mm) ranged from 17 to 712 ml

10 l-1 at reference and from 183 to 1,203 ml 10 l-1 at

impacted site (Fig. 3a, b). After gravel extraction, the

amounts of coarse sediments increased and were

higher in the RB than in GB at impacted site, while

at reference site the amounts were significantly lower

from the impacted site and higher in GB than in RB

(three-way ANOVA, interaction site*habitat, F =

11.28, P \ 0.01) (Table 3). The amount of particulate

organic matter (POM [ 0.1 mm) significantly chan-

ged over the time (Table 3, P \ 0.001) with mean

values ranging from 46 to 748 mgDW 10 l-1 at

Table 1 Average values (±SD) for physical and chemical characteristics of surface water and hyporheic water from the river bed

(depth 30–60 cm) and gravel bars (depth 60–90 cm)

Reference site Impacted site

Surface water River bed Gravel bars Surface water River bed Gravel bars

Vertical hydrological gradient (cm) -1.2 ± 3.4 -4.8 ± 7.6

Temperature (�C) 9.2 ± 4.1 9.7 ± 4.3 10.4 ± 4.6 10.5 ± 5.0 10.8 ± 4.9 11.0 ± 5.8

Dissolved oxygen (%) 106 ± 6 90 ± 13 82 ± 12 100 ± 4 94 ± 7 82 ± 15

Conductivity (lS cm-1) 273 ± 7 275 ± 12 281 ± 13 273 ± 8 271 ± 9 280 ± 16

pH 8.3 ± 0.1 8.1 ± 0.1 8.1 ± 0.1 8.3 ± 0.1 8.2 ± 0.1 8.1 ± 0.1

NO3- (mg l-1) 4.3 ± 0.6 4.1 ± 0.2 4.1 ± 0.5 3.9 ± 0.2 4.0 ± 0.6 4.2 ± 0.4

SO4- (mg l-1) 7.6 ± 1.7 7.2 ± 0.5 7.8 ± 0.9 7.1 ± 0.7 7.5 ± 1.5 7.4 ± 1.6

20 Hydrobiologia (2011) 667:15–30

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reference site and from 42 to 1,250 mgDW 10 l-1 at

impacted site and being the lowest in the samples from

May 2005 (Fig. 3c).

Biofilm activity

The mean values of ETS activity of hyporheic water,

fine and coarse sediments ranged from 3.12 to 6.50 ll

O2 l-1 h-1, 2.80 to 3.69, and 0.19 to 0.26 ll O2

gWW-1 h-1, respectively. Mean oxygen consump-

tion rates were from 1.44 to 2.39 ll O2 gWW-1 h-1

for fine and from 0.15 to 0.24 ll O2 gWW-1 h-1 for

coarse sediments (Table 2). Oxygen consumption

rates of fine and coarse sediments significantly

changed over the time (P \ 0.05 and \ 0.001,

respectively) and oxygen consumption rates of coarse

Fig. 3 The average of a volume of fine sediments (\0.1 mm),

b volume of coarse sediments ([0.1 mm), and c dry weight of

organic matter extracted with a Bou-Rouch pump from six

sampling stations (RB and GB) at the reference and impacted

sites on seven sampling occasions (n = 3). Error barsrepresent 1 SE

Table 2 Average values (±SD) for ETS activity and oxygen consumption rates (R) in the hyporheic water, and fine and coarse

sediments from the river bed (depth 30–60 cm) and gravel bars (depth 60–90 cm)

Reference site Impacted site

River bed Gravel bars River bed Gravel bars

ETS activity—hyporheic water (ll O2 l-1 h-1) 3.12 ± 2.03 No data 4.91 ± 3.68 6.50 ± 3.94

ETS activity—fine sediments (ll O2 gWW-1 h-1) 2.80 ± 2.99 No data 3.69 ± 3.84 2.88 ± 1.34

ETS activity—coarse sediments (ll O2 gWW-1 h-1) 0.26 ± 0.20 No data 0.20 ± 0.11 0.19 ± 0.09

R—fine sediments (ll O2 gWW-1 h-1) 1.44 ± 0.94 No data 2.39 ± 1.28 2.39 ± 1.37

R—coarse sediments (ll O2 gWW-1 h-1) 0.24 ± 0.15 No data 0.18 ± 0.15 0.15 ± 0.05

Hydrobiologia (2011) 667:15–30 21

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sediments were significantly lower at impacted site

(P \ 0.01) (Table 3). The amounts of fine sediments

and ETS activity of fine sediments were negatively

correlated (r = -0.60, P \ 0.001) (Fig. 4).

Hyporheic invertebrate community

The most frequent taxa in the majority of samples were

Chironomidae, Leuctra sp. and Baetoidea (occasional

hyporheos), and Nematoda, Oligochaeta and juvenile

Cyclopoida (permanent hyporheos). The most fre-

quent stygobitic species was Diacyclops languidoides

(Lilljeborg, 1901). Stygobionts occurred in much

lower abundance and frequency than occasional and

permanent hyporheos (Supplementary material—

Appendix A).

Total invertebrate density ranged from 96 to 1,309

individuals 10 l-1 at reference site and from 10 to

1,191 individuals 10 l-1 at impacted site, while

taxonomic richness at reference site was from 8 to

19 taxa and at impacted site 4 to 16 taxa 10 l-1

(Fig. 5). Total invertebrate density, density of occa-

sional and permanent hyporheos, as well as total

taxonomic richness and number of taxa of occasional

and permanent hyporheos did not differ between RB

and GB, but significantly changed over the time

(decreased after flood and gravel extraction). The

density and number of stygobitic taxa did not

significantly change over the time. The impact of

the site was significant for the density of permanent

hyporheos and stygobionts, total taxonomic richness

and taxa number of all three ecotypes, but not for

total density and density of occasional hyporheos

(Table 4).

Significant correlations were found for the

amounts of fine sediments (\0.1 mm) extracted from

Table 3 Analysis of variance of physico-chemical and biofilm characteristics in the hyporheic zone, using a factorial design (dates,

sites and habitats as fixed factors)

Source of variation df MS F P df MS F P df MS F P

Temperature

(n = 52, log transformed)

Oxygen


Conductivity


Site 1 0.02 3.62 0.07 1 0.00 0.25 0.62 1 0.00 2.87 0.10

Date 6 0.36 80.40 \0.001 6 0.03 5.17 \0.01 5 0.00 10.19 \0.001

Habitat type 1 0.00 0.03 0.86 1 0.01 1.87 0.18 1 0.00 4.88 \0.05

Date*site 3 0.02 4.50 <0.05

Organic matter


Fine sediments (\0.1 mm)

(n = 61, log-transformed)

Coarse sediments ([0.1 mm)


Site 1 0.09 0.57 0.45 1 1.08 3.12 0.09 1 0.77 2.30 0.14

Date 6 1.45 9.47 \0.001 5 0.15 0.43 0.82 6 0.19 0.56 0.76

Habitat type 1 0.14 0.89 0.35 1 0.04 0.11 0.74 1 0.01 0.02 0.90

Site*habitat 1 3.79 11.28 \0.01

ETS—hyporheic water


ETS—fine sediments


ETS—coarse sediments


Site 1 0.19 1.97 0.17 1 0.30 2.31 0.14 1 0.04 0.52 0.48

Date 5 0.09 0.94 0.47 5 0.13 1.04 0.41 5 0.06 0.91 0.49

Habitat type 1 0.27 2.90 0.10 1 0.02 0.14 0.71 1 0.01 0.08 0.78

Oxygen consumption rate—fine sediments


Oxygen consumption rate—coarse sediments


Site 1 0.30 3.48 0.08 1 0.23 11.56 \0.01

Date 5 0.35 4.04 \0.05 5 0.22 10.96 \0.001

Habitat type 1 0.00 0.05 0.82 1 0.00 0.00 0.99

Site*habitat 5 0.24 11.97 \0.001

The significance tests are shown only for the three main effects and significant interactions

df degrees of freedom, MS mean square, F F-statistics, P probability

22 Hydrobiologia (2011) 667:15–30

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the hyporheic zone and total invertebrate density and

taxonomic richness, as well as densities and taxo-

nomic richness of all three ecotypes, while the

amounts of coarse sediments were in significant

correlation with total density, and density and taxa

number of occasional hyporheos (Table 5).

Principal component analysis ordination resulted

in the clustering of the November samples (SD1–3)

and the samples from the January and March (SD4–5)

from the impacted site into two relatively homoge-

neous and distinct groups, while the samples from the

pre-disturbance date and May samples (SD6) from

the impacted site grouped together with the samples

from the reference site. The samples SD4 and SD5

were associated with higher densities of Baetoidea,

while the samples from the reference site were the

most distinct from the other two groups due to the

presence of Acanthocyclops gmeineri Pospisil 1989,

Hydracarina, Dytiscidae and Polycentropodidae

(Fig. 6).

Canonical correspondence analysis conducted on

data from the impacted site explained 44.9% of the

community variability. The first axis correlates

positively with conductivity, nitrates and sulphates

and accounts for 18.7% of the species–environment

relationship. The second axis represents a gradient of

decreasing organic matter and coarse sediments, and

increasing ETS activity in the hyporheic water and

accounts for further 14.1% of the species–environ-

ment relationship (Fig. 7). CCA indicates that inver-

tebrate community at the impacted site was

significantly related to sampling occasion (pre- or

Fig. 4 Relationship

between the amount of fine

sediment in 10 l of sample

(particles \0.1 mm) and

ETS activity of the fine

sediment fraction in

samples from the hyporheic

zone of the Baca River

(n = 46)

Fig. 5 The average of a hyporheic invertebrate densities and b taxonomic richness at the reference and impacted sites on seven

sampling occasions (n = 3). Error bars represent 1 SE

Hydrobiologia (2011) 667:15–30 23

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post-disturbance dates), temperature, conductivity

and nitrate. In contrast, at the reference site, where

CCA explained 54.7% of the community variability,

invertebrates were significantly related to sampling

occasion, conductivity, fine sediment amounts and

ETS of hyporheic water.

Table 4 Analysis of variance in various descriptors of hyporheic invertebrate community, using a factorial design (dates, sites and

habitats as fixed factors)

Source of variation df MS F P df MS F P

Total density


Total number of invertebrate taxa

(n = 75, square root-transformed)

Site 1 0.47 1.57 0.22 1 3.49 7.74 \0.01

Date 6 2.38 7.90 \0.001 6 1.83 4.06 \0.01

Habitat type 1 0.00 0.01 0.91 1 0.00 0.00 0.98

Density of permanent hyporheos


Number of taxa—permanent hyporheos


Site 1 1.67 5.37 \0.05 1 1.22 4.05 \0.05

Date 6 3.58 11.55 \0.001 6 1.19 3.94 \0.01

Habitat type 1 0.07 0.22 0.64 1 0.10 0.34 0.57

Density of occasional hyporheos


Number of taxa—occasional hyporheos


Site 1 0.03 0.09 0.77 1 1.10 4.27 \0.05

Date 6 1.88 5.12 \0.001 6 0.79 3.06 \0.05

Habitat type 1 0.14 0.39 0.54 1 0.39 1.52 0.22

Density of stygobionts


Number of taxa—stygobionts


Site 1 3.56 12.83 \0.001 1 0.91 5.18 \0.05

Date 6 0.22 0.80 0.57 6 0.36 2.07 0.07

Habitat type 1 0.61 2.21 0.14 1 0.05 0.31 0.58

The significance tests are shown only for the three main effects. The tests for interactions were not significant and are not presented

df degrees of freedom, MS mean square, F F-statistics, P probability

Table 5 Spearman rank correlation coefficients between selected physico-chemical and biofilm characteristics in the hyporheic zone

and hyporheic community descriptors

n Total

density

Total taxa

number

PH

density

PH taxa

number

OH

density

OH taxa

number

Sty

density

Sty taxa

number

Temperature 52 -0.20 -0.11 0.18 0.01 -0.36** -0.15 -0.24 -0.25

Conductivity 51 -0.07 0.06 -0.33* -0.03 0.07 0.04 0.24 0.22

Oxygen 43 0.20 0.11 -0.04 0.07 0.37* 0.10 0.14 0.21

Organic matter 75 0.22 0.28* 0.04 0.18 0.31** 0.29* 0.19 0.20

Fine sediments 63 0.42** 0.44** 0.38** 0.29* 0.37** 0.39** 0.39** 0.36**

Coarse sediments 75 0.27* 0.21 0.14 0.07 0.31** 0.24* 0.15 0.16

ETS—fine sediments 46 0.22 -0.02 0.09 -0.03 0.22 -0.01 -0.01 -0.03

ETS—coarse sediments 51 0.06 0.00 0.06 -0.05 0.06 0.08 0.06 -0.03

R—fine sediments 36 -0.18 -0.28 -0.32 20.42* -0.08 -0.17 -0.05 -0.06

R—coarse sediments 50 -0.10 -0.12 0.06 -0.20 -0.22 -0.02 -0.14 -0.09

ETS respiratory electron transport system activity of biofilm, R oxygen consumption rate of biofilm, PH permanent hyporheos,

OH occasional hyporheos; Sty stygobionts

Significance level: * P \ 0.05, ** P \ 0.01

24 Hydrobiologia (2011) 667:15–30

123

Discussion

Characteristics of the hyporheic zone in the river

Baca

The measurements of vertical hydraulic gradient

(VHG) and physico-chemical characteristics (temper-

ature, conductivity, oxygen) of surface and hyporheic

water from the RB and GB in the river Baca indicate

high rates of surface–subsurface exchange, vertically

(into the RB) and laterally (into GB), as well as short

retention times of stream water in the hyporheic zone

due to the high permeability (hydraulic conductivity)

of sediments. Moreover, the measurements of nutrient

concentrations revealed relatively low trophic level of

this river system. Consequently, the biofilm activity

measured as respiratory ETS activity and oxygen

consumption rates were relatively low in all three

fractions (water, fine and coarse sediments). From

previous studies it is well known that sediment grain

size, as well as hydrological exchange patterns and

sediment stability, influence biogeochemical pro-

cesses in the hyporheic zone and shape the hyporheic

invertebrate communities (Gibert et al., 1994;

Findlay, 1995; Brunke & Gonser, 1997; Mulholland

& DeAngelis, 2000; Boulton, 2007; Datry et al.,

2007). The hyporheic zone of the river Baca, was

inhabited by a highly resilient hyporheic invertebrate

community composed mainly of Cyclopoida (with

predominance of copepodites), and Chironomidae,

Leuctra sp. and Baetoidea larvae. Cyclopoida have

been reported as a major component of hyporheos

(Boulton et al., 1992; Hunt & Stanley, 2003), and

juvenile Copepods were found to dominate in the

hyporheic zone (72% of all individuals), in which harsh

environmental conditions shape the community compo-

sition (Malard et al., 2003). Stygobionts (groundwater

dwelling species) were present at low density and low

taxonomic richness, as found by Fowler & Death (2001)

in river sediments frequently disturbed by flood.

The effect of gravel extraction on hydrologic

exchange and biogeochemical processes

In-stream gravel extraction caused structural changes

in the river channel (incision and change in grain size

Fig. 6 PCA ordination

diagram of species (arrows)

and samples (points) from

the hyporheic zone

collected before and after

gravel extraction at

reference and impacted site.

Filled square reference site,

pre-disturbance date; filledcircle reference site, post-

disturbance dates; opensquare impacted site, pre-

disturbance date; opencircle impacted site, post-

disturbance dates

Hydrobiologia (2011) 667:15–30 25

123

distribution). The upper layer of mostly gravel (3 m in

depth) was replaced by finer sediments, originating

from upstream. The incision altered the pattern of

hydrological exchange at the impacted site with

increased input of surface water into the hyporheic

zone (strong down-welling). The sediment composi-

tion at the sampling stations was estimated by the

volume of sediment extracted by the Bou-Rouch

pump, a method that has been shown to be a good

indicator of permeability and rate of consolidation of

RB sediments (Malard et al., 2002b). The particles of

the size 5 mm were the largest particles, which were

still possible to extract with the piston pump. The

amounts of sediment extracted do not show the true

sediment composition in the hyporheic zone, but they

give the information about the proportion of small

gravel and sands (\5 mm) there. Since grain size

distribution is linked to permeability (Malard et al.,

2002a), increased amounts of extracted sediments

probably led to decreased permeability at the impacted

site. Changes in hydrological exchange and sediment

permeability (hydraulic conductivity) can affect the

residence time of water in the hyporheic zone (Freeze

& Cherry, 1979), and the residence time of advected

channel water within the subsurface influences the

type of biogeochemical processes operating within the

site (Malard et al., 2002a). In our study the assumed

decrease in hydraulic conductivity at impacted site

have not been found to affect the mayor physical and

chemical characteristics, as well as have not influ-

enced a respiratory ETS activity of microorganisms in

the hyporheic water and those attached to the

sediments. However, the oxygen consumption rates

(R) on coarse sediments have been shown to be

significantly lower at impacted than at reference site in

a month after gravel extraction (SD1–3). Those results

indicated the link between permeability and biofilm

activity. The reason that significant differences were

found (sites, P \ 0.01; time P \ 0.001) in oxygen

consumption rates but not in ETS activity is probably

due to the fact that the ETS activity of microbes

responds more slowly to environmental change than

respiration rate (Bamstedt, 1980). Relatively small

and insignificant variations in ETS activity could be

explained by the low values of POM and low water

temperatures (10.1 ± 4.3�C in 2004/2005). This is in

agreement with the results of Craft et al. (2002), who

found equivalent aerobic microbial activity on a

macro-scale (metres to kilometres) in an oligotrophic

gravel-bed river. However, the analysis of ETS

Fig. 7 CCA biplot of

hyporheic samples taken at

impacted site on seven

occasions relative to 15

environmental parameters.

The value (%) under each

axis label represents the

percentage of the species–

environment relationship

accounted for by that axis.

Open square pre-

disturbance date, RB; filledsquare pre-disturbance date,

GB; open circle post-

disturbance dates, RB; filledcircle post-disturbance

dates, GB

26 Hydrobiologia (2011) 667:15–30

123

activity on different sediment fractions and in surface

and hyporheic water showed that different fractions

contribute differently to the total mineralization in the

areas of different intensity of surface–subsurface

water exchange and the consolidation rate of sedi-

ments (Simcic & Mori, 2007). Hyporheic water and

fine sediment particles (\0.1 mm) are more important

components for mineralization in more consolidated

sediments, in which water exchange is less intense,

while coarser sediment particles (0.1–5 mm) contrib-

ute significantly to the mineralization in less consol-

idated sediments. Furthermore, we observed a strong

negative correlation between the volume of fine

sediment (\0.1 mm) and ETS activity (R = -0.60,

P \ 0.001), suggesting that increased fine sediment

amounts could impede biofilm activity, probably as a

result of consolidation and clogging of interstices as

shown by Songster-Alpin & Klotz (1995). Clogging of

the sediments with silt (colmation) fills interstitial

spaces and impairs hydrological exchange with the

overlying water, reducing the influx of dissolved

oxygen, nutrients and organic matter in the hyporheic

zone (Brunke & Gonser, 1997).

The response of the hyporheic invertebrate

community

Stream invertebrates from the rivers frequently

disturbed by floods are characterized by high resis-

tance and resilience (Townsend & Hildrew, 1994).

The previous observations of recovery rates due to

flood in the hyporheic zone are highly variable. Dole-

Olivier et al. (1997) observed the recovery of

hyporheic invertebrates in 7 days, Olsen & Townsend

(2005) in one month and Hancock (2006) in four and

a half months. The differences in recovery rates

occurred most probably due to different hydrological

regimes in the rivers studied (Hancock, 2006). The

hyporheic community of the Baca River recovered

after gravel extraction in two and a half month by

means of density and taxonomic richness. However,

the community composition recovered much later

(after 7 months). Due to the fact that coincidently a

flood occurred 2 days after gravel extraction (Fig. 2),

we had the opportunity to compare the effect of

anthropogenic disturbance versus natural one. Our

results suggest that density and taxonomic richness

was more seriously affected after anthropogenic

disturbance than after flood, and that recovery in

taxonomic richness after spate occurred sooner

(1–2 weeks) than that after gravel extraction

(2.5 months), while density needed 2.5 months at

both sites to recover. The former was previously

shown by Matthaei et al. (1997), who demonstrated

that experimental disturbance has more severe

impacts on benthic invertebrates than flood. The

reason could be that experimental disturbances,

which can be comparable in some way to gravel

extraction, are very sudden, whereas discharge

increases more gradually during a spate and inverte-

brates are able to search for refugee in the spatial

heterogenic structure of the RB. Moreover, during

gravel extraction, the whole upper layer of the river

sediments is suddenly removed over larger area (in

this study—100 m in length), in this way little or no

refugees is left for invertebrates. The invertebrate

community at the site of that kind of impact is most

probably recovered by colonization through drift and

upstream and downstream migration through the

sediments, which took in our case between one to two

and a half months. Invertebrate density and taxo-

nomic richness recovered in 2.5 months while the

community composition needed between 5 to

7 months to recover. The samples collected in a first

month after gravel extraction were characterized by

low densities in general, and January and March

samples (SD4–5) at impacted site were composed

mainly of large numbers of Baetoidea larvae (occa-

sional hyporheos).

Canonical correspondence analysis of environ-

mental and invertebrate data revealed the importance

of sampling occasion and conductivity for the

hyporheic community at both sites. It seems that

the hyporheic invertebrate community exhibited great

seasonal variation due to high variation in discharge

and a range of different annual life cycles and

reproductive patterns of occasional and permanent

hyporheos, while the populations of stygobionts

remains more stable and more likely respond to

changes in surface–subsurface water flow. Since

conductivity is indirect indicator of surface–subsur-

face hydrological exchange (Pospisil, 1994) this

could be the reason why this parameter was recog-

nized as an important factor for shaping the inverte-

brate community. Moreover, at impacted site,

temperature and nitrate contents, and at reference

site, fine sediments and ETS activity in the hyporheic

water revealed as important factor for invertebrates.

Hydrobiologia (2011) 667:15–30 27

123

Temperature is also an indicator of hydrological

exchange between surface water and groundwater

(Pospisil, 1994), while the other factors suggest

the importance of food resources in shaping the

hyporheic community. The majority of stygobionts

and permanent hyporheos at the impacted site

occurred along the gradient of decreasing biofilm

activity and organic matter content, and in the areas

with coarser sediments (decreasing amounts of sed-

iment extracted). In the samples where finer sedi-

ments prevailed and organic matter content and

biofilm activity were higher, occasional hyporheos

dominated. The great importance of the presence of

the fine sediment fraction (particles\0.1 mm) for the

composition of the hyporheic community is also

indicated in our study. Olsen & Townsend (2003)

found similar correlations between fine sediment

(0.063–1 mm) and hyporheic invertebrate distribu-

tion. Furthermore, analysis of hyporheic communities

from Oklahoma (USA) streams revealed the impor-

tance of substrate composition in determining the

composition and abundance of invertebrates (Hunt &

Stanley, 2003). Fine sediment may have a direct

effect on invertebrates through its particular habitat

characteristics, such as pore size, or by restricting

their ability to feed, respire or move (Olsen &

Townsend, 2003). Indirect effects of increasing

amounts of fine sediment include lowering the

permeability and residence time of water, which

affects the physical and chemical conditions in the

hyporheic zone (Jones & Holmes, 1996), and conse-

quently biofilm activity as noted earlier. Biofilm is a

potential food resource for many invertebrates inhab-

iting the hyporheic zone. Those observations were

supported by the correlation between the amount of

fine sediment and its ETS activity. The latter

decreased following an increase in fine sediment

amounts in the hyporheic zone, which probably

resulted in decrease in the food resources for

invertebrates.

The results of this study indicate that discharge

and gravel extraction activities in the river channel

were the major forces in shaping the hyporheic

invertebrate community in the river Baca. The in-

stream gravel extraction has been shown to affect

surface–subsurface water exchange (increased down-

welling) and to change the sediment composition at

the impacted site. Removal of the upper sediment

layer and the consequent changes in permeability led

to short-term decrease in biofilm activity (measured

as oxygen consumption rates) and invertebrate den-

sity and richness. Occasional hyporheos revealed to

be more resilient than stygobionts and permanent

hyporheos, most probably due to higher mobility and

habitat generalist traits of the former taxa. Moreover,

the shift in invertebrate community composition was

observed following gravel extraction at impacted site

with higher proportion of occasional hyporheos in

comparison with reference site. The above observa-

tions suggest that in-stream gravel extraction could

be more severe distraction for hyporheic invertebrate

community than extreme flood events that occur

every few years.

Acknowledgments The authors thank C. Fiser, C. Meisch, I.

Sivec, B. Sket, G. Urbanic, and D. Zabric for their help in

determining Ostracoda, Amphipoda, Isopoda, Plecoptera,

Trichoptera and Ephemeroptera and A. Jerebic for chemical

analyses of water samples. Special thanks go to D. Jesensek

from Tolmin Angling Club for providing information about

gravel extraction activities in the river Baca. Critical and

constructive comments from the reviewers and an editor

greatly improved the manuscript. The research was supported

by the Slovenian Ministry of Higher Education, Science and

Technology.

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