[Water Quality Measurements] Biological Monitoring of Rivers (Applications and Perspectives) ||...

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1.2Instream and Bankside Habitatin Rivers

Patrick D. Armitage

1.2.1 Introduction

1.2.2 Habitat Hierarchies

1.2.3 Habitat Types

1.2.4 Habitat/Fauna Associations

1.2.4.1 Choice of scale

1.2.4.2 Reach level and mesoscale

1.2.4.3 Spatial and temporal aspects

1.2.5 Factors Affecting Stream Habitat

1.2.6 Habitat Assessment Methods

1.2.7 Future Directions

Acknowledgements

References

1.2.1 INTRODUCTION

The main concerns of water managers in the past were water supply, pollution,power generation and flood control. However, with increasing knowledge of thecomplexities of the environment and cause and effect relationships between catch-ment disturbances and the condition of the river, a more holistic ecological viewof river management has emerged. This has resulted in truly interdisciplinary andcollaborative studies, particularly in the field of flow regulation, where since 1979there has been a triennial series of symposia dedicated to the amalgamation of

Biological Monitoring of Rivers: Applications and Perspectives Edited by G. Ziglio, M. Siligardi and G. Flaim © 2006 John Wiley & Sons, Ltd. ISBN: 0-470-86376-5


18 Instream and Bankside Habitat in Rivers

science with management issues (Lane, 2001). In addition, several publicationshave appeared specifically addressing the application of scientific knowledge to en-vironmental management of rivers (Gore and Petts, 1989; Boon et al., 1992; Calowand Petts, 1992a,b; Rosenberg and Resh, 1993; Harper and Ferguson, 1995; Pettsand Amoros, 1996). A theme common to most of this work is the recognition thatimpacts and disturbances affect not only the water quality but also the condition anddistribution of riverine habitat.

Management interest in habitat has arisen from a number of separate sources.First, the relation between discharge and wetted usable habitat is fundamental to thesetting of ecologically acceptable flows and this relationship has been explored in thedevelopment of the Instream Flow Incremental Methodology (IFIM) (Bovee, 1995).This system has focused attention on the relationship between stream hydrology andhydraulics and ecology and given rise to a new area of collaborative studies ‘ecohy-draulics’ (see Petts, 2003). Secondly, the restoration and rehabilitation of river sec-tions for recreational, environmental and aesthetic purposes (Brookes and Shields,1996; Boon and Raven, 1998; Lane, 2001) requires knowledge of the relationship be-tween channel geomorphology and habitat distribution. Thirdly, the United NationsConvention on Biological Diversity demands a commitment to the conservation ofbiodiversity, a goal which requires detailed information on the habitat requirementsof a wide range of biotic communities. This, in conjunction with EEC regulations,particularly the Habitats (92/43/EEC) and Water Framework (2000/60/EC) Direc-tives, has focused interest on the role of habitat in resource management (Logan andFurse, 2002).

This chapter will focus on the importance of habitat in determining river bio-coenoses with particular reference to macroinvertebrate communities. The specificobjectives are as follows:

� To describe instream and bankside habitat in relation to the hierarchical structureof rivers.

� Provide examples of how this may be altered or impacted by natural and anthro-pogenic means and briefly consider current habitat assessment methodologies andoutline future developments and needs.

1.2.2 HABITAT HIERARCHIES

The hierarchical organization of rivers has long been recognized by geomorpholo-gists and several classification systems have been developed. For the present pur-poses, the system devised by Frisell et al. (1986) forms a convenient framework fora discussion of ecological habitat.

Lotic systems incorporate a number of levels that are nested at successively smallerspatio–temporal scales. These range from the entire catchment, with a high temporalstability to the microhabitat (stick and leaf, detritus, sand over cobbles, etc.), that maylast as little as one month or even less. When this conceptual approach is blended


Habitat Hierarchies 19

with ‘River Continuum’ theory (Vannote et al., 1980), which stresses the role ofthe downstream gradient of physical factors as a control on biological strategies anddynamics of river systems, we have a broad holistic view of river structure and func-tion. Further developments incorporating anthropogenic influences and a historicalperspective have led to the view that rivers (‘fluvial hydrosystems’), (Amoros et al.,1987, Petts and Amoros, 1996) are four-dimensional systems which are dependenton longitudinal, lateral and vertical transfers of energy, material and biota over arange of time-scales (Ward, 1989).

It is useful to simplify the complex array of environmental variables that deter-mine the occurrence and distribution of river biota, by classifying sections of riversinto major types or functional sectors (Amoros et al., 1987). Figure 1.2.1 presents a

FLOODPLAIN UNITSDrained pasture, marsh, ponds,

ditches

RIPARIAN UNITSRiparian vegetation, vegetation

structure, bank structure

POOL

RIFFLEBoulder/cobbles, gravel,submerged macrophytes

RIVER BANKEmergent vegetation, bareearth, tree roots, artificial

BACKWATERSilt, woody debris, macrophytes,

floating leaved, emergent

GLIDE/RUN

Bedrock, boulders/cobbles,gravel, sand/silt

Boulders/cobbles, gravel,sand, submerged macrophytes

Figure 1.2.1 A hierarchical classification of habitat types found in a lotic system



schematic showing habitat hierarchies partially adapted from the ‘Fluvial Hydrosys-tem’ approach with the main emphasis on the instream component. Sectors maybe defined as lengths of river within which there is a uniformity of major physi-cal characteristics such as geology and slope. Sector boundaries are usually relatedto a major change in the flow regime, water chemistry and/or channel form. Theyusually show predictable changes with increasing distance from source, from smallupland relatively unmanaged sectors to lowland regions that may be intensively man-aged. Each sector type is composed of a series of reaches which are lengths of riverwithin which there is a uniformity of local habitat features. Reach boundaries mayrelate to localized features such as weirs, which create ponded reaches upstream andfaster-flowing gravel reaches downstream.

Alternatively the boundaries may be associated with local changes in land usefrom open pasture to woodland, or local changes in channel management (dredg-ing or channel straightening) (Petts and Bickerton, 1997). Reaches themselves aremade up of sets of habitats associated with particular flow velocity and substratumcombinations and bounded by bankside and floodplain habitats. This classificationprovides a useful framework to view habitat relationships with each other and withtheir position along the stream. In addition, when information is available from allcomponents, this approach provides a comprehensive description of the water systemwhich allows the integration of basic and applied knowledge in a manner suitablefor use by water managers.

1.2.3 HABITAT TYPES

Figure 1.2.1 identifies a range of habitats found throughout a lotic system. Some largemobile mammals and fish may cover a wide range of habitat types. Invertebrates, incontrast, although widely dispersed in running water, have a more focused habitatrange which is best considered at the ‘mesoscale’, intermediate between microhabitat(leaf tips, individual stones, etc.) and reach level.

There are many accounts of the types of habitat to be found in rivers (see Harperet al. (1995) for a review) and their occurrence and relative proportions at a site willreflect both sector and reach characteristics which are themselves largely controlledby catchment hydrology. A generalized and condensed list based on the UK RiverHabitat Survey Methodology (Raven et al., 1997) is presented below.

Instream mineral habitats:Bedrock, boulders, cobbles, pebbles, gravel, sand, silt, clay, hyporheic sedimentsInstream vegetation habitats:Macrophytes

Emergent and marginal (reeds, rushes, grasses and sedges)Emergent broad-leaved (Apium, Rorippa spp.)Submerged broad-leaved (Elodea spp., Callitriche spp.)Submerged fine-leaved (Ranunculus spp., Myriophyllum spp.


Habitat/Fauna Associations 21

Floating-leaved and rooted (Nuphar lutea)Free-floating (Lemna spp.)Submerged mosses/liverworts/lichensFilamentous algae

Other categoriesTree rootsAggregations of coarse particulate organic matter (detritus)Submerged wood

Riparian and floodplain habitats (not covered by the above categories):Bare earth banksVegetated river bankCattle drinksBackwaters (connected and isolated) and side channelsDitchesArtificially modified (iron pilings, concrete, rip rap, etc.)

The river ecosystem is composed of combinations of these basic units which maythemselves be modified by prevailing flow conditions Superimposed on this are thetemporal dynamics of habitat change, such as siltation of coarse substrata duringseasonal low-flow periods and the growth and senescence of vegetative substrata. Inaddition, the habitat requirements of instream fauna may change with time. Exam-ples are seen in the pupation of riffle beetles (Elmidae) in the wet banks of streams(Holland, 1972) and the temporal shifts in the physical habitat of the crayfish,Orconectes neglectus (Faxon), throughout its development (Gore and Bryant, 1990).Therefore, although different types of habitat are relatively easy to recognize it isimportant to be aware that the communities of biota they support are dynamic entitiesresponding to seasonal changes in discharge and hydraulics, vegetation growth andintrinsic biotic interactions. These in turn, are subject to the modifying effects of nat-ural and anthropogenic disturbances in the catchment area and in the channel itself.

1.2.4 HABITAT/FAUNA ASSOCIATIONS

1.2.4.1 Choice of scale

The association of faunal communities with habitat patches has been a common areafor study by freshwater ecologists but it is only relatively recently that emphasis hasbeen placed on habitat availability – a feature central to the IFIM methodology andof major interest to environmental management. Habitat availability has referred inthe main to habitat for single species (usually fish) but there is merit in extending thisconcept to habitat of faunal assemblages. By placing emphasis on the proportionsof habitat and the faunal communities which live in them, we have a tool that can beapplied in assessment of biological quality, conservation, and classification.



The scale of study chosen for ecological investigations will have a major influenceon the results obtained and their interpretation (Armitage and Cannan, 1998). In riversystems, the importance of scale in research studies has been addressed with respectto classification systems (Naiman et al., 1992) and ‘pattern and process’ (Cooperet al., 1998). It is recognized that at very large scales, assemblages of lotic biota arepredictable and persistent in the absence of any catastrophic natural or anthropogenicdisturbance. Observation of faunal assemblages at a microscale will in contrast beless predictable and more susceptible to environmental change. An intermediate scaleof study is required which will provide reliable data that can be used in managementdecisions.

1.2.4.2 Reach level and mesoscale

Fish biologists have placed importance on investigations of available habitat at reachlevel (Plafkin et al., 1989; Kershner et al., 1992; Parasiewicz, 2001) but macroin-vertebrate studies have in general not followed this research route, due mainly to thehigh cost of data processing and different research needs (assessment of water qual-ity). There is little in the published literature on the application of macroinvertebratestudies at reach level, except in broad longitudinal zonation studies (Hawkins, 1984;Statzner and Higler, 1986; Palmer et al., 1991). A description of a river in terms ofthe distribution of habitats along it and their faunal associations has, however, beencentral to studies on the Rhone (Amoros et al., 1987; Statzner et al., 1994; Petts andAmoros, 1996).

Research efforts into macroinvertebrate/habitat associations at the reach scale inother countries have been less intensive and floodplain issues and historical aspectsof change have not been much studied. Instead, the stimulus for ecological instreamhabitat investigations with application to management has come mainly from flowregulation, conservation and rehabilitation issues.

Studies of flow-related impacts on rivers, such as impoundment, abstraction andnatural low flows, have shown that it is habitat which is being affected by thesedisturbances (Armitage, 1984; Armitage and Petts, 1992; Gore, 1994). Informationon the faunal assemblages of specific habitats was required because flow modifica-tions affected the proportion and distribution of these habitats and hence the faunalcharacteristics of the river.

In one series of studies (Armitage et al., 1995; Armitage and Pardo, 1995), vi-sually distinct areas of river bottom (weed beds intermixed with patches of gravel,sand and silt) were identified from the bank. These were referred to as mesohabi-tats to introduce a scalar dimension, which the term biotope does not have, and todistinguish them from microhabitats such as a leaf tip or stone surface. A mesohab-itat may be defined as ‘a medium-scale habitat that arises through the interac-tions of hydrological and geomorphological forces which may include instreammacrophyte growth’. This choice of habitat unit was deliberately anthropocen-tric because changes in mesohabitat or their proportion are easily recorded. The


Habitat/Fauna Associations 23

question was asked – do mesohabitats support specific faunal communities thatremain distinct throughout the seasons? If so, information on their distribution inrelation to hydrological/hydraulic variables will provide a way of assessing distur-bances that affect the river bottom. This study and its application to a regulatedreach and a channelized stream (Armitage and Pardo, 1995; Tickner et al., 2000)have shown that the mesohabitat approach can be used to assess disturbance in caseswhere most standard biotic indices would be unsuitable.

Similar work at this scale, where the habitat units are called ‘functional habitats’,has been carried out to provide ecological guidance to those whose work affectedthe river environment (Smith et al., 1991). The work has now developed into amethodology for providing advice on conservation of river habitat and may alsoprovide a means of assessing river restoration works and have application in bothriparian zones and the floodplain (Harper et al., 1995).

Despite the varied nomenclature, mesohabitats (introducing a scale aspect), func-tional habitats and biotopes, are all essentially the same thing where river manage-ment is concerned. That is, areas of the river bottom or river system which are usuallyvisually distinct. They may be defined by resident hydraulic conditions, macrophytegrowth, or deposition of woody debris or combinations of these, and may supportspecific biotic communities. Work at this scale (Newson and Newson, 2000; Beiselet al., 2000; Buffagni et al., 2000; Brunke et al., 2002; Usseglio-Polatera and Beisel,2002) has provided information appropriate to the management of rivers and as partof a nested set of habitats (Figure 1.2.1) (Armitage and Cannan, 1998), can be appliedthroughout the catchment.

1.2.4.3 Spatial and temporal aspects

Habitats exist in time as well as space and it is therefore important that data onhabitat characteristics are gathered throughout the year, or at least seasonally. Thespecies assemblages of mesohabitats in a river in southern England (Pardo andArmitage, 1997) were observed in spring, summer and autumn. Macrophyte meso-habitats showed seasonal variations and were not discrete units throughout the year.‘Ranunculus’ constituted a distinct habitat in spring but as discharge decreasedthrough summer and autumn this mesohabitat became similar faunistically to twomarginal macrophyte habitats, ‘Nasturtium’ and ‘Phragmites’. In contrast, ‘gravel’mesohabitats showed a more persistent species structure although this also showedsome seasonal variation. It was concluded that species assemblages could only bedescriptors of mesohabitats if the seasonal distinctiveness is taken into account.

Seasonality is of major importance when considering bankside habitat (Armitageet al., 2001). The interactions between plants and their effects on flow hydraulics,and the associated fauna of invertebrates, fish, birds and mammals, are most highlydeveloped in bankside habitat. In certain rivers, the bankside may contribute mostof the faunal diversity (Cogerino et al., 1995). Production and organic matter reten-tion may be several times higher in the littoral than in mid-channel (Chauvet and



Arrows representpossible emergence,swarming andoviposition pathways

Floodplainforest

Riparian shrubsHerbaceousplants

Submerged andemergent macrophytes

Thalweg of channel

Figure 1.2.2 Bankside habitats and their relationship to the channel and floodplain

Jean-Louis, 1988) and bankside vegetation will furnish cover for both adult andjuvenile fish (Schiemer and Zalewski, 1992). Bankside habitat will also providerefugia for macroinvertebrates and fish during periods of high flow (Cogerino et al.,1995). In addition, the bankside habitat provides an important link between instreamfauna and the terrestrial environment (Figure 1.2.2). Species migrate from the mainchannel to marginal areas to complete their life-histories (Holland, 1972; Gore andBryant, 1990) and use marginal vegetation for emergence and oviposition and theriparian vegetation as refugia for adults and as swarm markers (Gibbons and Pain,1992; Armitage, 1995).

Generally speaking, this physically dynamic zone, which lies between the riparianstrip and instream habitats proper, has been neglected, particularly in regard to man-agement issues. Comprehensive ecological study of macroinvertebrate assemblageshas been concentrated on the Rhone (Cogerino et al., 1995). Armitage et al. (2001)found that bank profile and structure were major determinants of macroinvertebrateassemblages. Total abundances were five to six times greater in shallow-slopingvegetated sites compared with steeply sloped and artificial banks. Highest abun-dances were found in spring but the greatest biodiversity was observed in Augustand September, both findings having particular relevance to management issues.

1.2.5 FACTORS AFFECTING STREAM HABITAT

Any disturbances to stream structure and/or function will affect the habitat availableto riverine biota. The natural annual hydrological cycle will result in seasonal mod-ifications to depth, velocity, bed hydraulics and channel morphometry to which the


Habitat Assessment Methods 25

Table 1.2.1 Major disturbances and their primary effects on stream habitat

Disturbance Impact Primary effect

Flow regulation Increased flow Substratum instabilityReduced flow Loss of wetted area, sedimentationConstant flow Substratum stability, growth of macrophytes,

loss of floodplain habitatVariable flow Substratum instabilityFlood relief channel Reduction of flushing flows in main channel,

loss of floodplain habitatEngineering Bridge construction Substratum disturbance

Channelization Bank structure, substratum, floodplaindisturbance, loss of riparian habitat

Dredging Substratum disturbance, sedimentationDam construction Altered flow regime, sedimentationRun-of-river diversions Altered flow regime, substratum modifications

Water supply anddisposal

Abstraction Reduced wetted area, sedimentation

Transfer Flow patterns, water chemistryPollution from effluents Increased nutrient load, algal growth.

subtratum hydraulicsCatchment

activitiesAgriculture Nutrients, pesticides, sedimentation, loss of

riparian habitatFlood relief / drainage Loss of riparian and wetland habitatsLand clearance Sedimentation, riparian modificationForestry SedimentationQuarrying and mining SedimentationConstruction work SedimentationUrbanization and industrial Channelization, altered hydrology, pollutionCatastrophic events

(vulcanism, earthquakes)Total environmental disturbance

biotic communities are adapted. Extreme natural events such as floods and droughts,together with anthropogenic disturbances, will further modify habitat conditions.

Major disturbances and their primary effects on stream habitat are listed in Table1.2.1. These disturbances will induce a variety of responses, depending on theirintensity, the river type in question and whether they are acting alone or with otherimpacting agents. Most disturbances have some effect, either direct or indirect,on riverine habitat and many of the resultant changes are deleterious to primaryproducers, macroinvertebrates and fish populations (see Wood and Armitage (1997)for a review of these impacts)

1.2.6 HABITAT ASSESSMENT METHODS

It is clear that most stresses/disturbances on the lotic system involve changes, eitherdirectly or indirectly, to the quantity and quality of instream and marginal habitat.



Habitat assessment and classification methodologies have arisen from the need toprotect and conserve the environment by monitoring the effects of disturbances andpredicting their possible impacts. These methods range from basic descriptions ofthe environment incorporating instream and riparian features (River Habitat Survey(Raven et al., 1997); SERCON – System for Evaluating Rivers for Conservation(Boon et al., 1997)) to those which relate habitat availability or characteristics to thecomposition and distribution of biotic communities (Rapid Bioassessment Protocols(Plafkin et al., 1989); HABSCORE (Milner et al., 1985); RIVPACS (Wright et al.,1993)). Lastly, there are systems such as the Instream Flow Incremental Methodology(IFIM) and Physical Habitat Simulation Modeling (PHABSIM) (Bovee, 1995) whichattempt to predict habitat availability in relation to flow conditions.

These systems can be used to classify and assess the quality and quantity of riverhabitats (Boon and Raven, 1998), provide tools for maintaining a sustainable man-agement regime for rivers (Raven and Boon, 2002) and present a means of assessingthe ecological integrity of running waters (Jungwirth et al., 2000). However, it isimportant when evaluating environmental quality that habitat modification is con-sidered alongside water quality. At present, it is quite possible to record top waterquality conditions in a river whose habitat has been severely modified.

1.2.7 FUTURE DIRECTIONS

The overwhelming importance of habitat in determining river biocoenoses is clear.A wealth of data are now available to demonstrate the need to maintain a diversityof habitat in the face of increasing pressures arising from catchment disturbanceand the demand for water for domestic and industrial purposes. What remains to beinvestigated are the mechanisms that give rise to habitat and the particular featuresof that habitat to which the benthic communities respond. Recent symposia haveaddressed the need to maintain ‘environmental flows’ (Petts, 2003) and it is therelationship between these flows, available habitat and the communities they supportthat requires more study.

In order to improve the use of the mesohabitat/habitat unit approach, it is importantthat habitat occurrence is predictable. That is to say, the physical conditions thatgive rise to a specific mesohabitat need to be defined in a range of channel andriver types. A number of authors have related the occurrence and distribution ofpools runs and riffles to geomorphological and hydrological features (Jowett, 1993;Cohen et al., 1998; Rowntree and Wadeson, 1996) and near-bed hydraulics havebeen used to develop a model (CASIMIR) which can be used to simulate the impactof different minimum flow regulations (Jorde and Bratrich, 1998). Further researchof this type, together with approaches for linking habitats, flow types and speciesrequirements (Newson et al., 1998), are necessary requirements to understand fullycommunity/habitat interactions and facilitate river management.

In recent years, there has been an increasing interest in habitat mapping and mod-eling, mainly in relation to environmental flow assessment (Tharme, 2003). Studies


References 27

may be divided into three basic types – those mainly concerned with mapping habitatover small and large scales, those whose prime interest is in the hydraulics of habitattypes, and those whose main aim is to model habitat response to change (see Hardy(1998) for a review of this subject area). The rapid advances in mapping technologyand the quantification of riverine habitats using airborne multispectral imagery(Whited et al., 2002) now provide a means of describing river habitat along its entirelength and in relation to landscape features in both large and small water courses.

The ability to predict changes in the relative proportions of habitat units in areach is central to the further development of successful tools for environmentalmanagement because such changes will affect the balance of faunal communitiesand provide a comprehensive assessment of environmental disturbance (Armitageand Cannan, 2000). Mapping and modelling approaches, in conjunction with habitat-specific faunal studies, will eventually provide the information needed to predict theoccurrence and distribution of habitat units and assess comprehensively ecologicalconditions in the whole river system.

Much current research tends to be fragmented, whereas management requires co-hesive long-term data which will build towards comprehensive data bases (Armitageet al., 2001). It is hoped that funding organizations will encourage the development ofstudies which will help build knowledge of habitat/biota interactions in a systematicway.

ACKNOWLEDGEMENTS

I am grateful to my colleagues at the Centre for Ecology and Hydrology for providinginformation and useful discussions, and to Marty Gurtz (US Geological Survey) andthe Environment Agency (UK) for supplying relevant reports. This work was partlyfunded by the Natural Environment Research Council.

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