A review of two rapid in stream habitat bio-assessments to evaluate surface aquatic impacts from bulk water pipelines in different streams in Gauteng

A review of two rapid in stream habitat bio-assessments to evaluate surface aquatic impacts from bulk water pipelines in different in AQUATIC HEALTH in the FACULTY OF SCIENCE at the U

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How to cite this thesis

Surname, Initial(s) (2012) Title of the thesis or dissertation (Doctoral Thesis / Master’s

Dissertation) Johannesburg: University of Johannesburg Available from:

http://hdl.handle.net/102000/0002 (Accessed: 22 August 2017)

A review of two rapid in stream habitat bio-assessments to evaluate surface aquatic impacts from bulk water pipelines in different

in AQUATIC HEALTH

in the FACULTY OF SCIENCE

at the

UNIVERSITY OF JOHANNESBURG

SUPERVISOR: DR AMINA NEL

JUNE 2018

LIST OF FIGURES vii

LIST OF TABLES ix

ABBREVIATIONS x

TERMS xii

ACKNOWLEDGEMENT xiv

ABSTRACT xv

CHAPTER 1 - GENERAL INTRODUCTION 16

1.1 Introduction 16

1.2 Hypothesis 21

1.3 Aims 21

1.4 Objectives 22

1.5 Study overview 22

CHAPTER 2 - LITERATURE REVIEW 24

2.1 Introduction 24

2.2 Bio-assessment for stream habitat quality 25

2.2.1 Water quality against guidelines and standards 26

2.2.2 Macro-invertebrates using SASS-5 26

2.2.3 Habitat assessment 33

2.2.4 The Rapid Habitat Assessment Method (RHAM) (DWAF, 2009) 34

2.2.5 Visual assessment approaches 36

2.2.6 The United States Environmental Protection Agency (US EPA) visual based assessments of river habitat integrity (Barbour et al., 1999) 36

2.2.7 Visual Biotopes assessment for macro-invertebrate habitat/ Integrated Habitat Assessment (IHAS) (McMillan, 1998) 37

2.3 Disturbances to in-streams habitat from Below Ground Bulk Water Pipelines (BGBWPL) 37

2.3.1 Rand Water Below Ground Bulk Water Pipeline (BGBWPL) 41

2.3.2 Methodology of installing pipelines 42

2.3.3 Rehabilitation after construction and maintenance 43

2.4 Description of the study area 44

2.4.1 Topography and Geology 47

2.4.2 Climate 49

2.4.3 Vegetation 49

2.5 Conclusion from the literature review 50

CHAPTER 3 – MATERIALS AND METHODS 54

3.1 Introduction 54

3.2 Primary objectives and approach of the study methods and materials design 54

3.3 Sampling sites 56

3.4 Bio-assessment tools 66

3.4.1 Water quality 66

3.4.2 Description of the water clarity tube: 67

3.4.3 Macro-invertebrate analysis using the South African Scoring System version 5 SASS-5 (Dickens and Graham, 2002) 68

3.4.4 Rapid Habitat Assessment Method (RHAM) (DWAF, 2009) 71

3.4.5 Figure 3.24: The use of a velocity flow plank (VFP) Depth measurement using the VFP parallel to flow (source, G Andrews, October 2017) 73

3.4.6 Visual Bio-assessment methods 73

CHAPTER 4 - RESULTS 78

4.2. In situ Water quality parameters analysis 78

4.1.1 pH 78

4.1.2 Temperature 78

4.1.3 Dissolves oxygen (DO) 80

4.1.4 Total dissolved Solids (TDS) 80

4.1.5 Clarity 80

4.2 South African Scoring System version 5 (SASS-5) 81

4.2.1 Composition of macro-invertebrates 81

4.2.1.1 Site 1: Composition of macro-invertebrates 81

4.2.1.2 Site 2: Composition of macro-invertebrates 82

4.2.1.3 Site 3: Composition of macro-invertebrates 82

4.2.2 Spatial trends 82

4.2.2.1 Site 1: spatial trends 82

4.2.2.2 Site 2: spatial trends 82

4.2.2.3 Site 3: spatial trends 83

4.2.3 Temporal trends Error! Bookmark not defined. 4.2.3.1 Site 1: Temporal trends Error! Bookmark not defined. 4.2.3.2 Site 2: Temporal trends Error! Bookmark not defined. 4.2.3.3 Site 3: Temporal trends Error! Bookmark not defined. 4.2.4 Biotopes 85

4.2.4.1 Site 1: Biotope results 85

4.2.4.2 Site 2: Biotope results 85

4.2.4.3 Site 3: Biotope results 85

4.3 Rapid Habitat Assessment Method for rivers (RHAM) 87

4.3.1 Temporal changes in velocity flow classes 87

4.3.1.1 Site 1: RHAM velocity class composition results 90

4.3.1.2 Site 2: RHAM velocity class composition results 90

4.3.1.3 Site 3: RHAM velocity class composition results 90

4.3.2 Substrate composition 90

4.3.2.1 Site 1: RHAM substrate composition results 92

4.3.2.2 Site 2: RHAM substrate composition results 92

4.3.2.3 Site 3: RHAM substrate composition results 95

4.4 Visual Bio-assessment methods 95

4.4.1 US EPA visual tool 95

4.4.1.1 US EPA spatial changes 95

4.4.1.2 US EPA temporal changes 95

4.4.1.3 US EPA tool results at the different sites 95

4.4.1.3.1 Site 1: US EPA 96

4.4.1.3.2 Site 1: US EPA 96

4.4.1.3.3 Site 1: US EPA 96

4.4.2 IHAS visual tool 97

4.4.2.1 IHAS spatial changes 97

4.4.2.2 IHAS temporal changes 97

4.4.2.2.1 Site 1: IHAS 98

4.4.2.2.2 Site 1: IHAS 98

4.4.2.2.3 Site 2: IHAS 99

4.4.2.2.4 Site 3: IHAS 99

CHAPTER 5 – DISCUSSION 101

5.1. In-situ Water quality parameters 101

5.1.1 pH 101

5.1.2 Temperature 102

5.1.3 Total Dissolved Solids (TDS) 102

5.1.4 Dissolved oxygen (DO) 103

5.1.5 Clarity 104

5.1.6 Summary remarks on in situ water quality 104

5.2 South African Scoring System version 5 (SASS-5) 104

5.2.1 Composition of macro-invertebrates 104

5.2.1.1 Site one Composition of macro-invertebrates 105

5.2.1.2 Site Two Composition of macro-invertebrates 106

5.2.1.3 Site three Composition of macro-invertebrates 107

5.2.2 Spatial and temporal trends across sites 107

5.2.2.1 Site 1 biotope discussion: 109

5.2.2.2 Site 2 biotope discussion: 111

5.2.2.3 Site 3 biotope discussion: 114

5.2.3 Summary remarks on SASS-5 for bio-assessment monitoring 115

5.3 Rapid Habitat Assessment Method for rivers (RHAM) 116

5.3.1 Velocity class composition observations 116

5.3.1.1 Site 1 (RHAM) velocity classes composition 117

5.3.1.2 Site 2 (RHAM) velocity classes composition 117

5.3.1.3 Site 3 (RHAM) velocity classes composition 118

5.3.2 Substrates composition observation 118

5.3.2.1 Site 1 (RHAM) substrate composition 119

5.3.2.2 Site 2(RHAM) substrate composition 119

5.3.2.3 Site 3 (RHAM) substrate composition 119

5.3.3 Temporal observations of substrate compositions 120

5.3.4 Concluding remarks on RHAM 120

5.4 Visual Bio-assessment methods 120

5.4.1 (US EPA) United States environmental protection agency 121

5.4.1.1 Site 1 US EPA 121

5.4.1.2 Site 2 US EPA 122

5.4.1.3 Site 3 US EPA 122

5.4.2 Summary remarks on US EPA 123

5.4.3 (IHAS) visual bio-assessment discussion 123

5.4.3.1 Site 1 IHAS 127

5.4.3.2 Site 2 IHAS 127

5.4.3.3 Site 3 IHAS 128

5.4.4 Summary remarks on IHAS 128

CHAPTER 6 – CONCLUSION 129

6.1 Conclusion and recommendations 129

6.2 Aims 129

6.3 Objectives 131

6.4 Hypothesis 132

6.5 Recommendations 133

Annexures 169

Annexure A: In-situ Water Quality 169

The following Extracts from the: SOUTH AFRICAN WATER QUALITY GUIDELINES, Volume 7: Aquatic Ecosystems, First Edition, 1996 Are provided as further information to interpreted the data 169

Annexure B: SASS-5 172

Annexure B: ITEM 1 Extracts from : The South African Scoring System (SASS) Version 5 Rapid Bio-assessment Method for Rivers (Dickens and Graham, 2002) are provided for further clarification on sampling method 172

Annexure B: ITEM 2 The river health program, DWAAF, WRC, DEAT, SASS-5 official field sheet 176

Annexure C: RHAM 181

Annexure C: ITEM 2 RHAM spread sheet 183

Annexure D: US EPA 188

The US EPA visual-based habitat assessment manual 188

The US EPA visual-based habitat assessment field sheet 188

Annexure E: IHAS 191

FIGURE 2.1: A CONCEPT OF THE THRESHOLD AT WHICH A RIVER BECOMES

UNHEALTHY AND WHEN A DISTURBANCE BECOMES UNSUSTAINABLE (MEYER,

1997 ADOPTED FROM KARR, 1999) 24

FIGURE 2 2: A TYPICAL PIPELINE CONSTRUCTION SHOWING RIGHT-OF-WAY (ROW),

TOPSOIL STRIPPING AND A TRENCH IN WHICH THE PIPE IS BURIED (DESSERUD

ET AL., 2010) 42

FIGURE 2 3:PIPE JACKING UNDER A RIVER (ZOLMAT, 2018) 43

FIGURE 2 4:DIFFERENT STUDY SITES AND QUATERNARY DRAINAGE REGIONS

(GENERATED BY RAND WATER GIS SECTION, 2018) 46

FIGURE 2 5:SAMPLING SITES AWAY FROM POTENTIAL ACID MINE DRAIN POLLUTION AND SURROUNDING HEAVY INDUSTRIES LOCATED AROUND MINES (ADAPTION

FROM WEPENER ET AL., 2015) 47

FIGURE 2.6: A CONTOUR MAP OF THE STUDY AREA (SOURCE, RAND WATER GIS SECTION) 48

FIGURE 2.7: A VEGETATION MAP INDICATING THE THREE SAMPLING SITES (SANBI, 2017) 50

FIGURE 2.8: SUMMARY APPROACH TO BIOMONITORING BGBWPL PRODUCED FROM INFORMATION IN THE LITERATURE REVIEW 52

FIGURE 3.1: SITE 1, (US) VIEW FROM THE ROAD BRIDGE ON COLUMBINE AVE

(PHOTOGRAPH SOURCE, N ANDREWS, NOVEMBER 2017) 57

FIGURE 3.2: SITE 1 SUB SITES TRANSECTS AND PIPELINE POSITIONS DELIMITATED (ADAPTED FROM GOOGLE MAPS, OCTOBER 2017) 58

FIGURE 3.3: SITE 1 IN 2008 DURING THE CONSTRUCTION OF THE ROCK MATRICES (SOURCE, G ANDREWS) 58

FIGURE 3.4: SITE2 (US), DEMONSTRATES THE SITE TRANSECT POSITIONS FROM THE UPSTREAM (US) VIEW (SOURCE,, G ANDREWS, JULY 2017) 59

FIGURE 3.5: SITE 2 (ON), DEPICTING THE SITE TRANSECTS POSITIONS FROM ON THE PIPELINE (ON) (SOURCE,, G ANDREWS, JULY 2017) 59

FIGURE 3.6: SITE 2(DS), DEPICTING THE SITE TERRAIN AND LOCATION FROM

DOWNSTREAM OF THE PIPELINE (DS) (SOURCE,, G ANDREWS, JULY 2017) 60

FIGURE 3.7: SITE 2 DEMONSTRATES THE SITE LOCATION FROM ABOVE NEAR SILVER

A (ON) VIEW (SOURCE, N ANDREWS, NOVEMBER 2017) 60

FIGURE 3.8: SITE 2 SUB SITES TRANSECTS AND PIPELINE POSITIONS DELIMITATED (ADAPTED FROM GOOGLE MAPS, OCTOBER 2017) 61

FIGURE 3.9: SITE 2, CONSTRUCTION OF THE ROCK MATRICES DURING 2008

FIGURE 3.15:SITE 3 (ON) DETAIL OF CONCRETE ENCASEMENT OVER THE

PIPELINE(SOURCE,, G ANDREWS, JULY 2017) 64

FIGURE 3 16: SITE 3 (US) POSITION OF TRANSECTS (SOURCE, G ANDREWS, JULY

2017) (SOURCE,, G ANDREWS, JULY 2017) 65

FIGURE 3.17:SITE 3 (ON) POSITION OF TRANSECTS SHOWN IN YELLOW LINES

(SOURCE, G ANDREWS, JULY 2017) 65

FIGURE 3.18:SITE 3 (DS) POSITION OF TRANSECTS (SOURCE, G ANDREWS, JULY

2017) 66

FIGURE 3.19:YSI PRO PLUS MULTI-METER USED TO MONITOR IN SITU WATER

QUALITY PARAMETERS (SOURCE, G ANDREWS, 2017) 67

FIGURE 3.20:WATER CLARITY TUBE IN USE (SOURCE, G ANDREWS, 2017) 68

FIGURE 3.21:EQUIPMENT USED FOR SASS-5 SAMPLING INCLUDE: A) BAGS AND

CONTAINERS, B) BOOTS, C) NET, D) TRAY, E) STOP WATCH, F) MAGNIFYING LENSES AND G) MICROSCOPE 69

FIGURE 3.22:A DEMONSTRATION OF SASS-5 SAMPLING OF THE BIOTOPES STONE CURRENT (SIC) AND GRAVEL, SAND AND MUD (GSM) (SOURCE, G ANDREWS, OCTOBER 2017) 70 3.4.5 FIGURE 3.24: THE USE OF A VELOCITY FLOW PLANK (VFP) DEPTH

IN-MEASUREMENT USING THE VFP PARALLEL TO FLOW (SOURCE, G ANDREWS, OCTOBER 2017) 73

FIGURE 3 23: A SCHEMATIC LAYOUT OF SITE 1, ON (NOT TO SCALE), AND A

CORRESPONDING DELINEATED TRANSECTS AND NUMBER NOTATION 74

FIGURE 4.1: SASS-5 PARAMETERS WITHIN SUB SITES – UPSTREAM (US) ON THE

PIPELINE (ON) AND DOWNSTREAM (DS) ERROR! BOOKMARK NOT DEFINED FIGURE 4.2: SASS-5 SCORES WITHIN BIOTOPES (STONES (S), VEGETATION (VEG), GRAVEL SAND AND MUD (GSM)) 86

FIGURE 4.4: SITE 1:1 ST AND 2 ND SAMPLING PERIOD SHOWING THE SPATIAL

TEMPORAL COMPOSITIONS OF THE VARIOUS WATER VELOCITY CLASSES AT DIFFERENT SUB SITES IN THE RIVER 89

FIGURE 4.5: SITE 1:TEMPORAL CHANGES IN THE PERCENTAGE PROPORTION OF WATER VELOCITY CLASSES BETWEEN THE 1 ST AND 2 ND SAMPLING PERIODS AT SITE 1 91

FIGURE 4.6: SUBSTRATE COMPOSITION ON SITE 2 93

FIGURE 4.7: TEMPORAL CHANGES IN SUBSTRATE COMPOSITION AT SITE 1, 2 AND 394

FIGURE 4.8: COMPARATIVE DATA FROM IHAS AND US EPA FOR 1 ST AND 2 ND SAMPLING PERIOD 100

FIGURE 5.1: SUBSTRATE COMPOSITIONS FROM SITE 1, ON, DURING THE 1 ST

SAMPLING PERIOD (A) AND 2 ND SAMPLING PERIOD (B) USING THE RHAM METHOD DISPLAYED THE DOMINANT SAND BIOTOPE IN SITE 1 111

FIGURE 5.2: SUBSTRATE COMPOSITIONS FROM SITE 1 ON (1 ST (A) AND 2 ND (B)

SAMPLING PERIODS) USING THE RHAM METHOD DISPLAYED THE DOMINANT COBBLE/STONE BIOTOPE AT SITE 2 112

FIGURE 5.3: 1 ST AND 2 ND SAMPLING PERIOD DATA, OVERLAY OF VISUAL METHODS SASS-5 TAXA AND SASS SCORES 125

FIGURE 5.4: SASS-5 TAXON WITHIN BIOTOPES STONES (S), VEGETATION (VEG), GRAVEL SAND AND MUD (GSM) AND SUB SITES (UPSTREAM (US), ON THE

PIPELINE (ON) AND DOWNSTREAM (DS)) INCLUDING INSTREAM VISUAL

ASSESSMENT (IHAS) 126

ANNEXURE C: FIGURE 1 DIAGRAM OF A CROSS-SECTION INDICATE THE POSITIONS

FOR TAKING READINGS ALONG THE LINE (SOURCE, DWAF., 2009) 181

ANNEXURE C: FIGURE 2: GUIDELINE ON SPACING CROSS-SECTION FOR DATA

COLLECTION (SOURCE, DWAF., 2009) 182

ANNEXURE C: FIGURE 3 DIAGRAM OF AN EXAMPLE OF THE SPACING OF CROSS

SECTIONS (SOURCE, DWAF., 2009) 182

ANNEXURE C: FIGURE 4 1 ST SAMPLING, ALL SITES AND SUB SITES SPATIAL AND TEMPORAL COMPARATIVE VELOCITY CLASSES 184

ANNEXURE C: FIGURE 5 SUBSTRATE COMPOSITIONS USING RHAM METHOD FOR

ANNEXURE C: FIGURE 6 SUBSTRATE COMPOSITIONS USING RHAM METHOD FOR

SITE 2 186

ANNEXURE C:: FIGURE 7 SUBSTRATE COMPOSITIONS USING RHAM METHOD FOR

LIST OF TABLES

TABLE 2.1: WATER QUALITY VARIABLES IN THE AQUATIC LANDSCAPE 30

TABLE 2.2: POTENTIAL VISUAL OBSERVATION AND HOW IT RELATES TO HABITAT INTEGRITY 35

TABLE 2.3: THE US EPA HABITAT RESPONSE VISUAL PARAMETERS AND BGBWPL

(ADAPTED FROM BARBOUR ET AL., 1999) 40

TABLE 3.1: ATTRIBUTES OF THE THREE SAMPLING SITES 55

TABLE 4.1: IN SITU WATER QUALITY RESULTS FOR THE 1ST AND 2ND SAMPLING PERIOD (SP), WITH THE RELEVANT TARGET WATER QUALITY RANGE (TWQR) OF THE WATER QUALITY GUIDELINES FOR AQUATIC ECOSYSTEMS (WQG/AE),

(DWAF, 1996) 79

TABLE 4.2: SUMMARY OF SASS-5 RESULTS FROM THE 1 ST AND 2 ND SAMPLING

PERIOD 83

TABLE 4.3: SASS-5 TEMPORAL CHANGES BETWEEN THE 1ST AND 2 ND SAMPLING

PERIOD ERROR! BOOKMARK NOT DEFINED TABLE 4.4: FIRST SAMPLING PERIOD VELOCITY FLOW CLASSES 88

TABLE 4.5: SECOND SAMPLING VELOCITY FLOW CLASSES 88

TABLE 4.6: TEMPORAL DIFFERENCES OF VELOCITY CLASSES BETWEEN THE 1ST SAMPLING PERIOD AND THE 2ND SAMPLING PERIOD (*RED FIGURES ARE

NEGATIVE VALUES.) 88

TABLE 4.7: US EPA RESULTS ON SPATIAL AND TEMPORAL VARIATION 96

TABLE 4.8: IHAS RESULTS ON SPATIAL AND TEMPORAL VARIATION 97

TABLE 4.9: INTEGRATED HABITAT ASSESSMENT SYSTEM (IHAS) ADAPTED FROM MCMILLAN (1998) 98

Annexure B: Table 1 SASS-5 Field Sheet……… …157

Annexure B: Table 2 1st and 2nd sampling list of macro-invertebrates

encounter indicating sensitivity scores, (Adapted from Gerber and Gabriel 2002)……….………158

Annexure B: Table 3 Data collected during the 1st SASS-5 sampling, only

listing applicable taxa (Adapted Dickens and

Annexure B: Table 4 Data collected during the 2nd SASS-5 sampling, only

listing applicable taxa (Adapted Dickens and Graham, 2002)……… …….160

Annexure D: Table 1 Extract from field data sheet of US EPA…………168

Annexure D: Table 2 :US EPA results for 1st and 2nd sampling period 170

Annexure E: Table 1 IHA results for 1 st and 2 nd sampling period ………171

ABBREVIATIONS

ANZECC Australia and New Zealand Environment and Conservation Council ASPT Average Score per Taxon

BGBWPL Below Ground Bulk Water Pipelines

BGIS Biodiversity Geo-referenced information

CMA’s Catchment Management Agencies

DEA Department of Environmental Affairs

DO Dissolved oxygen

DWAF Department of Water and Forestry

DWAS Department of Water and Sanitation

EI Ecological Infrastructure

EPA Environmental Protection

EU European Union

GIS Geographic Information System

GSM Gravel Sand and Mud

MEPC Ministry of Environmental Conservation of China

NEMA South Africa National Environmental Management Act

NWA National Water Act

OEH The Australian Office of Environment and Heritage

ON On the pipeline footprint

PDA Primary Drainage Area

QDA Quaternary Drainage Area

RBPs Rapid Bio-assessment Protocols

RHAM Rapid Habitat Assessment Method

SA South Africa

SANBI South African National Biodiversity Institute

SASS-5 South African Scoring System Version 5

TDS Total dissolved Solids

TWQR Target Water Quality Range

US EPA United States Environmental Protection Agency

VEG Vegetation

VFP Velocity Flow Plank

WHO World health organisation

WMA Water Management Area

WQ Water Quality

WQG/AE Water Quality Guideline for the Aquatic Ecosystem

NEMBA National Environmental Management Biodiversity Act No 10 of 2004

TERMS

TRANSECT: A river transect line intercept, is a line determined by two points on

opposite stream banks and is useful as the location reference for the measurement of habitat conditions This line intercept allows for repeated measurements at exactly the same location at different times and yet allows the randomness in site selection needed to meet statistical requirements (Figure 3.7)

(Platts et al., 1983)

EPIFAUNAL SUBSTRATE/AVAILABLE COVER

Includes the relative quantity and variety of natural structures in the stream, such

as cobble (riffles), large rocks, fallen trees, logs and branches, and undercut banks, available as refuge, feeding, or sites for spawning and nursery functions

of aquatic macro fauna A wide variety and/or abundance of submerged structures in the stream provide macro-invertebrates and fish with a large number

of niches, thus increasing habitat diversity (Table 2.3) (Barbour et al., 1999)

EMBEDDEDNESS

Refers to the extent to which rocks (gravel, cobble, and boulders) and snags are covered or sunken into the silt, sand, or mud of the stream bottom Generally, as rocks become embedded, the surface area available to macro-invertebrates and fish (shelter, spawning, and egg incubation) is decreased Embeddedness is a result of large-scale sediment movement and deposition, and is a parameter

evaluated in the riffles and runs of high gradient streams (Table 2.3) (Barbour et al., 1999)

CHANNEL ALTERATION

Is a measure of large-scale changes in the shape of the stream channel Many streams in urban and agricultural areas have been straightened, deepened, or diverted into concrete channels, often for flood control or irrigation purposes Such streams have far fewer natural habitats for fish, macro-invertebrates, and plants than do naturally meandering streams Channel alteration is present when artificial embankments, riprap, and other forms of artificial bank stabilization or structures are present; when the stream is very straight for significant distances; when dams and bridges are present; and when other such changes have

occurred Scouring is often associated with channel alteration (Table 2.3)

(Barbour et al., 1999)

BANK STABILITY

Measures whether the stream banks are eroded (or have the potential for erosion) Steep banks are more likely to collapse and suffer from erosion than are gently sloping banks, and are therefore considered to be unstable Signs of erosion include crumbling, un-vegetated banks, exposed tree roots, and exposed soil Eroded banks indicate a problem of sediment movement and deposition, and suggest a scarcity of cover and organic input to streams Each bank is evaluated separately and the cumulative score (right and left) is used for this

parameter (Table 2.3) (Barbour et al., 1999)

ACKNOWLEDGEMENT

My supervisor Dr Nel, for taking me on as a student and making the time to give attention to my work She showed professionalism throughout the study Her commitment and dedication with sharp precision and attention to detail; throughout the project was spot on She provided an enabling environment with calm, balance, patience and positive outlook I will always be proud to have been her student

My co supervisor, Mr Hoy, for his support, guidance, intellectual input, editing and attention to detail For sharing his own experiences while undertaking his doctorate He has also been my manager for a greater part of my working career and has always supported me with much needed articulate editing detail Thank you for walking this path with me as well I will be proud to see your name as a

me to better understand RHAM Irwin from ARMOUR for the company during field work and sharing data Klipriverberg Nature Reserve for the access to the property My dog Co Co and the cat Ploppy that stayed with me while working

My family for support and encouragement throughout the study My daughter Gainor for photography and help with field work My brother-in-law Noel, for aerial photography My husband Norman for support and love Granting me the space and time to undertake the study and taking up the slack while I was working on the thesis I hope that my colleagues will be encouraged by my work and also want to undertake further studies

ABSTRACT

The purpose of the study was to review selected bio-assessment tools for suitability to monitoring the habitat impacts of below ground bulk water pipelines (BGBWPL) The need for this study arose from the fact that BGBWPL are required to provide essential services, but, it also impacts on rivers temporally

(Reid et al., 2010; Castro, 2015), by altering river and stream channels as well

as disrupting the bed and banks of rivers (Lévesque and Dubé, 2007) However, very little research could be found to explain how these potential impacts (BGBWPL) affected habitat integrity Also, very little could be found as to how to

go about biomonitoring habitat integrity impacts specifically from BGBWPL Research and monitoring of BGBWPLs are required to mitigate and manage

these impacts (Marzin et al., 2013) To achieve the purpose of the study, selected

available bio-assessment tools were reviewed at three sites and two sampling periods Each selected bio-assessment tool was used as per the manuals The results showed that all the selected methods could provide spatial trend data that could with replication be used to confirm impacts of BGBWPLs None of the tools provided a “one stop shop” for use in biomonitoring of BGBWPLs and should be used in combination with each other By the overlaying physical habitat observation on the SASS data, a correlation could be indicated regarding the response from the macro-invertebrates It was found that the selected bio-assessment tools provide promise to be suitable to monitor the recovery of construction sites after installation of BGBWPLs but further research and investigations are required

CHAPTER 1 - GENERAL INTRODUCTION

1.1 Introduction

“Water is life, and clean water means health.” Audrey Hepburn

species extinction However, freshwater environments have higher occurrences of

species extinction than in terrestrial ecosystems (Revenga et al., 2005) This has

resulted in heightened global awareness for the need for sustainability of the health and habitat integrity of rivers (Karr, 1991; Griffiths, 2002)

Rivers are globally affected by a variety of stressors, including anthropogenic pollution

and various degradations of river habitat (Vörösmarty et al., 2010) River research in

turn provide a framework for mitigation strategies to avert negative impacts on “river

health” (Marzin et al., 2013) Habitat availability is only one aspect of “river health”

(Figure 1.1) but habitat degradation through anthropogenic development is a key

driver of biodiversity loss (Chong, 2014; Giersch et al., 2014; Jones, 2014; Joppa et al., 2016) and tropic collapse (Dobson et al., 2006). A direct relationship between

stressors and integrity can be noted (Dudgeon et al., 2006) Physical habitat is a

fundamental requirement in maintaining diverse, functional aquatic communities in surface waters (Rankin, 1995) Thus, the physical habitat is a template for observing the dynamics of ecosystems responses including macro-invertebrates to anthropogenic activities Habitat quality is a key driver to which macro-invertebrates

respond (Parsons et al., 2004)

Figure 1.1: Concept of river “health” (adapted from Karr, 1996; Meyer, 1997; Boulton,

1999)

Globally, there is a recognition that anthropogenic activities in natural surface water require management as this has become unsustainable This has encouraged a global alignment towards regulations to protect natural surface water such as rivers Terrado

et al (2016), included examples of the 2012 European Parliament to halt the loss of

biodiversity and ecosystem services in the European Union (EU) by year 2020 (WHO, 2004), the United States of America (USA) Endangered Species Act of 1973 (Scott, 2006), and the establishment of the Environmental Protection Agency (EPA) in 1986

Laws oriented to restoring and maintaining the biological integrity of freshwater ecosystems include the Water Framework Directive of 2000 in the European Union (EU), the Clean Water Act of 1965 in the United States of America (USA) (Karr, 1991; Griffiths, 2002; and Scott, 2006) Major conservation efforts exist in emerging economies such as China with their Strategy and Action Plan for Biodiversity Conservation of 2010 (MEPC, 2011) Similarly, some Latin American countries have progressive conservation policies such as Costa Rica's Biodiversity Law of 1998 and Colombia's National System of Protected Areas of 2010 (Solís-Rivera and Madrigal-

Cordero, 1999;) The Canadian Water Quality Guidelines (Saffran et al., 2001), is a

Ecological integrity:

Capacity to support/maintain natural and

balanced, integrative, adaptive

Clean water for drinking and washing;

Environment for recreation and

spiritual renewal

Services:

Cleansing/detoxifying water Producing fish and shellfish;

Providing aesthetic pleasure;

Maintaining water supply;

Storing/regenerating essential elements

further example of the thrust to protect aquatic environments South Africa (SA) has implemented similar legislation that include the National Environmental Management Biodiversity (NEMBA) Act No 10 of 2004, Alien and Invasive Species Regulations of

2014 and the Draft National Biodiversity offset policy (DEA, 2017)

The National Water Act (NWA) Act No 108 of 1989, through the ecological reserve, aims to satisfy both human needs as well as to protect the aquatic ecosystems, so that sustainable development can be obtainable (DWAS, 2017) People are required

to strive to protect and manage these scarce water resources strategically (Nel et al.,

2013) South Africa has increasing infrastructure demands that contribute to

unsustainable degradation of the environment (De Klerk et al., 2016) In SA a strong

urban development agenda is present guided by the role of Ecological Infrastructure

Development (EID) and Built Infrastructure to enable growth and development (Dini et al., 2016; Maze and Driver, 2016) This however, must meet the Sustainable Development Goals (SDGs) (Cumming et al., 2017) Thus, in SA developing essential

services such as the supply of water, must account and mitigate potential negative impacts to these scarce water resources (NWA, 1998)

Essential services, such as below ground bulk water pipelines (BGBWPL) across the world provide water for development to economic urban hubs of countries However, BGBWPLs are also another anthropogenic human impact in the system with the

potential of short and long-term negative impacts (Reid et al., 2010; Castro et al.,

2015) Below Ground Bulk Water Pipelines alter river and stream channels, hence may have detrimental effects on aquatic ecosystems (Lévesque and Dubé, 2007) Literature indicates that BGBWPL can have an impact on in-stream habitat integrity and a bio-monitoring tool for BGBWPL has become pertinent to establish the extent

of this potential impact to the “river health” (Figure 1.1)

The habitat integrity of a river refers to the maintenance of a balanced composition of physico-chemical and habitat characteristics These parameters are evaluated on temporal and spatial scales Habitat integrity is comparable to the characteristics of natural habitats of the region or alternative a reference site (Kleynhans, 1996) Habitat integrity is also a surrogate for the assessment of biological responses to drivers of

The habitat-heterogeneity hypothesis states that an increase in habitat heterogeneity leads to an increase in species diversity due to nice space (creation of appropriate habitats) (Cramer and Willig, 2004) Environmental heterogeneity affects population dynamics and community structure Although community-level analyses of effects of habitat heterogeneity on species diversity are important, this does not reveal the

mechanism through which heterogeneity affects diversity (Palmer et al., 1990; Cramer and Willig, 2002; Cramer and Willig, 2004; Merz et al., 2005) O’loughlin (1986), noted that vegetation recovery may not necessary indicate the functional recovery of a watercourse Thus, the critical aspects that should be monitored to establish resilience and/or recovery after BGBWPL’s are installed, include the following from the Relative Risk Method by O’Brien and Wepener (2012):

 The possible identified habitat stressors that are altering the composition and intensity of macro-invertebrates, habitat change, flow alteration (Nelson and

Lieberman, 2002), erosion or sedimentation (Jun et al., 2011), fragmentation of natural areas and loss of habitat complexity/heterogeneity (Frissel et al., 1996; Merz et al.,

2005)

 The receptor would be the in-stream habitat (Habitat integrity) which include Hydrological modification, physico-chemical modification, bed modification and connectivity modification (Kleynhans and Louw, 2007)

This study attempts to evaluate various methods for use in understanding the role that BGBWPL have as an anthropogenic impact in rivers Bio-assessment tools assess the health of aquatic ecosystems Aquatic ecosystems partly consist of abiotic (physical and chemical) and biotic components, as well as the habitats and ecological processes contained within rivers (DWAF, 1996) The identified bio-assessment tools under review were selected to discern differences and comparisons between a reference point upstream (US), changes occurring on the pipeline footprint (ON), and then the receiving environment downstream (DS)

Three sites (streams) were selected within the same quaternary catchment of the Klip River system (Figure 1.1) Site 1 and 2 are part of the Bloubos Spruit and had been

rehabilitated with rock matrices Site 3 is part of the Glenvista Spruit with a concrete encasement

The selection of assessment tools included the following:

Physical habitat integrity: using tools to review the effectiveness of visual assessment for monitoring in stream integrity such as:

 The United States Environmental Protection Agency (US EPA) visual based

assessments of river habitat integrity (Barbour et al., 1999)

 Integrated habitat assessment system (IHAS version 2)(IHAS)(McMillan, 1998)

 Rapid Habitat Assessment Method (RHAM) (DWAF, 2009)

Biota composition was determined by sampling macro-invertebrates using SASS-5 (Dickens and Graham, 2002)

Figure 1.2: The location of the three sites in two tributaries of the headwaters of the

Klip River (Generated by Rand Water GIS, 2017)

In-situ water quality assessment included parameters such as temperature, electrical

conductivity, oxygen (mg/L and % saturation), pH, and clarity (Holmes, 1996; Davies and Day 1998; Dallas and Day, 2004; Dallas, 2007a)

Blouboss

1.2 Hypothesis

First Hypothesis

Ho a - the South African Scoring System, version 5 (SASS-5) bio-assessment tool, is suitable for use, to indicate the response of macro-invertebrates to below ground bulk water pipelines

Second Hypothesis

Ho b - the visual based habitat bio-assessments, United States Environmental Protection Agency (US EPA), Integrated Habitat Assessment System, version 2 (IHAS) and Rapid Habitat Assessment Method (RHAM), are suitable to monitor below ground bulk water pipeline river crossings

1.3 Aims

Four aims were set for this study

The first aim of the study was to confirm the suitability of SASS-5 for monitoring invertebrate responses to BGBWPL

macro-Secondly, to confirm the relevance of The Rapid Habitat Assessment Method (RHAM)

to provide guidance to manage and mitigate instream physical habitat anthropogenic impacts from BGBWPLs

Thirdly, to confirm the relevance of visual - Integrated Habitat Assessment (IHAS) for instream biotope assessment methods when compared to measuring habitat indices for monitoring instream habitat suitability for macro-invertebrates

Fourthly, to confirm the relevance of visual geomorphic assessment method of river integrity protocols from United States Environmental Protection Agency (US EPA) are suitable to assess habitat quality of BGBWPLs

1.4 Objectives

Six objectives were set for the study in reviewing selected bio-assessment tools for the purpose of BGBWPL management and monitoring

1 The assessment of physico-chemical water quality variables of selected sites

2 The assessment of spatial and temporal variation of aquatic macro-invertebrate communities of selected sites

3 The assessment of spatial and temporal variation of aquatic macro-invertebrate communities between biotopes of selected sites

4 The assessment of spatial and temporal variation of water velocity flow classes

5 The assessment temporal variation of substrates

6 The comparison of spatial and temporal variation between aquatic invertebrate communities and visual habitat assessments- (Integrated Habitat Assessment IHAS and United States Environmental Protection Agency - US EPA) of selected sites

macro-1.5 Study overview

CHAPTER 1 - GENERAL INTRODUCTION

In the introduction, a general summary of the project and study area is presented The study hypothesis, aims and objectives are set out

CHAPTER 2 - LITERATURE REVIEW

The literature review provides the background to river integrity concepts in terms of habitat A background of BGBWPLs and installation is provided followed by the impacts that BGBWPLs have to the in stream river habitat integrity A basic outline of rehabilitation after construction of BGBWPL is provided This is followed by a description of the study area, topography and geology, climate, and vegetation Then the application of the selected bio-assessment tools is discussed The literary review

is concluded with a summary that provides direction for the materials methods to follow

CHAPTER 3 – MATERIALS AND METHODS

A background of the sampling sites and sub sites is provided It also describes the catchment attributes within the quaternary drainage area as well as the methods undertaken to gather data for the project

CHAPTER 4 – RESULTS

The results of each of the selected methods are presented This included in situ water

quality parameters, response of macro-invertebrates to BGBWPL habitats i.e quantification of velocity flow classes for macro-invertebrates with their substrate compositions Two different visual evaluation methods, one in stream and the other a general geomorphological approach, are presented

Statistical analyses were not provided as the study consists of a review of the methods and not to prove the impacts from pipelines

CHAPTER 5 – DISCUSSION

The results are discussed and relevant literature is recapped Noteworthy observations are highlighted and suggestions as to what the data could mean in context to BGBWPL are proposed It concludes with insights as to how the information may be applied to meet monitoring and maintenance of BGBWPL

CHAPTER 6 – CONCLUSION AND RECOMMENDATIONS

The concluding remark of the study revisits the study hypothesis, aims and objectives

as set out in chapter 1

CHAPTER 2 - LITERATURE REVIEW

“river health” (Figure 1.1), is a balance between ecological and human values (Karr, 1996; Meyer, 1997; Karr, 1999) The resilience of biological systems contributing to its

“health” are difficult to define and measure (Nilsson and Grelsson, 1995; Karr, 1999) The interaction of biogeographic and evolutionary processes in the regional climatic and geological context may be small but, the cumulative impacts even when small, may be more substantial (Karr, 1999) (Figure 2.1)

Figure 2.1: A concept of the threshold at which a river becomes unhealthy and when

a disturbance becomes unsustainable (Meyer, 1997 adopted from Karr, 1999)

Nothing

Alive

Severe

Disturbance

Gradient of Biological Condition

Gradient of Human Disturbance

Pristine

No of Minimal Disturbance

Integrity

2.2 Bio-assessment for stream habitat quality

The monitoring of rivers is not a new concept Empirical records of the Nile dating back

to 3000 BC showed the use of the Roda Nilometer which recorded the annual flood that fertilised the delta with nutrient rich silt (Newson, 2009)

The monitoring of rivers through bio-assessments however, can provide insight of aquatic responses to land use (Allan, 2004) and remediation (Karr, 1996) The habitat integrity of a river refers to the maintenance of a balanced composition of physico-chemical and habitat characteristics on a temporal and spatial scale that are comparable to the characteristics of natural habitats of the region (Kleynhans, 1996) Water quality along with habitat assessment and biota observations, are all aspects of biomonitoring (Bredenhand, 2005)

Davies and Day (1998) state that an ecosystem comprises of living and non-living attributes The water quality, river channel and its embankments are non-living, while the living components are the biotic aspects e.g macro-invertebrates The non-living

habitat components include biotopes It is accepted internationally (Pashkevich et al.,1996; Merz et al., 2005; Saliu et al., 2007; Jiang et al., 2010) and in South Africa

(SA) that biotopes for macro-invertebrates can be differentiated between, based on hydraulic, substratum (stones, vegetation or sand) and vegetation characteristics (Dickens and Graham, 2002; Thirion, 2016)

Each river is unique and functions in a slightly different way Understanding these interrelationships requires bio-assessments (O’Keeffe, and Dickens, 2000) However, rivers are also dynamic and change constantly (Karr, 1999) Instream biota is naturally ever changing in response to geomorphology (Braat and Kleinhans, 2017) or in line with the river continuum concept (Brooks, 2017) Extreme seasonal, cyclic, or unpredictable hydrologic fluxes are considered natural events rather than disturbances (Karr, 1996; Davies and Day, 1998; Dale and Beyeler, 2001) In fact, rivers are in a state of flux between one set of equilibriums and the next (Tucker and Whipple, 2002)

2.2.1 Water quality against guidelines and standards

Water quality is essential to the health of the ecosystem It is an assessment against parameters for specific purposes (recreation; environmental; drinking and industrial) (Kleynhans, 1996)

International examples of guidelines for the water quality include the World Health Organisation (WHO, 2004) that produced international norms used as the basis for regulation and standard settings worldwide The Australian and New Zealand Guidelines for Fresh and Marine Water Quality are used for the national management strategy (ANZECC, 1992; ANZECC, 2000; OEH, 2017)

The South African Water Quality Guidelines (WQG) Vol 1 – 6 and 8 are for drinking water and Vol 7 relates to the aquatic environments (DWAF, 1996) and can be found

in Annexure A

Aquatic ecosystems’ water quality focuses on the issue-based management of water quality and the measurement of biological parameters that relate to physical and

chemical parameters in both water and sediment (Jun et al., 2011)

Water quality variables for aquatic health always include pH, water temperature, dissolved oxygen (DO), turbidity (TDS) and electrical conductivity (EC) Water quality often exhibit more variability than physical properties such as depth and flow in aquatic habitat that biota respond to (Holmes, 1996; Day, 2002) Electrical conductivity (EC), temperature, TDS and DO however, are the most important variables to track for habitat change caused by pollution, illegal dumping, litter, sediment from erosion (Jun

et al., 2011), point and defused discharges from storm water, sewerage works,

industrial and agricultural contaminants sources (Davies and Day, 1998) Each variable may have an impact on aquatic life and their ability to function optimally Table 2.1 lists the water quality variables and some known function and responses that can

be expected from each variable (For further detail on the understanding of the variable

please refer to Terms)

2.2.2 Macro-invertebrates using SASS-5

Fresh water ecosystems support remarkable biodiversity and abundance of

macro-group of organisms (i.e fish) available that are suitable for biomonitoring invertebrates form an essential component of the riverine ecosystem, as they play a role in purifying the water and providing a food source, that supports a huge food chain (Allan, 1995; Skorozjewski and De Moor, 1999; O’Keeffe and Dickens, 2000) The observation and monitoring of macro-invertebrates indicate community effects due to specific “stressors which are the drivers of response from macro-invertebrates Macro- invertebrates are thus considered acceptable indicators of river integrity, internationally” (Pretti and Cognetti-Varriale, 2001)

Macro-The advantages of using macro-invertebrates for biomonitoring include that:

 These organisms tend to move very little and are therefore representative of the

area where collected, ideal for comparative studies (Barbour et al., 1999)

 The macro-invertebrate’s short life cycle compared to that of fish, allows a quicker reaction to changes through changes to population and community

structure (Bonada et al., 2006; Bonada et al., 2007)

 As sediment dwellers, these organisms live and feed in, on, and around

sediments and can accumulate toxins, passing it up the food chain (Simpson et al., 2005; Jun et al., 2011)

 The assemblages occupy different trophic levels and react to pollution with varying degrees of tolerance making macro-invertebrates ideal for assessing

cumulative effects (Barbour et al., 1999)

 Macro-invertebrates exist abundantly in a wide range of aquatic habitats and water quality, unlike fish that often require conditions that are more specific and are therefore not commonly used (Thirion, 2007)

 Invertebrates respond to the quality of habitat type (Wohl et al., 1995)

However, benthic communities may change seasonally as invertebrates move though life cycles (Chutter, 1998)

Disadvantages of macro-invertebrate sampling for biomonitoring as per Dickens and Graham (2002), include:

 Quantitative sampling can be difficult

 Knowledge of life cycles is necessary to interpret absence of species

 Some groups are difficult to identify

Biological monitoring programs that assess the status of shallow streams in which it is possible to safely walk, are now well established in most states within the United

States of America (USA) (Barbour et al., 1999) and South Africa (Dickens and Graham, 2002; Thirion, 2007; Wepener et al., 2015) Short and long-term responses

to changes in the aquatic environment are well noted, since it interacts with each other and many macro-invertebrates occupy unique niche functions (i.e collectors, decomposers, predators, and grazers) (Brook, 2017) This interaction is more

descriptive than a purely taxonomic approach (Bonada et al., 2006) The use of

macroinvertebrates for bio assessment works best when the diversity of biotopes is wide and includes riffles or rapids, but it also produces valuable results from poor

habitats (Li et al., 2012) It is necessary to interpret the data in relation to habitat

quality, availability and diversity and ultimately also in relation to the ecological region from which it comes It is also necessary to interpret the data in relation to the season

of collection, as some natural variation will occur during the course of the year and between years

Riffle habitat, for example, have higher abundances and taxa richness when compared

to pools (Dudgeon, 2000; Nijboer and Smidt-Kloiber, 2004) It has also been noted that homogeneous streambed habitats with greater fine particles support lower

diversity and abundance (Li et al., 2012) Additionally, organic pollution could

transform the coarse substrate into an organic rich soft bottom, altering the community

structure to fewer tolerant species (Helson et al., 2006)

In SA, the South African Scoring System (SASS), Version 5, a Rapid Bio-assessment Method for Rivers (SASS-5)(Annexure B) is a recognised tool used by the National River Monitoring Program (NRMP) (Dickens and Graham, 2002)

The SASS-5 bio-monitoring tool for macro-invertebrates is based on the British Monitoring Working Party Method (BMWP) (Walley & Hawkes, 1996) and adapted for South African conditions by Chutter (1998) Since then it has undergone various upgrades to the current version 5 This version is also ISO 1400 compliant, cost effective, rapid and simple (Dickens and Graham, 2002)

The index makes use of family level macro-invertebrate data, collected under specific conditions in selected biotopes at each site It also provides sensitivity scores for each

taxon calculated and based on the derived sensitivity to organic pollution (Dickens and Graham, 2002) Individual taxon such as Ephemeroptera, Plecoptera and Trichoptera are associated as good water quality indicators (Suhaila and Che Salmah, 2014; Ab Hamid and Rawi, 2017) and are scored with higher sensitivity values

The tool presents the following applications:

 Monitoring of specifically organic pollution within streams (Dickens and Graham, 2002)

 Assessment of the current ecological state of a river or stream, based on the River Health Programme biomonitoring protocol and the National River Health Programme (DWS, 2017)

 Ecological Reserve determination as required by the South African National Water Act (1998)

According to Dickens and Graham (2002), the SASS-5 method is best for low/moderate flow hydrology and is not applicable in wetlands, impoundments, estuaries and other lentic habitats

It is important to follow a standard that is well tested for improving knowledge but also for comparing data When habitat complexity is poor, there will be less biotic diversity and consequently a lower SASS score Average Species per Taxon (ASPT) will be less affected (Dallas, 1997; Chutter, 1998), because the few organisms present may have the appropriate sensitivity The ASPT score may be depressed where, for example, a sand bed river in pristine condition may produce a low ASPT, as it may be occupied by hardy, adaptable taxa Chutter (1998), also points out that ASPT is a more reliable measure of the health of good quality rivers (as opposed to poor quality rivers) than purely taxon count scores or sensitivity scores The degree to which taxon are responsive to water quality varies in sensitivity (Gerber and Gabriel, 2002)

Table 2.1: Water quality variables in the aquatic landscape

Variable Function in aquatic life Invertebrate response

pH Determines ionic balance, chemical species

availability and gill functioning of aquatic life (Dallas and Day, 2004)

Reduction of sensitive species like the mayflies (Ephemeroptera) at pH<4 In comparison, Plecoptera, Trichoptera and Diptera abundances may show no statistically significant differences (Courtney and Clements, 1998)

Temp Determines: metabolic rate, growth, nutrient and

toxins availability, oxygen saturation levels

Reproduction, migration and general fitness, influence physical, chemical and biological processes as well as microbial activity Metabolic rates double for every 10°C increase in water

temperature (Vought et al., 1998; Dallas and Day, 2004; Eady et al., 2013)

Lower temperature result in lower metabolic functioning and organisms take longer to mature, producing less offspring At higher temperatures, there is less dissolved oxygen for biological reaction However, invertebrates, are more active leading to stress, particularly in high density (Eady et al., 2013).

Variability of temperature by more than 2°C or 10% can lead to exclusion of taxa unable to tolerate extreme highs or lows (DWAF,

1996; Hawkins et al., 1997; Newson, 2009; Davies and Day, 1998;

Dallas and Day, 2004)

Table 2.1: Continued

Variable Function in aquatic life Invertebrate response

DO Respiration of all aerobic organisms and all life

stages, eggs, larvae, adult Also for feeding and

reproduction (Li et al., 2012)

Mayflies which are wide spread are probably the most sensitive to low oxygen conditions, and lethal effects have been observed at DO levels <20% saturation Mortality of Chironomidae, which are tolerant to low oxygen, are observed when oxygen concentrations

are below 8% saturation (Helson, et al., 2006) Macro-invertebrates

that remain at a location and do not drift, at DO concentrations of 25

to 35% and 10 to 20% saturation, survive sub lethal effects by suppressing emergence This mechanism enables species to persist

in hypoxic conditions in the short term (Connolly et al., 2004)

Reduction in species biodiversity as the juvenile stages (larvae and

eggs) are most negatively affected by high TDS (Rutherford et al.,

2000)

Community structure is strongly associated with EC (Kefford, 2000)

Table 2.1: Continued

Variable Function in aquatic life Invertebrate response

Turbidity Poor visibility from high TDS, affects the food

searching ability of predators (Henley et al., 2000; Burkhead and Jelks, 2001; Hancock et al., 2005; Sutherland et al., 2007)

High turbidity resulting in sedimentation negatively affects organism The sedimentation smothers organisms (their sensitive gill

structures), their eggs, their food base and algae (Jun et al., 2011)

Sediments and turbidity block light, reducing photosynthetic production (Wood and Armitage, 1997)

Sediments fill up voids under cobbles riffles and pools changing

habitat quality (Dallas and Day, 2004; Li et al., 2012)

Disruption of sediment could potentially disturb latent pollution buried in the river bed Alternatively, nutrient loading could occur as sediment can potentially be released back into the water column

(Mount, 1995; Boix-Fayos et al., 2007)

2.2.3 Habitat assessment

Aquatic habitat is organised by the instream and surrounding topographical features, and is a major determinant of aquatic community potential (Southwood, 1977; Plafkin

et al., 1989; Barbour and Stribling, 1991) The habitat integrities, quality and quantity

available, affect the structure and composition of biota (Southwood, 1977; Karr, 1981;

Sedell et al., 1990; Maddock, 1999; Álvarez-Cabria et al., 2017) Thus, habitat assessment is defined as “the evaluation of the structure of the surrounding physical habitat that influences the quality of the water resource, and the condition of the resident aquatic community ” (Barbour et al., 1996) Furthermore, a habitat functions

as a temporally and spatially variable within which aquatic organisms can exist (Poff and Ward, 1990) Therefore, monitoring and assessment of lotic systems should demonstrate an ability to describe impacts and the progression of the success or deterioration from one state to another This is particularly true when tracking

restoration interventions (Palmer et al., 1997; Karr, 1999; Palmer et al., 2005;

Aquatic organisms have preferred habitats (Thirion, 2007), in terms of physical, chemical and other biological features such as vegetation Variation in one or more of these can lead to stress on individuals and possibly a reduction in the total numbers

of species (Chapman, 1996, Richards et al., 1997) According to Chapman (1996), physical alterations of a habitat can affect aquatic organisms as follows:

 changes in the species composition of aquatic communities,

 changes in the dominant groups of organisms in a habitat,

 impoverishment of species,

 high mortality of sensitive life stages, e.g eggs, larvae,

 mortality in the whole population,

 changes in behaviour of the organisms,

 changes in physiological metabolism, and

 Histological changes and morphological deformities

species and increases in others (Saliu et al., 2007) This in turn may provide conditions

for a range of new or otherwise scarce species to flourish An increase in habitat

complexity alternatively known as heterogeneity can increase species abundance in

habitats that have been degraded (Lepori et al., 2005; Merz et al., 2005; Miller et al.,

Merz et al., 2005; Thirion, 2007; Thirion, 2016)

Thirion (2007) classified SA’s macro-invertebrate taxon preferences to habitat biotopes as follows: 6 taxa prefer bedrock, 31 prefer cobbles, 24 prefer vegetation, 20 gravel sand and mud, and 11 prefer open water However, macro-invertebrates can also occupy more than one biotope in one location even though they exhibit habitat preference

2.2.4 The Rapid Habitat Assessment Method (RHAM) ( DWAF, 2009 )

Water quality parameters often vary more prominently than physical variables among river watersheds Variability among the macro-invertebrate-based stream groups can

be better explained by altitude gradients together with streambed composition and

water velocity, then chemical variables (Metcalfe, 1989; Brabec et al., 2002; Kirchner,

2006)

The South African Rapid Habitat Assessment Method (RHAM) (Annexure C) is able

to quantify the stratum type, depth and velocity It is cost effective for Ecological Water Habitat Requirement for both baseline and follow-on monitoring The RHAM does not provide an eco-status assessment of the environment It is ideally suited to monitor change in river morphology, or before and after characteristic of a disturbance or natural events affecting in-stream habitat characteristics (DWAF, 2009)

Table 2.2: Potential visual observation and how it relates to habitat integrity

Visual aspect Potential impact

Organic sediments Organic sediments reduce oxygen content due to changes in invertebrate assemblages (; Odum, 1985;

DWAF, 1996) such as mayflies (Ephemeroptera), stoneflies (Plecoptera) and caddisflies (Trichoptera)

are often replaced by Chironimidae midges (Diptera) (Dudgeon, 1994; Quinn et al., 1997)

Habitat complexity The loss of habitat heterogeneity correlates with the reduction in community complexity and stability of

aquatic macro-invertebrates (Merz et al., 2005; Dudgeon, 2006; Lévesque and Dubé, 2007; Reid et

al., 2010)

Homogeneous streambed habitats with greater fine particles support lower diversity and abundance

(Li et al., 2012; Reid et al., 2010)

Concrete encasement

can act as weirs if above

the river bed leading to

loss of connectivity

Fragmentation, interactions and ultimately abundance of species result if any barriers to movement patterns occur The impact of the barrier depends on the perception of the barrier or territory boundary

or used as an avenue for travel and invasion into habitats previously inaccessible (Warren and Pardew,

1998; Norman et al., 2009; Ramirez and Mosley, 2015)

Wire baskets structures

filled with rock are

known as gabion

baskets

Aquatic Macro-invertebrates prefer rock baskets for habitat when compared with concrete as these baskets have voids, aerate the water and trap debris suitable for feeding, found that rock filled baskets could be used to improve aquatic macro-invertebrate habitat in trout farms, as it harboured vital macro-invertebrates which were useful for trout feeding (Ramirez and Mosley, 2015)

2.2.5 Visual assessment approaches

Many physical aspects of aquatic habitat are observable such as organic sediment and habitat complexity / heterogeneity and anthropogenic structures (Table 2.2) Other aspects include depths and flow of water (Nelson and Lieberman, 2002) Measurements are more precise than visual estimates However, visual estimation

procedures can be nearly as precise as measurements (Kaufmann et al., 1999) Kaufmann et al., (1999) further advised that visual observations are limited to

measurable characteristics (e.g cover or presence), rather than judgements of habitat

quality, at multiple locations within a river reach Kaufmann et al., (1999), also noted

that visual judgement methods are attractive because of its rapidity in the field and in data reduction but the lack of precision, limits its use in many applications

2.2.6 The United States Environmental Protection Agency (US EPA) visual

based assessments of river habitat integrity (Barbour et al., 1999)

According to Barbour et al (1999) “The habitat assessment matrix developed for Rapid Bio-assessment Protocols (RBPs) by Plafkin et al (1989), were originally based

on the Stream Classification Guidelines for Wisconsin developed by Ball (1982) and Methods of Evaluating Stream, Riparian, and Biotic Conditi ons” developed by Platts

et al (1983) Barbour and Stribling (1991), modified the habitat assessment approach originally developed for the RBPs to include additional assessment parameters for high gradient streams and a more appropriate parameter set for low gradient.”

The British equivalent of bio-assessment by Raven et al (1997) and Raven et al

(1998), “The physical character of rivers and streams in the UK and Isle of Man”,

provided the basis for the US EPA rapid bio-assessment protocol The visual based assessment is one component of the protocol used for instream assessments Key visual habitat quality parameters are assessed The quality of each parameter is rated and scored against predetermined criteria The final score is a percentile

The matrix in the form of a field data sheet (Annexure D) is used to evaluate in stream habitat, channel morphology, bank structural features and riparian vegetation It rates ten parameters into categories of optimal, suboptimal, marginal, or poor condition A detailed description with photographs describes each category are provided to guide the visual assessment

2.2.7 Visual Biotopes assessment for macro-invertebrate habitat/ Integrated

Habitat Assessment (IHAS) (McMillan, 1998)

This method developed by McMillan (1998), forms part of the SASS-5 field sheet and focuses on the quality of the biotopes This information assists in interpreting the data collected on the SASS-5 field sheet It is alternatively also referred to as Integrated Habitat Assessment (IHAS) Each biotope is rated on a 0-5 scale, where 0 is absent and 5 represents full availability and suitability (McMillan, 1998)

The ultimate aim is to summarise and numerically reflect the quantity, quality and diversity of biotopes available for habitation by macro-invertebrates at a sampling site (Dallas, 1997; McMillan, 1998; Dallas, 2007c; Dallas, 2007d) This scoring system provides for a total of 100 points (percentile) and is split into two sections Firstly, Sampling Habitat for 55 points and secondly, Stream Condition/Characteristics for 45 points The Sampling Habitat section is further divided into three sub-sections: Stones-in-Current (20 points), Vegetation (15 points), and Other Habitat (20 points) which includes stones-out-of-current, gravel, sand and mud The Stream Condition section provides an evaluation of a site in terms of its physical characteristics and the degree

of disturbance present, including estimates of aspects such as stream width, depth and velocity

Total IHAS scores of greater than 75 indicate excellent macro-invertebrate habitat conditions, whilst total scores of between 65 and 75 indicate adequate habitat conditions (McMillan, 1998)

2.3 Disturbances to in-streams habitat from Below Ground Bulk Water Pipelines (BGBWPL)

Globally, in Africa and in SA (Gauteng), the large scale below ground bulk water pipelines (BGBWPL) that supplement water to developmental urban hubs, crosses through rivers and add to anthropogenic impacts, adding to habitat degradation within

aquatic eco systems (NWA, 1998; NEMA, 1998; Clarke-Sather et al., 2017; Maniatis,

2017; Strijdom, 2017) The BGBWPL alters river and stream channels, hence may have detrimental effects on aquatic ecosystems (Lévesque and Dubé, 2007; Maniatis, 2017) resulting in loss of habitat complexity, becoming less heterogeneous after

pipeline installation (Harding et al., 1998; Brown, 2003; Lévesque and Dubé, 2007)

Streambed composition is one of the most important factors that directly influence richness and abundance of macro-invertebrates on local scales (Halwas and Church,

2002; Merz et al., 2005, Jiang et al., 2010)

Linear activities are known to have the following negative impacts:

 Impede drainage, causing upslope flooding and desiccation of vegetation

downslope (Laurance et al., 2009)

 Change flow patterns that result in elevate stream velocity, which scours

streambeds and simplifies downstream habitats (Laurance et al., 2009)

 Cause fragmentation of species (Goosem, 2007)

 Result in barriers for aquatic fauna from linear corridors, alter movement patterns, species interactions and ultimately abundance (taxa use streams as corridors for dispersal) The impact of the barrier depends on whether the corridor is perceived

as a barrier or territory boundary or used as an avenue for travel and invasion into

habitats previously inaccessible (Warren and Pardew, 1998; Norman et al., 2009; Latham et al., 2011)

 Instream pipeline crossings can also effect water quality such as total suspended

solids (Vezza et al., 2014)

 Physical habitat indices are affected (substrate particle size, channel morphology)

(Vezza et al., 2014)

 Alteration of hydrological pattern, leading to sedimentation and possible erosion (Ramirez & Mosley, 2015)

 Introduction of invasive species (Ramirez and Mosley, 2015)

 Benthic invertebrate community structure and drift (abundance, species composition, diversity, standing crop) (Lévesque and Dubé, 2007)

 Fish behaviour and physiology changes (Lévesque and Dubé, 2007)

 Instream and riparian zone perturbations can be regarded as primary causes of degradation of a river ecosystem (Dallas, 2005)

Physical variables create diverse microhabitats in streambed conditions Loss of habitat can have more impact than water quality resulting from physical anthropogenic

impacts such as BGBWPL (Braccia and Voshell, 2017)

The temporal and spatial scale of synchronized species replacements and distribution

construction activity or generally less than one month Short term impacts last between

1 month to 1 year, medium term impacts last between 1 and 5 years, while long term impacts persists longer than 5 years (Balloch, 2017) Sediment plumes flow down the river for up to six months However, once the bed and bank are stabilized, no further sediment dislodgement is expected (Lévesque and Dubé, 2007)

Table 2.3 (adapted from Barbour et al., 1999) provides scenarios where by the

parameters could produce negative and positive habitat changes on BGBWPLs The ability of a watercourse to recover from disturbances such as BGBWPLs, necessitates the adoption of response measurements to quantify ecological condition and monitor ecological change in terms of acceptable and unacceptable ranges of impacts to the habitat (Roux, 1999) There is a need to protect rather than to use and abuse, and has become a first line approach to conservation in SA (Roux, 1999) The degree of resilience in a watercourse according to Roux (1995), is the inherent capacity of an ecosystem to return to its original state, given the removal of all human alterations, stresses and degree of change However, if any component is greater than 50%, relative to the original state, the ecosystem is unlikely to be able to tolerate the change Hughes (1995), suggested rated impacts from 90% of the reference condition intact is of high quality and perhaps within the range of natural and measurement variability, 75% of the reference condition is considered acceptable, 50%–75% of the reference condition could be considered marginal Although these references are old and more updated opinions have not been confirmed, the concept provides a scale on which the anthropogenic activity of BGBWPLs can be considered

Table 2.3: The US EPA habitat response visual parameters and BGBWPL

(Adapted from Barbour et al., 1999)

Visual Aspect Detail

Embeddedness Pipelines may result in erosion adding to the sediment load

of a river (Lévesqu and Dubé, 2007) Excessive flow combined with sediments cause embeddedness, loss of

riffles, and pools (Li et al., 2012) Stone packed gabion

baskets could be filled and become embedded (Allan, 2004;

to go into suspension and later deposited (Mount, 1995; Reid

et al., 2004; Boix-Fayos et al., 2007)

The decreases in the mean substrate size and increases in the percentage of fine sediments are indicative of destabilisation and erosion (Kaufmann, 1999; Reid et al.,

2008) These fine substrate particles also fill the voids of coarser bed materials, reducing habitat space availability to

macro-invertebrates (Carling, 1984; Gayraud, 2003; Merz et al., 2005)