Accepted Manuscript

Using MODIS data for understanding changes in seagrass meadow health: a case
study in the Great Barrier Reef (Australia)

Caroline Petus, Catherine Collier, Michelle Devlin

PII: S0141-1136(14)00048-8
DOI: 10.1016/j.marenvres.2014.03.006
Reference: MERE 3866

To appear in: Marine Environmental Research

Received Date: 11 December 2013

Revised Date: 3 March 2014
Accepted Date: 7 March 2014

Please cite this article as: Petus, C., Collier, C., Devlin, M., Using MODIS data for understanding
changes in seagrass meadow health: a case study in the Great Barrier Reef (Australia), Marine
Environmental Research (2014), doi: 10.1016/j.marenvres.2014.03.006.

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 ACCEPTED MANUSCRIPT

• We use MODIS data to map turbid plume waters in the Great Barrier Reef.
• We use these data to understand changes in seagrass meadow areas and abundance.
• Correlations are found between seagrass changes and exposure to turbid plume waters.
• Potential of remote sensing data to predict GBR seagrasses health changes is proved.

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 ACCEPTED MANUSCRIPT
1 Using MODIS data for understanding changes in seagrass meadow health: a case study

2 in the Great Barrier Reef (Australia)

3 Petus, Caroline a*, Collier, Catherine b, Devlin, Michelle a

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4 Centre for Tropical Water and Aquatic Ecosystem Research, Catchment to Reef Research Group,

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5 James Cook University, Townsville, QLD 4811, Australia

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6 School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia

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7 Corresponding author: caroline.petus@jcu.edu.au, Phone: +61 7 4701 4680, Fax: +61 7 4781

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8 5589

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9
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10 Abstract
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11 Stretching more than 2,000 km along the Queensland coast, the Great Barrier Reef Marine

12 Park (GBR) shelters over 43,000 square km of seagrass meadows. Despite the status of
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13 marine protected area and World Heritage listing of the GBR, local seagrass meadows are
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14 under stress from reduced water quality levels; with reduction in the amount of light available

15 for seagrass photosynthesis defined as the primary cause of seagrass loss throughout the
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16 GBR. Methods have been developed to map GBR plume water types by using MODIS quasi-
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17 true colour (hereafter true colour) images reclassified in function of their dominant colour.
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18 These data can be used as an interpretative tool for understanding changes in seagrass

19 meadow health (as defined in this study by the seagrass area and abundance) at different

20 spatial and temporal scales. We tested this method in Cleveland Bay, in the northern GBR,

21 where substantial loss in seagrass area and biomass was detected by annual monitoring from

22 2007 to 2011. A strong correlation was found between bay-wide seagrass meadow area and

23 biomass and exposure to turbid Primary (sediment-dominated) water type. There was also a

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24 strong correlation between the changes of biomass and area of individual meadows and

25 exposure of seagrass ecosystems to Primary water type over the 5-year period. Seagrass

26 meadows were also grouped according to the dominant species within each meadow,

27 irrespective of location within Cleveland Bay. These consolidated community types did not

28 correlate well with the exposure to Primary water type, and this is likely to be due to local

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29 environmental conditions with the individual meadows that comprise these groupings. This

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30 study proved that remote sensing data provide the synoptic window and repetitivity required

31 to investigate changes in water quality conditions over time. Remote sensing data provide an

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32 opportunity to investigate the risk of marine-coastal ecosystems to light limitation due to

33 increased water turbidity when in situ water quality data is not available or is insufficient.

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34 Key words: seagrass health, MODIS, water clarity, ecological consequences.

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36 1. Introduction
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37 River plumes are the major transport mechanism for sediments, nutrients, and other land-
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38 based pollutants and are a major threat to coastal and marine ecosystems worldwide (e.g.
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39 Halpern et al., 2008). Identifying the movement, duration, frequency of occurrence and

40 composition of river plumes and associated water quality, is critical to measure the risk of
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41 marine ecosystems to reduced water quality such as reduced light availability due to
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42 increased water turbidity (e.g., Warrick et al., 2004; Novoa et al., 2012a, b; Petus et al., in

43 press). Satellite sensors provide an effective means for frequent and synoptic water quality

44 observations over large areas. The input of Total Suspended Sediments (TSS), Coloured

45 Dissolved Organic Matters (CDOM) and phytoplankton (measured through the

46 concentrations of chlorophyll-a (chl-a)) by river discharges alter the turbidity, colour and

47 optical properties of the water and Moderate Resolution Imaging Spectroradiometer

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48 (MODIS) satellite images have been used to monitor river plumes worldwide (e.g., Devlin et

49 al., 2011, 2012a; Petus et al., 2009, 2014; Saldías et al., 2012).

50 In the Great Barrier Reef Marine Park (hereafter GBR) and World Heritage Area, recent

51 studies have focused on developing innovative MODIS methods to map the spatial extent and

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52 frequency of occurrence of the different river plume water types existing within the GBR

53 river plume gradient; as well as the exposure of local ecosystems to land-based pollutants

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54 discharged through river plumes (e.g., Álvarez-Romero et al., 2013; Devlin et al., 2013a;

55 Petus et al., in press). Three main river plume water types (Primary, Secondary and Tertiary

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56 plume water types) were described from the inshore to the offshore boundary of GBR river

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57 plumes (e.g., Devlin et al., 2011b, 2012b; Petus et al., in press). Each plume water type
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58 (hereafter water type) is associated with different levels of pollutants and optically active

59 components (OACs), including TSS, chl-a and CDOM levels (Devlin et al., 2012b, Petus et
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60 al., in press and Appendix A). TSS, aCDOM and Kd(PAR) levels in river plume waters

61 decrease from the inshore/Primary to the offshore/Tertiary plume water types (Devlin and
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62 Schaffelke., 2009, Devlin et al., 2012a, 2013a, b; Petus et al., in press) and the relative
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63 concentrations of these OACs affect the light attenuation properties of the water types
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64 (Devlin et al., 2008, 2009).

65 Comparisons between GBR water types mapped through MODIS images and in situ TSS (in
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66 mg L-1), chl-a (in µg L-1), and diffuse attenuation coefficient of photosynthetically active
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67 radiation (Kd(PAR), in m-1) measurements have validated the use of MODIS true color

68 images to classify GBR plume water types (Devlin et al., 2013b). TSS and Kd(PAR) in the

69 Primary water type are typically around (mean ± 1SD) 36.8±5.5 mg L-1 and 0.73 ± 0.54 m-1,

70 respectively; in the Primary water type (Devlin et al., 2013b and Appendix A). Devlin et al.

71 (2013b) also described higher in-situ TSS measurements (and thus light limiting conditions

72 due to increase of water turbidity) related to areas that were more frequently (greater than 50

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73 % of the wet season) exposed to the Primary waters type. Primary waters are thus

74 characterized by high turbidity levels and light attenuation properties (Devlin et al., 2008,

75 2009), and light reduction is the most likely driver of seagrass loss in the region (Collier et

76 al., 2012a, b).

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77 Seagrasses are marine flowering plants that occur in shallow waters (<50m) across the globe

78 except in the Polar Regions. There are approximately 70 species arising from three separate

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79 lineages, which have convergent biological traits and similar ecological roles (Short et al.,

80 2011; Les et al., 1997; Waycott et al., 2006). Their ecological roles also have high economic

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81 value, including nutrient cycling, nursery habitat for commercial fish species, sediment

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82 stabilisation, carbon storage and they are a direct source of food for numerous herbivores and
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83 their high rates of productivity subsidize adjacent ecosystems such as coral reefs (Costanza et

84 al., 1997; Heck et al., 2008; Cullen-Unsworth et al., 2013; Fourqurean et al., 2012). In
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85 tropical regions, such as the GBR, seagrass meadows support turtles, manatees and dugongs,

86 which are seagrass specialists (Marsh et al., 2011). Seagrass meadows have relatively high
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87 light requirements compared to other marine plants such as macroalagae and phytoplankton
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88 (Dennison, 1993), and so they are often restricted to the shallow waters fringing islands and
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89 coasts. This places them at high risk of exposure to plume waters from adjacent watersheds

90 and this is contributing to accelerating loss of seagrass across the globe. This loss has placed
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91 them amongst the worlds most threatened ecosystems (Waycott et al., 2009; Hughes et al.,
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92 2009).

93 In the GBR, dugong foraging grounds and dugong protection areas largely occur in coastal

94 seagrass meadows. These meadows have a distinct senescent season, which is initiated in the

95 wet season (McKenzie et al., 2013). During the wet season, seagrasses are exposed to water

96 types that are detrimental to seagrass productivity because water clarity is reduced in turbid

97 and nutrient-rich waters (Collier et al., 2012b). The close association between runoff and

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98 seagrass senescence in the GBR makes seagrasses a good habitat for exploring the

99 relationship between ecological health and plume water types.

100 Multi-scale studies of seagrass species distributions is often the starting point for examining

101 environmental drivers and interpreting responses of seagrass meadows to climate change and

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102 decreased water quality (Kendrick et al., 2008). The main objective of this study was to test if

103 relationships can be established between the frequency of exposure to Primary water type

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104 (used to monitor waters with reduced light levels caused by turbidity) and changes in seagrass

105 health (as defined in this study by the seagrass area and abundance) in the GBR at different

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106 spatial and temporal scales. We focused on Cleveland Bay, bordering the city of Townsville

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107 (North Queensland, Figure 1), as a case study. Two local rivers drain the study area: the Ross
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108 River and Alligator Creek. Both river catchments are impacted by anthropogenic

109 developments and sediment and nutrient exports have increased since European settlement in
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110 the region (Furnas, 2003, Kroon et al., 2012). Substantial seagrass loss has occurred in

111 Cleveland Bay over the period 2007 to 2011 and changes in seagrass area and above-ground
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112 biomass (hereafter biomass) have been regularly monitored for selected meadows (see
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113 references in Rasheed and Taylor, 2008 and McKenna and Rasheed 2012).
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114 The seagrass data were coupled with exposure to Primary water type , which was derived

115 from MODIS true color images and the classification method developed by Álvarez-Romero
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116 et al. (2013), in order to test the response of these sensitive ecosystems to Primary water,
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117 characterised by reduced light levels.

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119 2. Study area

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120 Cleveland Bay is located on the eastern coast of north Queensland, Australia, 1,359

121 kilometres north of Brisbane. Cleveland Bay is located in the dry tropics and experiences a

122 summer wet season (December to April) and a winter dry season (May to November). The

123 average rainfall is about 1120 mm an-1, the majority of which falls during the wet season

124 (Furnas, 2003).

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125 The Bay is bordered to the west by the city of Townsville (Figure 1) and to the east by

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126 Magnetic Island; an inshore continental island of the GBR located about 8 km offshore from

127 Townsville. The Port of Townsville is Queensland’s third largest commercial port and has

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128 undergone large extensions over the past few years. Cleveland Bay reaches a maximum depth

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129 of 15 m at its seaward edge and the bay is protected from the south-easterly trade winds that
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130 dominate the dry season by Cape Cleveland. The Ross River and Alligator Creek with

131 catchment areas of 998 km2 and 265 km2, respectively, discharge into the Bay and the
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132 average fine sediment discharge in Cleveland Bay has been estimated around 25900 t y-1

133 (Lambrechts et al., 2010). The bay can also receive fine sediments from the Burdekin River
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134 located 100 km to the South (Bainbridge et al., 2012; Lambrechts et al., 2010).
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135
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136 INSERT FIGURE 1

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137 Figure 1: Bathymetry of Cleveland Bay (Bathymetry: © www.deepreef.org) and location of

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138 meadows monitored during the 2007 wet season baseline survey. Meadow areas selected for

139 the seagrass health long term monitoring (meadows 3, 4, 5, 6, 10, 12, 13, 14, 15, 16, 17, 18)

140 are indicated with a bright green color and the location of monitoring survey boundaries with

141 black dashed lines. Red star of the inset map indicate the location of Cleveland Bay within

142 Queensland (in light grey). See Table 1 for description of selected meadows.

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143 Numerous intertidal and shallow subtidal seagrass meadows, comprised of six seagrass

144 species, are located along Cape Cleveland, from the Bohle River to Ross River, and around

145 Magnetic Island (Figure 1 and Table 1). The combination of seasonal terrestrial run-off,

146 regular cyclones, strong south-easterly trade winds and large tidal runs creates significant

147 coastal turbidity and reduces light levels available for primary production. To survive this

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148 regime seagrasses need to exhibit high vegetative growth rates and prolific seed banks

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149 (Waycott et al., 2005). This has led to the predominance of opportunistic species, such as

150 Halodule uninervis and Halophila spinulosa in Cleveland Bay. Other main seagrass species

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151 in shallow waters near Townsville are, Zostera muelleri (also known as Zostera capricorni),

152 and Cymodocea serrulata, while the other two species – Halophila ovalis and Halophila

153
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decipiens were less dominant at the time of this study, though H. ovalis in particular, is
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154 widespread throughout the region.
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155 Cleveland Bay is typical of anthropogenically-modified shallow turbid environments

156 impacted by seasonal terrestrial run-off and it has widespread seagrass meadows. Cleveland
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157 Bay was thus selected in this study for testing the response of seagrasses to reduced light
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158 levels, as measured by the frequency of exposure to Primary water type.

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159
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160 3. Methods
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161 3.1. Seagrass surveys in Cleveland Bay

162 The sampling approach for the seagrass surveys in Cleveland Bay is described in detail in

163 e.g., Rasheed and Taylor (2008), Unsworth et al. (2009) and McKenna and Rasheed (2012,

164 2013). Two baseline surveys of seagrass distribution and abundance were conducted within

165 port limits of Townsville in the 2007/2008 wet season (November 2007 – February 2008)

166 (Figure 1) and 2008 dry season (June 2008). The surveyed area included intertidal and

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167 subtidal areas extending from the Bohle River through to Cape Cleveland, including the

168 southern side of Magnetic Island. A total of 634 and 761 sites were surveyed in the wet

169 season baseline 2007 and dry season baseline 2008. Twelve mixed species meadow types of

170 varying density and eight meadow types were identified and were categorised according to

171 each meadow’s dominant species (Rasheed and Taylor, 2008).

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172

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173 Table 1: Description of meadows selected for long term monitoring (Rasheed and Taylor,

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174 2008), including unique meadow ID, and species composition. Hu: Halodule uninervis; Cs:

175 Cymodocea serrulata, Ho: Halophila ovalis, Zm: Zostera muelleri, Hd: Halophila decipiens,

176

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Hs: Halophila spinulosa. Meadows are regrouped into four consolidated communities
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177 according to the dominant species within each meadow at the start of the monitoring

178 program: Hu*: Halodule uninervis (thin)-dominated communities, Cs*: Cymodocea

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179 serrulata-dominated communities, Zm*: Zostera muelleri-dominated communities, and Hs*:

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180 Halophila spinulosa-dominated communities. Int: Intertidal, Sub: subtidal. mix sp.: mixed
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181 species.

182 INSERT TABLE 1

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183
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184 This baseline information was used to select a subset of 12 meadows and design a long-term
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185 monitoring program to assess seagrass health from 2007 to 2011 (Table 1 and Figure 1).

186 These selected meadows represented the range of meadow types found in the area suitable for

187 monitoring and also captured areas of interest and likely water quality impact (including

188 resuspension of sediments and reduction in light levels) related to Townsville port

189 development. Monitoring meadows included both intertidal and subtidal seagrasses as well as

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190 meadows preferred as food by dugong and those likely to support high fisheries productivity

191 (Rasheed and Taylor, 2008). In this study, we reclassified the 12 selected meadows into four

192 consolidated communities (Hu*, Cs*, Zm*and Hs*; Table 1) according to the dominant

193 species within each meadow at the start of the monitoring program.

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194 The monitoring program surveyed seagrass biomass, area, distribution and species

195 composition each spring/summer (October/November) from 2007 to 2011 using methods

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196 developed by the James Cook University Marine Ecology Group for their network of

197 established seagrass monitoring programs, including Cairns, Mourilyan Harbour, Gladstone,

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198 Karumba, and Weipa (McKenna and Rasheed, 2013). The boundary of the seagrass meadow

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199 was mapped from aerial (helicopter) surveys conducted at low tide when the seagrass
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200 meadows were exposed, or by free diving and underwater camera techniques. Waypoints

201 were recorded around the edge of the meadow using a global positioning system (GPS) and
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202 were digitised on to a Geographic Information System (GIS) base map. The GIS base map

203 was constructed from a 1:25,000 vertical aerial photograph rectified and projected to
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204 Geodetic Datum of Australia (GDA 94) coordinates. Each seagrass meadow was assigned a
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205 mapping precision estimate based on the mapping methodology utilised for that meadow
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206 (McKenzie et al., 2001). Mapping precision estimates ranged from 10 m for isolated intertidal

207 seagrass meadows to 500 m for larger subtidal meadows (see Table 3 in Unsworth et al.,
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208 2009). The mapping precision estimate was used to calculate a range of meadow area for
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209 each meadow and was expressed as a meadow reliability estimate in hectares. Additional

210 sources of mapping error associated with digitising aerial photographs onto basemaps and

211 with GPS fixes for survey sites were embedded within the meadow reliability estimates.

212 Biomasses were estimated using a modified “visual estimates of biomass” technique

213 described by (Mellors, 1991). This method has been utilised in surveys throughout

214 Queensland and peer reviewed on several occasions (Rasheed et al. 2008; Rasheed and

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215 Unsworth 2011). The method involves an observer ranking above-ground seagrass biomass

216 within three randomly placed 0.25m2 quadrats at each site. Measurements for each observer

217 are later calibrated to previously obtained biomass values from seagrass harvested from

218 quadrats and dried in the lab to determine mean above-ground biomass in grams dry weight

219 per square metre at each site.

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220

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221 3.2. Mapping MODIS Primary water type, representing turbid water

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222 Flood plumes were mapped in this work using the method presented in Álvarez-Romero et al.

223 (2013) and described in Appendix B. In this method, daily MODIS Level-0 data acquired

224
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from the NASA Ocean Colour website (http://oceancolour.gsfc.nasa.gov) are converted into
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225 true colour images with a spatial resolution of about 500×500 m using SeaWiFS Data
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226 Analysis System (SeaDAS; Baith et al., 2001). True colour images are then spectrally

227 enhanced (from RGB to HSI colour system) and classified into six colour classes through a
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228 supervised classification using spectral signature from river plume waters in the GBR.
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229 The six colour classes are further reclassified into 3 plume water types corresponding to the
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230 three GBR water types (Primary, Secondary, Tertiary) defined by e.g., Devlin and Schaffelke

231 (2009) and Devlin et al. (2012a). The turbid sediment-dominated waters or Primary water
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232 type is defined as corresponding to colour classes 1 to 4 of Álvarez-Romero et al. (2013), the
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233 chl-a dominated waters or Secondary water type is defined as corresponding to the colour

234 class 5 and the Tertiary water type is defined as corresponding to the colour class 6 (Álvarez-

235 Romero et al., 2013, Devlin et al., 2013b) (Appendix A). Satellite/in-situ match-ups analyses

236 were performed by Devlin et al. (2013a, b) and validated plume water type maps produced at

237 the multiannual time scale and GBR spatial scale from the re-classification of the colour

238 classes of Álvarez-Romero et al. (2013).

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239 The supervised classification of Álvarez-Romero et al. (2013) was used to classify 5 years of

240 MODIS images (from 2007 to 2011, focused on the summer wet season i.e., December to

241 April inclusive), and to produce daily Primary water type maps over the 2007 (i.e., December

242 2006 to April 2007) to 2011(i.e., December 2010 to April 2011) wet seasons. Secondary and

243 Tertiary water type maps were not included in this study as we wanted to focus our study on

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244 the potential ecological effects of highly turbid waters on seagrass meadows. Weekly Primary

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245 water type composites were created to minimize the amount of area without data per image

246 due to masking of dense cloud cover, common during the wet season (Brodie et al., 2010),

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247 and intense sun glint (Álvarez-Romero et al., 2013).

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248 Weekly composites were resampled at the minimum MODIS spatial resolution (250×250 m)
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249 using the resampling function of ARCGIS 10.1 and a nearest interpolation resampling

250 technique to allow comparison between the MODIS images and the smallest seagrass beds of
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251 Cleveland Bay. This technique uses the value of the closest cell to assign a value to the output

252 cell when resampling. Weekly composites were thus overlaid (i.e., presence/absence of
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253 Primary water type) and normalized, to compute annual normalised frequency maps of
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254 occurrence of Primary water type (hereafter annual Primary water frequency maps). Finally,
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255 annual Primary water frequency maps were overlayed in ArcGIS to create multi-annual

256 (2007-2011) normalised frequency composites of occurrence of Primary water types

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257 (hereafter multi-annual Primary water frequency composites). Three composites were created
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258 by calculating the median, maximum and standard deviation frequency values of each

259 cell/year. The annual/multi-annual frequency of occurrence of Primary water type represent

260 the number of week the Primary plume water type was present in each MODIS pixel during

261 one/several (2007 to 2011) consecutive wet season(s), respectively.

262 3.3. Using MODIS annual turbid water maps for understanding changes in seagrass

263 meadow health

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264 Relationships in Cleveland Bay were investigated between annual Primary water type maps

265 and seagrass at three different spatial scales, including: (i) the individual meadow scale (i.e.,

266 for every respective 12 individual meadows (Table 1); (ii) the consolidated community scale

267 (i.e., for the four consolidated communities: Hu*, Cs*, Zm*and Hs* ; Table 1), and; (iii) the

268 bay-wide scale (i.e., for the Cleveland combined 12 monitored meadows; Table 1),

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269 respectively. Relationships were investigated by correlating seagrass health measurements

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270 with the exposure of seagrasses to Primary water type at these three different scales (Figure

271 2). The 12 meadows were consolidated into four communities because we aimed to test if

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272 correlation between the turbid waters and the seagrass changes could be explained by the

273 dominant seagrass species (and its specific growth requirements) in each of the seagrass

274
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meadows. Methods are further described in sections 3.3.1 and 3.3.2. Appendix C presents the
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275 ranges of scales (in pixel, km2 and Ha) for the individual, the consolidated community and
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276 the bay-wide seagrass meadow scales.

277
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278 INSERT FIGURE 2

279 Figure 2: methods used to investigate relationships between seagrass meadow health
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280 measurements and the exposure of seagrass beds to Primary water type: a: annual, ma:
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281 multiannual; dArea and dBiomass: total changes over the 5-year monitoring in the individual
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282 meadow area and biomass and; Freq(P): exposure of seagrasses to Primary water type. Areaa

283 and Biomassa of the consolidated communities and bay-wide seagrasses are calculated by

284 summing the corresponding individual meadow Areaa and Biomassa measured from 2007 to

285 2011 and Freq(P)a are calculated following methods of Figure 3. dArea and dBiomass are

286 calculated following Eq. 1 and Freq(P)ma extracted from the multi-annual Primary water

287 frequency composites (median, maximum and standard deviation composites).

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288 3.3.1. Measurements of seagrass health

289 Areas and biomasses were computed annually (Areaa and Biomassa) for the three seagrass

290 scales. Areas of the consolidated communities and bay-wide seagrasses were calculated by

291 summing the corresponding individual meadow areas measured every year from 2007 to

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292 2011. To fully quantify changes in seagrass area and abundance, the biomass recorded for

293 each meadow was multiplied by its respective area to derive an individual meadow estimate.

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294 Consolidated community and bay-wide biomasses were calculated by summing the

295 corresponding meadow biomass. Finally, in order to better assess individual meadow area

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296 and biomass total changes over the 5-year monitoring period, the difference (d) of seagrass

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297 areas and biomasses were estimated following Eq. 1.
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298 dArea / dBiomass = ( Area / Biomass2011 − Area / Biomass2007 ) / Area / Biomass2007 × 100 Eq. 1
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299 With the difference (d) in %, the Area in hectares (Ha) and the biomass in mgDW (DW: Dry

300 Weight).
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301

302 3.3.2. Exposure to Primary water type

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303 The annual and multi-annual Primary water frequency maps and composites were used to
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304 inform turbidity changes and exposure of seagrasses to reduced light levels caused by
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305 turbidity. Exposure of seagrasses to Primary water type (i.e., to reduced light levels) was

306 estimated by calculating the mean annual Primary water frequency (Freq(P)a) measured over

307 the seagrass, considering the three different seagrass spatial scales. Every pixel (i.e., annual

308 frequency value) located over (i) each individual seagrass meadow (individual meadow scale;

309 Figure 3.4a); (ii) each of the consolidated communities (consolidated community scale;

310 Figure 3.4b); and, (iii) the combined 12 monitored meadows (bay-wide scale; Figure 3.4c) as

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311 measured during the 2007 wet season baseline survey, were selected and frequency values

312 were averaged, per year. The objective was to describe how changes in the frequency of high

313 turbidity waters related to changes in seagrass area and biomass. Multi-annual Primary water

314 frequency composites (median, maximum and standard deviation composites) were then used

315 to calculate the multi-annual exposure of every individual meadow to Primary water type

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316 (Freq(P)ma). Every pixel (i.e., multi-annual median, maximum and standard deviation

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317 frequency value) located over each individual seagrass meadow was selected and averaged.

318 All these exposure measurements to Primary water type were used for correlation analysis

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319 with the seagrass health measurements defined in the previous section.

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320
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321 INSERT FIGURE 3
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322 Figure 3: method used to report the mean annual Primary water frequency (Freq(P)a) over the

323 individual (4a), consolidated community (4b) and bay-wide (4c) seagrass meadow areas.
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324
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325 3.4. Relationship between reduced light levels caused by turbidity and frequency of
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326 occurrence of Primary water type

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327 Finally, the mean discharge recorded over each monitoring wet seasons at the gauging station
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328 of the Bohle River (http://watermonitoring.derm.qld.gov.au/) was compared to the

329 corresponding Freq(P)a in order to illustrate the relationship between reduced light levels

330 caused by turbidity and frequency of occurrence of Primary water type, as described in

331 Devlin et al., 2013b. This comparison is justified as runoff is assumed to be the main

332 parameter influencing the sediment supply and turbidity levels in the coastal waters during

333 the wet season (Fabricius et al., 2012; Logan et al., 2013) and maximum frequency of

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334 occurrence to Primary water type over the monitoring period should be correlated to the

335 maximum river discharge recorded.

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337 4. Results

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338 4.1. Changes in seagrass areas and biomasses

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339

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340 INSERT FIGURE 4

341 Figure 4: Monitored seagrass meadows: location and spatial extent from October 2007 to

342 October 2011.

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343
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344 Substantial seagrass loss occurred from 2007 to 2011 with total bay-wide seagrass meadow
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345 extent decreasing from 8161 Ha to 1268 Ha (84 % loss) (Figure 4, Figure 5b and Table 2).

Biomass loss also occurred, declining from a bay-wide estimate of 2.13 x 109 to 7.10 x 106
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346

347 gDW (>99 % loss; Figure 5a and Table 2). This estimated loss in seagrass biomass is due to
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348 the loss of extent, as well as large reductions in biomass within the meadows that remain. In

349 the 2010-2011 wet season the largest relative change in seagrass area occurred, with an 86 %
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350 loss in area compared to 2010. Earlier losses in area ranged from 7 % to 30 % per year. In
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351 contrast biomass reductions were large in each year, ranging from 70 % to 85 % per year.

352 All communities declined in meadow area over the five monitored years; however, the annual

353 change varied among the community groupings (Figure 4, Figure 5d and Table 2). H.

354 uninervis–dominated communities declined in area by 99 % overall with the greatest declines

355 in 2011 (98 %) and 2008 (43 %) relative to the area in the previous year. Only 6 Ha of H.

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356 uninervis-dominated meadows remained in 2011. Cymodocea serrulata-dominated

357 communities declined relative to the previous year by 65 % and 43 % in 2009 and 2010, but

358 then increased slightly in 2011, when all other communities declined. In total, C. serrulata-

359 dominated communities declined in area by 73 % over the entire monitoring period from

360 2007 to 2011. Zostera muelleri-dominated meadows were all very shallow, intertidal

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361 communities, with the largest area in southern Cleveland Bay. These meadows had the

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362 smallest overall decline (46 %), with 14 % and 40 % decline in 2010 and 2011, relative to the

363 previous year. Halophila spinulosa-dominated meadows, which also contained significant

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364 amounts of H. uninervis (Table 1), incrementally declined in meadow extent throughout the

365 monitoring period, with a total loss in area of 99 %. Only 7 Ha remained in 2011.

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366

367 INSERT FIGURE 5

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368 Figure 5: Bay-wide and consolidated community seagrass a) biomass and b) area at the long-
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369 term (2007 and 2011, inclusive) monitoring sites in Cleveland Bay. Changes of seagrass
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370 community re-grouped following: Hu*: Halodule uninervis (thin)-dominated communities,

371 Cs*: Cymodocea serrulata-dominated communities, Zm*: Zostera muelleri-dominated

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372 communities, and Hs*: Halophila spinulosa-dominated communities.

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373
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374 Table 2: Bay-wide and consolidated community (Com.) seagrass biomasses and areas

375 measured at the long-term (2007 and 2011, inclusive) monitoring sites in Cleveland Bay.

376 INSERT TABLE 2

377

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378

379 4.2. Mapping of turbid areas through MODIS Primary water type

380 Annual and multi-annual Primary water frequency maps and composites are presented in

381 Figure 6a and b.

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382

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383 INSERT FIGURE 6

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384 Figure 6: (a) Annual Primary water frequency maps. Frequency values are normalized with a

385 pixel value of 1 indicating that Primary water type was measured, for this pixel, 22 weeks

386
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over the 22 weeks of this wet season. (b) Multi-Annual Primary water frequency composites
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387 (2007-2011): median, maximum and standard deviation. Frequency values are normalized

388 with a pixel value of 1 indicating that Primary water type was measured, for this pixel, 110
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389 weeks over the 110 weeks of the 5 combined wet seasons.
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390
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391 Highest frequency of occurrence of Primary water type is located along the Townsville coast,
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392 with Primary frequency values reaching close to 100 % of the time (Figure 6a and b (Median,

393 Maximum)). Low variability in the annual frequency of Primary water type (Figure 6b(iii)) is
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394 observed in these inshore waters; i.e., all years during the study period had a relatively high
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395 level of exposure to Primary water. More offshore, coastal waters of Magnetic Island are

396 classified 10 to 40 % of the time as Primary water type. Along the south western coast of

397 Magnetic Island, lowest and relatively homogeneous frequency values recorded around

398 meadows 5 and 6 are related to the presence of clear water in Cockle Bay. This shallow bay,

399 south west of Magnetic Island, is protected from the prevailing SE winds by the island, and

400 from the ocean swells by the Great Barrier Reef (Birch and Birch, 1984) and is thus a low-

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401 energy bay where sediment resuspension is limited. At the individual meadow scale, Freq(P)a

402 couldn’t be calculated for individual meadows 4 and 15 as scales of these seagrass beds were

403 under the minimum detection limit of the MODIS images (i.e., < 1 pixel, see Appendix C).

404

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405 The mean wet season discharge measured at the Bohle River gauging station and the mean

406 Freq(P)a at the bay-wide scale follow the same increasing trend with the exception of the

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407 relationship measured in 2009 (Figure 7). This positive relationship proved that frequency of

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408 occurrence to Primary water type recorded in Cleveland Bay over the monitoring period is

409 correlated to the maximum river discharge recorded and validated the method used to classify

410 the plume water types in Cleveland Bay.

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411
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412 INSERT FIGURE 7

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413 Figure 7: Comparison between the mean wet season (WS) discharges (calculated as the
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414 average of the mean monthly discharge values recorded every respective monitored year

415 between December and April inclusive) at the gauging station of the Bohle River and the
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416 mean annual frequency of Primary water type (Freq(P)a). (Freq(P)a) values are indicated in

417 italic.
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418

419 4.3. Using MODIS Primary water type for understanding changes in seagrass

420 meadow health

421 4.3.1. Bay-wide scale

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422 At the Bay-wide scale, negative relationships between annual seagrass health measurements

423 and Freq(P)a (Figure 8) are observed with lowest biomass and area measurements associated

424 with the highest exposure to Primary water type.

425 Annual biomasses and areas of seagrass are generally well predicted by the annual frequency

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426 of primary water type, with again the exception of data collected in 2009. Excluding 2009, 98

427 % of variance in total biomass can be explained by changes in mean Primary water type

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428 frequency (Figure 8a, R2 =0.98, p<0.05) and 92 % of variance in total seagrass area can be

429 explained by changes in mean Primary water type frequency (Figure 8b, R2 =0.92, p<0.05).

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430

431
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INSERT FIGURE 8
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432 Figure 8: Correlation between annual total seagrass a) biomasses and b) areas and the mean
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433 annual frequencies of Primary water type. Trendlines and determination coefficient are

computed without considering the year 2009 (cross symbol).

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434
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435

436 4.3.2. Consolidated community scale

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437 At the community scale, data plotted for each community demonstrated non-significant
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438 responses within the community assemblages (Appendix D). The annual biomass and area of
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439 each consolidated seagrass communities (Hu*, Cs*, Zm*and Hs; Table 1) could not be

440 predicted by Freq(P)a. Negative relationships between annual seagrass health measurements

441 and Freq(P)a were nevertheless observed, similarly to the Bay-wide scale, for the Hu* and

442 Cs* consolidated communities, respectively.

443

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444 4.3.3. Individual meadow scale

445 At the individual meadow scale, the loss of seagrass biomass over the 5-year period

446 correlated well with the median and maximum multi-annual exposure values to Primary

447 water (Figure 9b). Loss of seagrass area also correlated with the median and maximum

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448 exposure to Primary water (Figure 9a), with exceptions of meadows 10 and 16, which are

449 both Z. muelleri –dominated meadows in intertidal habitats.

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450

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451 INSERT FIGURE 9

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452 Figure 9: Correlation between total (5-year: 2007-2011) loss in seagrass calculated following
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453 Eq. 1a) area and b) biomass and the multi-annual mean frequency of Primary waters type

454 extracted from the mean median, maximum and standard deviation combined maps (Figure
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455 6b). Color scale used is the same as Figure 5 i.e., blue: Hu*; violet: Cs*; Brown: Zm* and

green Hs* communities. Int: Intertidal, Sub: subtidal (see Table 1).
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456
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457

458 5. Discussion
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459 Changes in areas and biomasses of seagrass in Cleveland Bay have been documented in
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460 McKenna and Rasheed (2012). However, this study did not include collection of water
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461 quality or other environmental data, making interpretation of seagrass changes speculative

462 and based largely on climate information. Repeated and extended above average wet seasons

463 were monitored in the GBR between 2007 and 2011. Nearly all of the GBR rivers

464 experienced a high degree of flooding during the 2010-2011 wet season due to the very

465 strong ‘La Nina’ beginning early in the season in mid-2010 and three cyclones (Tasha in

466 December 2010, Anthony in January 2011 and the most damaging: Yasi in February 2011)

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467 that crossed the North Queensland coast over a period of three months (Devlin et al., 2012b,

468 Logan et al., 2013). The present study, which combines MODIS measurements and

469 ecological information across years, provided further information about interactions between

470 seagrass health (as measured by the area and biomass of seagrasses) and reduced light levels

471 caused by turbidity (as measured by the frequency of exposure to Primary water type); as

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472 well as recovery and resilience of these inshore ecosystems in a context of extreme weather

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473 conditions.

474 5.1. Changes in seagrass abundance and area

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475 The decline in meadow area in Cleveland Bay from 2007 to 2011 was unprecedented and

476

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striking (Figure 4), as meadow loss indicates an advanced state of exposure to stressful
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477 conditions. The loss in meadow area in Cleveland Bay from 2007 to 2011 was far in excess

478 of global seagrass losses (Waycott et al., 2009) and of that reported, for example, for
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479 Cockburn Sound in Western Australia (Cambridge and McComb, 1984), and suggests that
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480 earlier estimates of seagrass decline may have underestimated their losses at a global scale.
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481 Biomass loss also occurred and was quantitatively higher than reductions in area (>99 %

482 biomass loss). Biomass loss can be attributed to plant death, thinning of shoots (fewer shoots
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483 per plant), reductions in the number of leaves per shoot and even changes to morphology
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484 (Collier et al., 2012a; Ralph et al., 2007); however, these meadow and plant attributes were
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485 not documented as part of the long-term monitoring program (McKenna and Rasheed, 2012).

486 In addition, loss of seagrass biomass occurred faster than loss in area (Figure 5). This result is

487 consistent with our current understanding of meadow-scale responses to reductions in light

488 availability, whereby, for example, seagrass meadows which occur in reduced light

489 conditions, have lower biomass and as light reduces further meadows disappear i.e., biomass

490 loss followed by loss in area (Collier et al., 2007; Ralph et al., 2007).

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491 The substantial impacts to seagrass meadow area and abundance were not restricted to

492 Cleveland Bay, but occurred throughout the GBR from 2007 to 2011 (McKenzie et al.,

493 2012a, b; Collier et al., 2012b; Pollard and Greenway 2013). These widespread impacts can

494 be attributed largely to the extreme weather conditions occurring during the monitoring years

495 in which above-average rainfall exposed meadows to turbid plume waters that reduce light

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496 penetration: an impact that occurred throughout the central and southern Great Barrier Reef.

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497 Seagrass meadows of the GBR typically undergo a period of senescence in the wet season

498 when meadow abundance and productivity is reduced (Collier et al., 2012b, McKenzie et al.,

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499 2012a). The meadows then recover during the dry season as water warms and light increases.

500 However, during the study period, the repeated and extended above average wet seasons were

501
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followed by shortened dry season recovery periods (McKenzie et al., 2012a).
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502
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503 5.2. Using MODIS Primary water type for understanding changes in seagrass
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504 meadow health.

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505 Declines in seagrass meadow area and biomass from 2007 to 2011 in Cleveland Bay were

506 compared with the frequency of exposure of the Cleveland bay seagrass meadows to Primary
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507 water type, at different spatial scales (bay-wide, community and individual meadow scales).
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508 Relationships were found between bay-wide seagrass meadow area and biomass and
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509 exposure to Primary water type (Figure 8) as well as changes of biomass and area of

510 individual meadows and exposure of seagrass ecosystems to Primary water type over the 5-

511 year studied period (Figure 9). These results confirmed that MODIS data can be used to

512 explain changes in seagrass health at different spatial scales and indicated that declines in

513 seagrass areas and biomasses over the 2007-2011 period were linked to increased exposure to

514 Primary water type, i.e., reduced light levels caused by increase in water turbidity. These

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515 results are in agreement with an increase in sediment loads reported in the region (Kroon et

516 al., 2012; Waterhouse et al., 2012). The relationships confirmed correlations previously

517 observed in-situ between light availability and seagrass abundance at the site level (Collier et

518 al., 2012b; McKenzie et al., 2012a) and indicate that these correlations are also relevant at a

519 bay-wide scale.

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520 Although bay-wide and individual meadow-scales analysis did show a strong correlation with

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521 water type, no significant relationship was found between the biomass and area of

522 consolidated communities and the exposure of Primary water (Appendix D). Trends in both

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523 area and biomass reduction differed amongst the four main seagrass community types (Figure

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524 5). Z. muelleri and H. spinulosa are the most vulnerable to reductions in light availability
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525 most likely due to their low overall storage capacity (Collier et al., 2012a). However, Z.

526 muelleri occurs in very shallow intertidal meadows (Figure 4 and Table 1) which receive
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527 light before, during, and immediately after low tide (Petrou et al., 2013) which meant that

528 losses in area of this species were actually lower than the other species (overall decline of 46
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529 %, see Figure 5a). This is also well illustrated by Figure 9a, where the Z. muelleri-dominated
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530 meadows 16 and 10 are outliers in the meadow area vs. exposure analysis. In contrast, H.
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531 spinulosa, which only occurs in subtidal meadows and therefore does not get reprieve from

532 low light conditions at low tide, were highly sensitive and had lowest survival rates (total loss
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533 in area of 99 %, see Figures 5a and 9a.). These observations, indicating that subtidal
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534 seagrasses are more sensitive to light depletion, are consistent with other cases of seagrass

535 responses to short-term light reduction, typically associated with changes in water quality

536 (Collier et al., 2012a). Other studies worldwide nevertheless reported impact from reduced

537 water clarity for both subtidal and intertidal seagrasses species; with loss in seagrass areas

538 affecting first subtidal then intertidal species (Plus et al., 2010).

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539 C. serrulata-dominated communities were impacted strongly in 2008 and 2009 and lost

540 quantitatively less area and biomass in later years when exposure was even greater due to the

541 consecutive lowering of annual measurements of area and biomass in 2008 and 2009. Of the

542 subtidal meadows, C. serrulata has relatively high light requirements (summarised in Collier

543 and Waycott, 2009) and it also has more above ground biomass (i.e., leaves) to support,

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544 relative to the below-ground storage of reserves. The largest of the C. serrulata meadows

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545 (17) was subtidal (Table 1 and Figure 4), and therefore light penetration to the meadow was

546 reduced under turbid conditions making it more vulnerable to Primary waters compared to

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547 the adjacent, shallow, intertidal meadows (McKenzie et al., 2012). Cs* meadows showed the

548 strongest (though not significant) relationship between changes in area and biomass and the

549 frequency of exposure to primary water

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550 In addition to specific resilience characteristics of the four main seagrass community types,
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551 the consolidated communities considered in this study were also spread out amongst different

552 meadows (Figure 4) and, most certainly, amongst different physical (e.g., temperature,
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553 salinity, bathymetry and sediment type), chemical (e.g., nutrients and specific pollutant
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554 concentrations like PSII) and hydrological (e.g., local tidal currents and wave exposure)
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555 conditions. Seagrass require light, nutrients, and tolerable salinity, temperature and pH to

556 survive. Photosystem II inhibiting herbicide (PSII) diuron commonly found in inshore GBR
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557 waters also adversely affects seagrass productivity and physical factors, such as tidal
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558 variation, sediment type and wave exposure also influence seagrass distribution (see

559 references in Schaffelke et al., 2013). The environmental conditions within seagrass meadows

560 influence the response of meadows within the community groupings and further explain the

561 non-significant relationships obtained between the biomass and area of consolidated

562 communities and the exposure of Primary water. Finally, meadows were defined according to

563 the dominant species present at the start of the monitoring, but generally they were comprised

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564 of multiple species (Table 1), which may respond differently to exposure to reduced light

565 levels and local environmental conditions.

566 These observations underline the complexity of coastal ecosystems such as seagrass

567 meadows, where changes in health are linked to a combination of human-induced and

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568 environmental stressors as well as to the natural resilience of species to these combined

569 stressors. Environmental and biological components can also interact and Ganthy et al.

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570 (2013) showed that presence of meadows modifies the balance between particle trapping and

571 protection against erosion processes, depending upon the seasonal growth stage of seagrass.

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572 Decline of seagrass meadows facilitates the resuspension of sediment, leading to reduction in

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573 the amount of light available for seagrass photosynthesis and thus to further impact on
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574 seagrass ecosystem health. Remote sensing models are in development to try to incorporate

575 the cumulative effects of pollutants using MODIS data (Petus et al., in press). In the
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576 meantime, this study focused on light as reduction in the amount of light available for

577 seagrass photosynthesis was defined as the primary cause of seagrass loss throughout the
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578 GBR.
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579 Loss and recovery are a natural part of the seagrass dynamics in the Great Barrier Reef (Birch
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580 and Birch, 1984; Waycott, 2005), but whether Cleveland Bay can fully recover from this

581 series of extreme events that led to loss of more than 99 % of seagrass biomass will depend
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582 on availability of recruits (e.g. seed bank) (Waycott et al., 2005), and the occurrence of
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583 additional stressors such as further runoff events or cyclones, during the recovery period.

584 Underground parts (roots, rhizomes) were not considered in the monitoring and we thus have

585 no information about the possibility for a rapid recolonisation of Cleveland Bay seagrass

586 meadows; however the extreme level of loss indicates a high likelihood of rhizome mortality.

587 A number of these species, such as H. uninervis form persistent seed banks and these are

588 likely to be important in during recovery (Inglis, 2000).

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589 5.3. Technical limitations

590 The size of seagrass meadows presented a challenge in this study as some of the seagrass

591 mapping units are under or just in the satellite detection limit. For example, Freq(P)a couldn’t

592 be calculated for meadows 4 and 15 as scales of these meadows were less than one MODIS

593 pixel (Appendix C); and these seagrass beds were thus not included in the individual meadow

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594 analyses (Figure 9). Nevertheless, results obtained in this study were coherent with

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595 correlations previously observed in-situ between light availability and seagrass health

596 measurements and support the use of the MODIS data for monitoring of relative changes in

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597 water clarity over multi-annual time frame. MODIS data provides an effective means for

598 frequent and synoptic water clarity observations over Cleveland Bay; information not

599
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available in this study area through more classical in-situ measurements.
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600 Primary water type is characterised through the mapping of river plumes by MODIS true
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601 colour images recorded during the wet season (December to April inclusive; Álvarez-Romero

602 et al., 2013), as it is typically during these periods of high flow when water quality conditions
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603 can be across a gradient of high turbidity waters (Devlin et al., 2012a; Petus et al., in press).
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604 At the whole GBR scale, restricting the analysis to wet season months also minimizes the

605 occurrence of “false” river plume areas associated with wind-driven re-suspension of
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606 sediments during the strong trade winds typical of the dry season (Álvarez-Romero et al.,
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607 2013). However in the shallow coastal areas of Cleveland Bay and Magnetic Island (Figure
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608 1), muddy sediments can be resuspended (Lambrechts et al., 2010 ), and it is likely that

609 resuspension of sediment by wind, waves and tidal currents also affect the turbidity levels in

610 the coastal waters classified as Primary water type.

611 The mapping of exposure to water types depends on the frequency and availability of the

612 MODIS imagery. Cloud contamination preventing ocean colour observations and the

613 description of the water types through optical satellites images influence the number of

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614 images available to compute the annual frequency maps, and alter some of the existing water

615 quality/seagrass correlations. Significant breaks in relationships between the Bohle river

616 discharge, the bay-wide biomass, the bay-wide area and Freq(P)a measured in 2009,

617 respectively (Figure 7 and Figure 8), seems to underline a problem in the frequency maps of

618 Primary water produced for 2009.

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619 Number of MODIS cloud free images available for a specific study area is inversely

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620 proportional to the local River discharge conditions (Petus et al., 2014). More frequent cloud

621 cover over Cleveland Bay associated with stormy condition and high Boyle River discharge

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622 could be a possible explanation for underestimated Freq(P)a values in 2009 (Figure 7 and

623 Figure 8). These observations underline the climatic limitations of our satellite-based

624
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methodology. Similar limitations nevertheless apply when using in-situ measurements as
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625 shipboard surveys and sampling data quality are highly dependent of the wind and sea
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626 conditions. Satellite images offer the most extensive spatial and temporal coverage available

627 to monitor reduced light levels caused by turbidity over large scale and temporal periods.
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628 Mapping seagrass cover using remote sensing is impossible in turbid waters (Lyons et al
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629 2012) and in situ seagrass health measurements are still essential in shallow turbid
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630 environments such as Cleveland Bay. Furthermore, the degree of variability (Inter- and multi-

631 annual) and the timing issues between satellite water quality measurements and
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632 corresponding seagrass impacts can make it difficult to align the water quality pressure with
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633 the seagrass response. The correlative measures explored in this report require more

634 investigation. However, these are encouraging preliminary results, and further work on other

635 statistical measures and models may provide better explanation of the water quality-seagrass

636 relationship.

637 5.4. Future direction

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638 MODIS satellite data are available since 2000, offering potentially more than a decade of

639 synoptic water turbidity information; and expansion of the temporal scale would be useful.

640 Indeed, the seagrass exposure history possibly affects their vulnerability (Kendrick et al.,

641 2008); and a critical component in seagrass changes might be previous year exposures e.g.,

642 how was the community exposed to Primary water type pre-2007. Information on the number

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643 of continuous days or weeks seagrass beds were in contact with water types, and the

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644 maximum TSS concentrations or turbidity levels associated with each event could be

645 extracted from the MODIS true color images and through the processing of MODIS Level 2

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646 data (Petus et al., in press). This study tested sensitivity of seagrasses to turbid water

647 exposure over an entire wet season but recovery intervals in between periods of acute light

648
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limitation can enhance seagrass survival, and furthermore the duration of the recovery is a
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649 key predictor of survival (Biber et al., 2009). Work on persistence of Primary water would
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650 thus help to clarify drivers of change in seagrass meadow health. Furthermore, documenting

651 maximum concentrations of TSS or maximum turbidity levels associated with the exposure
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652 would help describing thresholds of acceptable changes for the seagrass ecosystems.
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653 This study was focussed on an anthropogenically-modified shallow turbid region impacted by
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654 seasonal terrestrial run-off and with high frequency of exposure to Primary water type. The

655 relationship between water type and seagrass meadow health needs to be validated for a
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656 greater range of physical, chemical and hydrological environmental conditions, water types
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657 (including Secondary and Tertiary water types), and frequency of occurrence levels. This

658 could be explored in the GBR using long-term monitoring data (seagrass health, as well as

659 MODIS water type data) that ranges from relatively low impact through to heavily impacted

660 such as Cleveland Bay (Collier et al., in prep.). Repeating this work at the whole GBR scale

661 or through the comparison of this data with reference areas (non/low impacted by

662 anthropogenic developments) would more clearly show the links between satellite water

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663 quality outputs and seagrass community measures. A similar methodology could also be

664 applied for regions outside of the GBR marine park, including the Torres Strait region where

665 extensive seagrass beds (Coles et al., 2003) shelter a large population of endangered dugongs

666 (Marsh and Kwan, 2008); if long-term seagrass health data were available for this region.

667 Nevertheless, spectral signatures used to classify the MODIS true color data into 6-color (and

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668 resulting 3 water types), should be adjusted as they were created using specific

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669 spectral/colour characteristics of the GBR region (see Appendix B and Alvarez-Romero et

670 al., 2013).

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671 Finally, and more particularly at the community scale, satellite data should be associated with

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672 physico-chemical and hydrological measurements (temperature, salinity, nutrient and specific
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673 pollutants concentrations) for a better understanding of seagrass community changes. MODIS

674 data used in this study could be combined with other satellite synoptic products, such as the
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675 MODIS sea surface temperature and load of nutrients from GBR rivers derived from MODIS

676 true color images (Álvarez-Romero et al., 2013), as well as with numerical hydrodynamic
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677 outputs into more complex seagrass productivity models to encompass combined stressors
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678 affecting the seagrass health. In the near future, these productivity models should help predict
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679 seagrasses health changes.

680 Conclusions
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681 This study looked at innovative remote sensing methods to test if relationships can be

682 established between the frequency of exposure to Primary water type (used to monitor waters

683 with reduced light levels caused by turbidity) and changes in seagrass health (defined in this

684 study by the seagrass biomasses and areas). This study demonstrated that exposure to Primary

685 water is strongly linked to seagrass area and biomass changes in Cleveland Bay at the bay-

686 wide and individual meadow scale and reaffirmed that turbidity is a priority concern for

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687 seagrass meadow health in the northern GBR (e.g., Collier et al., 2012b). Despite limitations,

688 this case study has demonstrated that water quality information derived from remote sensing

689 data can be used to interpret ecological change. This study opened a suite of possibilities for

690 exploring historical ecological data where environmental in-situ data are not available.

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691

692 Acknowledgement

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693 The authors of this report would like to thank the Queensland Department of Environment

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694 and Heritage Protection for providing funding for this project under the Reef Water Quality

695 Program and the Department of Heritage and the Great Barrier Reef Marine Park Authority

696
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for funding support under the Reef Plan Marine Monitoring Program. We would also like to
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697 acknowledge the Reef Plan Marine Monitoring Program which was the main source of in-situ
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698 data for this study. We thank the Townsville Port Authority for release of the long-term

699 seagrass monitoring data for Cleveland Bay. We also thank L. McKenzie and M. Rasheed for
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700 assistance in obtaining and interpreting the seagrass monitoring data. A number of people
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701 have also contributed to the development of remote sensing tools for detecting flood plume

702 impacts on seagrasses and we thank Eduardo Da Silva and Jorge Alvarez Romero.
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703
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704 References
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705 Álvarez-Romero, J. G., Devlin, M., Teixeira da Silva, E., Petus, C., Ban, N. C., Pressey, R.

706 L., Kool, J., Roberts, J., Cerdeira,S., Wenger, A., and Brodie, J., 2013. Following the flow: a

707 combined remote sensing-GIS approach to model exposure of marine ecosystems to riverine

708 flood plume. Journal of Environmental management, 119: 194-207.

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709 Bainbridge, Z., Wolanski, E., Álvarez-Romero, J., Lewis, S., Brodie, J., 2012. Fine sediment

710 and nutrient dynamics related to particle size and floc formation in a Burdekin River flood

711 plume, Australia. Marine Pollution Bulletin, 65: 236–248.

712 Biber, P.D. and Kenworthy, W.J. and Paerl, H.W., 2009. Experimental analysis of the

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713 response and recovery of Zostera marina (L.) and Halodule wrightii (Ascher.) to repeated

714 light-limitation stress. Journal of Experimental Marine Biology and Ecology 369, 110-117.

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715 Birch, W.R., Birch, M., 1984. Succession and pattern of tropical intertidal seagrases in

716 Cockle Bay, Queensland, Australia: A decade of observations. Aquatic Botany 19: 343-367.

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717 Brodie, J., Schroeder, Th., Rohde, K., Faithful, J., Masters, B., Dekker, A., Brando, V., and

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Maughan, M, 2010. Dispersal of suspended sediments and nutrients in the Great Barrier Reef
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719 lagoon during river discharge events: Conclusions from satellite remote sensing and

720 concurrent flood plume sampling, Marine and Freshwater Research, 61(6): 651–664.
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865 quality assessment using satellite-derived chlorophyll-a within the European directives, in the

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931 threatens coastal ecosystems. Proceedings of the National Academy of Sciences 106: 12377-

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Plume water types as described in Devlin et al. (2012a) and Álvarez-Romero et al. (2013), detailing the wate
Morel and Prieur,1977; Froidefond et al., 2002; McClain, 2009), and the mean TSS, chl-a and Kd(PAR) which
concentrations (modified from Devlin et al., 2013b)

Colour
Water type Description
classes

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Sediment-dominated waters: characterised by high
values of coloured dissolved organic matters (CDOM)
and total suspended sediment (TSS), with TSS

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concentrations dropping out rapidly as the heavier
1 to 4 Primary particulate material flocculates and settles to the sea

SC
floor (Devlin and Brodie, 2005; Brodie and Waterhouse,
2009). Turbidity levels limit the light (KdPAR) in these
lower salinity waters, inhibiting production by primary

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producers and limiting chl-a concentrations.
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Chlorophyll-a-dominated waters: characterised by a
region where CDOM is elevated with reduced TSS
concentrations due to sedimentation. In this region, the
5 Secondary increased light in comparison to primary water type
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condition (but still under marine ambient conditions)

and nutrient availability prompt phytoplankton growth
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measured by elevated chl-a concentrations.

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CDOM-dominated waters: offshore region of the plume

that exhibits no or low TSS that has originated from the
flood plume and above ambient concentrations of chl-a
6 Tertiary
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and CDOM. This region can be described as being the

transition between secondary water type and marine
ambient conditions.
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mero et al. (2013), detailing the water quality and optical properties (e.g., Clarke et al.,1970;
mean TSS, chl-a and Kd(PAR) which define the plume characteristics within each plume type
modified from Devlin et al., 2013b).

Mean concentrations
Colour properties (Devlin et al., 2013b; see
Figure 10)

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Greenish-brown to beige waters: Sediment particles are

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highly reflective in the red to infra-red wavelengths of -1
TSS: 36.8±5.5 mg L
the light spectrum. Sediment-dominated waters have a
chl-a: 0.98 ± 0.2 μg L-1
distinctive brown/beige colour, depending upon the

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Kd(PAR): 0.73 ± 0.54 m-1
concentration and mineral composition of the
sediments.

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Bluish-green waters: Due to this green pigment,
chlorophyll/phytoplankton preferentially absorb the red
and blue portions of the light spectrum (for TSS:8.9 ± 18.1 mg l-1
photosynthesis) and reflect green light. Chl-a-dominated chl-a: 1.3 ± 0.6 μg L-1
M

waters will appear as certain shades, from blue-green to Kd(PAR): 0.39 ± 0.20 m-1
green, depending upon the type and density of the
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phytoplankton population.
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Dark yellow waters: CDOM are highly absorbing in the TSS:2.9 ± 3.2 mg l-1
blue spectral domain. CDOM-dominated waters have a chl-a: 0.7 ± 0.3 μg L-1
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distinctive dark yellow colour. Kd(PAR): 0.24 ± 0.02 m-1

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Appendix B: method and techniques used to classify the true color images (modified from
Alvarez-Romero et al., 2013 and Devlin et al., 2013) into 6 color classes and Primary,
Secondary, Tertiary water types.

The method used to classify the MODIS true color images into 6 color classes and is
detailed in Alvarez-Romero et al., 2013, section 2.1.1 and summarize on Figure 1-step 1

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(Classify daily true color satellite images) below. This methods involve converting true
colour images from Red-Green-Blue (RGB) to Intensity-Hue-Saturation (HIS) colour
schemes, the definition of 6 colour classes corresponding to plume areas and that describe

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a gradient in the river borne pollutants as well as 2 classes corresponding to non-plume
areas (cloud and sun glint signatures), the creation of spectral signatures for these
respective areas, and the utilization of the created spectral signature to map the full extent

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of the plume.
Color classes (and their respective spectral signature) corresponding to plume and dense
clouds and sun glint, were created using a MODIS true color image with large plumes

U
occurring along the whole GBR coast to ensure that color variations within plumes along the
latitudinal gradient were incorporated into the spectral signature. The selected image
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included large areas with no plumes, varied atmospheric conditions (light to dense clouds,
haze and sun glint), and sections with no data (not covered by satellite swath). To create the
spectral signatures, we used the ArcMap Spatial Analyst (ESRI, 2010) isodata clustering tool
M

to perform an unsupervised classification of the selected image. The resulting structure

allowed characterization of the natural groupings of cells (i.e., pixels within an image) in
multidimensional attribute space, i.e. IHS and RGB spaces for plumes and clouds/sun glint,
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respectively.
Plume maps produced were assessed using different number of classes based on two
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criteria: how well the mapped classes identified the river plume boundary (we assessed the
classified images against visually interpreted true-color imagery); and whether the variation
of selected L2 parameters among the color classes showed the expected gradient (as
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described by Devlin et al., 2012a; see Section 3.1.1). For each classification the mean value of
the two L2 parameters for each color class was plotted. Due to reflectance similarities
between land and very turbid plumes occurring in the mouth of the rivers, the full image,
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was classified without masking out land. This allowed tomap very turbid/high TSS plume
areas commonly found near river mouths, which are frequently flagged incorrectly as land
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or very dense clouds. The classification was selected based on 6 color classes as the most
appropriate for plume mapping. These classes represent a gradient in exposure to
pollutants, from highest in class 1 to lowest in class 6.
Finally, a supervised classification was used to map the full extent of plumes and to create a
mask representing dense clouds and intense sun glint. Supervised classification uses labeled
training data (i.e., the color classes defined in the previous step) to create a spectral
signature for each class, which is then used to classify all of the daily input imagery into 6-
color classes. The ArcMap Spatial Analyst maximum-likelihood classification tool (ESRI, 2010)
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was used to produce: (1) daily 6-class plume maps representing variations in L2 parameters
(also used to identify the plume boundary) and (2) masks representing dense clouds and
intense sun glint, used to eliminate areas with insufficient information to map plumes. A
number of images covering different years, regions and months was selected to confirm the
plume extent and overall congruence of our classified plume maps against plume maps

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produced using the method proposed by Devlin et al. (2012b), and to visually validate the
clouds/sun glint masks.

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Weekly 6-classes composites were thus created to minimize the amount of area without
data per image due to masking of dense cloud cover, common during the wet season
(Brodie et al., 2010), and intense sun glint (Álvarez-Romero et al., 2013). The six colour

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classes were further reclassified into 3 plume water types corresponding to the three GBR
water types (Primary, Secondary, Tertiary) defined by e.g., Devlin and Schaffelke (2009) and
Devlin et al. (2012a) (see Figure 1 below; step 2: Create weekly 3-class plume maps). The

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turbid sediment-dominated waters or Primary water type is defined as corresponding to
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colour classes 1 to 4 of Álvarez-Romero et al. (2013), the chl-a dominated waters or
Secondary water type is defined as corresponding to the colour class 5 and the Tertiary
water type is defined as corresponding to the colour class 6 (Álvarez-Romero et al., 2013,
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Devlin et al., 2013b). Land is thus removed using a shapefile of the Great Barrier Reef (GBR)
marine National Resource Management (NRM) boundaries (source: GBRMPA, GBR: Features)
and by assigning ‘No Data’ values to any pixels outside of the shapefile boundaries
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(including land and offshore areas outside of the GBR marine park). Satellite/in-situ match-
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ups analyses were performed by Devlin et al. (2013a, b) and validated plume water type
maps produced from the re-classification of the colour classes of Álvarez-Romero et al.
(2013).
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Weekly composites were thus resampled at the minimum MODIS spatial resolution
(250×250 m) using the resampling function of ARCGIS 10.1 and a nearest interpolation
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resampling technique. This technique uses the value of the closest cell to assign a value to
the output cell when resampling ArcGIS., Weekly composites were thus overlaid (i.e.,
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presence/absence of Primary water type) and normalized, to compute annual normalised

frequency maps of occurrence of Primary water type (hereafter annual Primary water
frequency maps) (see Figure 1 below, step 3: Create annual 3-class plume maps). Multi-
annual (2007-2011) normalised frequency composites of occurrence of Primary water types
(hereafter multi-annual Primary water frequency composites) are created by overlaying the
weekly composites in Arcgis and calculating the median, maximum and standard deviation
frequency values of each cell/year
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Figure B-1 (from Devlin et al., 2012a, Modified from Álvarez-Romero et al. 2013 and Devin et al., 2013) :
Summary of the process followed to build plume water maps with examples of inputs and outputs: (a)
Plume mapping process: different shadings represent steps (light gray), analyses within steps (white),
intermediate outputs (dark gray), and final outputs (black); (b) A: MODIS-Aqua true colour image used to
create the spectral signature defining 6 color classes for GBR plumes (25/01/2011), B and C: daily 6-color
class map (25/01/2011) and weekly composite (19 to 25/01/2011) of 6-class map. D: reclassified map
into weekly P, S, T composite (19 to 25/01/2011); E: Frequency of occurrence of the secondary water
type in 2011; Figure C to E are zoomed in the Tully-Burdekin area (see red box on panel B).
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Ranges of scale (in pixel, km and Ha) for the individual, the consolidated community and
the bay-wide seagrass meadows

Number of pixels
Individual Community Bay-wide
3 3
4 <1
12 7
Hu* 774
13 10
15 <1

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18 754
Bay-wide 2130
5 127
Cs* 674
17 547

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6 29
10 Zm* 20 271

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16 222
14 Hs* 411 411
Corresponding scales (km2 and Ha)
0.1 -100 km 2 10 - 100 km 2 ≈ 100 km2

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10 - 10000 Ha 1000 - 10000 Ha ≈ 10000 Ha
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Consolidated
Meadow ID Location
communities

3 Hu*

4 Hu*
Magnetic Island
p
5 Cs*

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6 Zm*

10 Zm*

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12 Hu*

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13 Hu* Bohle River to Ross River

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14p Hs*
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15 Hu*

16p Zm*
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Ross River to Cape

17p Cs*
Cleveland
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18p Hu*
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Habitat type Community type Species present

Int / Sub Dense Hu (thin) Hu (thin)

Int / Sub Moderate Hu (thin) Hu (thin), Hu (wide), Ho

Cs, Hu (wide), Hu (thin),

Int / Sub Moderate Cs with mix sp
Ho, Zm, Hs
Zm, Ho, Hu (wide), Hu

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Int Light Zm with mix sp
(thin), Cs

Intl Light Zm with Hu (thin) Zm, Hu (thin), Cs, Ho

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Int / Sub Moderate Hu (thin) Hu (thin)

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Int / Sub Dense Hu (thin) Hu (thin), Hu (wide), Ho

Hs, Hu (wide), Hu (thin),

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Sub Light Hs with Hu (thin)
Ho, Hd
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Int / Sub Light Hu (thin) Hu (thin)

Zm, Cs, Hu (thin), Hu

Int Moderate Zm
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(wide), Ho
Cs, Hu (wide), Zm, Hs, Hu
Sub Dense Cs
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Hs, Hu (wide), Hu (thin),

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2007 MANUSCRIPT 2009 2010 2011
Bay-wide 2126 ± 201 800 ± 80 137 ± 35 46 ±9 7
Biomass Hu* 306 ± 54 39 ±7 18 ±5 34 ±5 0
and error Cs* 1020 ±77 343 ± 34 32 ±5 2 ±1 3
Com.
(mgDW ) Zm* 647 ± 50 383 ± 36 78 ± 22 8 ±2 4
Hs* 152 ± 21 35 ±4 9 ±3 2 ±1 0
Bay-wide 8161 ± 581 5858 ± 776 5443 ± 464 3786 ± 446 1268
Area and Hu* 3605 ± 223 1721 ± 320 2503 ± 254 2234 ± 341 25
error Cs* 1882 ± 198 1854 ± 138 635 ± 121 178 ± 25 513
Com.
(Ha) Zm* 1352 ± 78 1417 ± 73 1405 ± 50 800 ± 48 723

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Hs* 1321 ± 82 866 ± 245 900 ± 39 573 ± 32 7

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±1
±0
±1
±1
±0
± 246
±4
± 195
± 41

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Figure 1: Bathymetry of Cleveland Bay (Bathymetry: © www.deepreef.org) and location of
meadows monitored during the 2007 wet season baseline survey. Meadow areas selected for
the seagrass health long term monitoring (meadows 3, 4, 5, 6, 10, 12, 13, 14, 15, 16, 17, 18)
are indicated with a bright green color and the location of monitoring survey boundaries with
black dashed lines. Red star of the inset map indicate the location of Cleveland Bay within
Queensland (in light grey). See Table 1 for description of selected meadows.

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Table 1: Description of meadows selected for long term monitoring (Rasheed and Taylor,
2008), including unique meadow ID, and species composition. Hu: Halodule uninervis; Cs:
Cymodocea serrulata, Ho: Halophila ovalis, Zm: Zostera muelleri, Hd: Halophila decipiens,

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Hs: Halophila spinulosa. Meadows are regrouped into four consolidated communities
according to the dominant species within each meadow at the start of the monitoring

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program: Hu*: Halodule uninervis (thin)-dominated communities, Cs*: Cymodocea
serrulata-dominated communities, Zm*: Zostera muelleri-dominated communities, and Hs*:
Halophila spinulosa-dominated communities. Int: Intertidal, Sub: subtidal. mix sp.: mixed

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species.
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Figure 2: methods used to investigate relationships between seagrass meadow health
measurements and the exposure of seagrass beds to Primary water type: a: annual, ma:
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multiannual; dArea and dBiomass: total changes over the 5-year monitoring in the individual
meadow area and biomass and; Freq(P): exposure of seagrasses to Primary water type. Areaa
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and Biomassa of the consolidated communities and bay-wide seagrasses are calculated by
summing the corresponding individual meadow Areaa and Biomassa measured from 2007 to
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2011 and Freq(P)a are calculated following methods of Figure 3. dArea and dBiomass are
calculated following Eq. 1 and Freq(P)ma extracted from the multi-annual Primary water
frequency composites (median, maximum and standard deviation composites).
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Figure 3: method used to report the mean annual Primary water frequency (Freq(P)a) over the
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individual (4a), consolidated community (4b) and bay-wide (4c) seagrass meadow areas.
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Figure 4: Monitored seagrass meadows: location and spatial extent from October 2007 to
October 2011.

Figure 5: Bay-wide and consolidated community seagrass a) biomass and b) area at the long-
term (2007 and 2011, inclusive) monitoring sites in Cleveland Bay. Changes of seagrass
community re-grouped following: Hu*: Halodule uninervis (thin)-dominated communities,
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Cs*: Cymodocea serrulata-dominated communities, Zm*: Zostera muelleri-dominated
communities, and Hs*: Halophila spinulosa-dominated communities.

Table 2: Bay-wide and consolidated community (Com.) seagrass biomasses and areas
measured at the long-term (2007 and 2011, inclusive) monitoring sites in Cleveland Bay.

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Figure 6: (a) Annual Primary water frequency maps. Frequency values are normalized with a
pixel value of 1 indicating that Primary water type was measured, for this pixel, 22 weeks

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over the 22 weeks of this wet season. (b) Multi-Annual Primary water frequency composites
(2007-2011): median, maximum and standard deviation. Frequency values are normalized
with a pixel value of 1 indicating that Primary water type was measured, for this pixel, 110

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weeks over the 110 weeks of the 5 combined wet seasons.

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Figure 7: Comparison between the mean wet season (WS) discharges (calculated as the
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average of the mean monthly discharge values recorded every respective monitored year
between December and April inclusive) at the gauging station of the Bohle River and the
mean annual frequency of Primary water type (Freq(P)a). (Freq(P)a) values are indicated in
italic.
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Figure 8: Correlation between annual total seagrass a) biomasses and b) areas and the mean
annual frequencies of Primary water type. Trendlines and determination coefficient are
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computed without considering the year 2009 (cross symbol).

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Figure 9: Correlation between total (5-year: 2007-2011) loss in seagrass calculated following
Eq. 1a) area and b) biomass and the multi-annual mean frequency of Primary waters type
extracted from the mean median, maximum and standard deviation combined maps (Figure
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6b). Color scale used is the same as Figure 5 i.e., blue: Hu*; violet: Cs*; Brown: Zm* and
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green Hs* communities. Int: Intertidal, Sub: subtidal (see Table 1).

Appendix A: Plume water types as described in Devlin et al. (2012a) and Álvarez-Romero et
al. (2013), detailing the water quality and optical properties (e.g., Clarke et al.,1970; Morel
and Prieur,1977; Froidefond et al., 2002; McClain, 2009), and the mean TSS, chl-a and
Kd(PAR) which define the plume characteristics within each plume type concentrations
(modified from Devlin et al., 2013b).
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Appendix B: : method and techniques used to classify the true color images (modified from
Alvarez-Romero et al., 2013 and Devlin et al., 2013) into 6 color classes and Primary,
Secondary, Tertiary water types.

Appendix C: Ranges of scale (in pixel, km2 and Ha) for the individual, the consolidated
community and the bay-wide seagrass meadows.

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Appendix D: Correlation between annual seagrass a) biomasses and b) areas of the four

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consolidated community and the mean annual frequencies of Primary water type. Trendlines
and determination coefficient are computed without considering the year 2009 (cross
symbol).

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