The origin of suspended particulate matter in the Great Barrier Reef

River run-off has long been regarded as the largest source of organic-rich suspended particulate matter (SPM) in the Great Barrier Reef (GBR), contributing to high turbidity, pollutant exposure and increasing vulnerability of coral reef to climate change. However, the terrestrial versus marine origin of the SPM in the GBR is uncertain. Here we provide multiple lines of evidence (13C NMR, isotopic and genetic fingerprints) to unravel that a considerable proportion of the terrestrially-derived SPM is degraded in the riverine and estuarine mixing zones before it is transported further offshore. The fingerprints of SPM in the marine environment were completely different from those of terrestrial origin but more consistent with that formed by marine phytoplankton. This result indicates that the SPM in the GBR may not have terrestrial origin but produced locally in the marine environment, which has significant implications on developing better-targeted management practices for improving water quality in the GBR.

A and B: this sampling system allows large volumes of water (9,000 to 12,000 L) to be pumped through a 1 µm filter cartridge (Puretec ® sediment filter cartridge-wound GW011) over a relatively short period (2 to 3 hours); C and D: The SPM retained in the filter carousel was recovered by cutting the string filter cartridge to release the SPM.Table S1.Changes in proportion of organic carbon functional groups during transportation of organic matter along the plant-soil-riverine-estuarine-marine continuum as identified by solid-state 13 C nuclear magnetic resonance ( 13 C NMR) spectroscopy.

Origin of microbial communities in the marine environment
A Bayesian-based approach Sourcetracker2 was used to predict the contribution of different habitats (riverine, inner estuarine mixing zone (IEMZ) and outer estuarine mixing zone (OEMZ)) to bacterial and fungal communities associated with marine trap samples.The boxplots were generated in R, and Tukey Honest Significant Differences (TukeyHSD) was used to test the significance among different habitats.On average, 88.6% of the bacterial community associated with marine trap sediment was unique, while the remainder could be traced back to their potential habitat origin (Fig. S8).Of the three habitat sources, most bacteria associated with marine trap samples (10.8%) had OEMZ origins which was significantly (p < 0.001) higher than the contributions of soil, riverine and IEMZ combined (sum of which contributed only 0.6%).Results also showed that 99.54% of the fungi attached to marine trap sediments were unique, and only a small proportion could be traced back to the three habitat sources (0.09%-soil, 0.13%-riverine and IEMZ, 0.23%-OEMZ).These results show that microbial community composition and structure significantly change at the interface of freshwater and marine environments.Microbes in soil, riverine and IEMZ habitats comprise a very small proportion of microbial communities associated with marine trap sediment.
Table S3.Changes in the bacteria to fungi gene copy number ratio (bacteria:fungi ratio), bacterial and fungal richness (BactRich and FunRich), diversity (Shannon index -BactShann and FunShann) and community structure (BactNMDS and FunNMDS) across habitats.

Fig. S4 .
Fig. S4.The variation and correlation among biogeochemical variables across habitat types.

Fig. S6 .
Fig. S6.Bacterial community composition and structure.This figure presents a) the

Fig. S7 .
Fig. S7.Fungal community composition and structure.This figure presents a) the relative

Fig. S8 .
Fig. S8.The Origin of microbial communities in the marine environment.This figure

Table S2 .
Redundancy analysis (RDA) outputs showing the percentage of variation in organic matter (OM) characteristics across soil, riverine, estuarine and marine habitats explained by explanatory variables of microbial diversity and community structure (MDCS).The characteristics Means (SD) within a column followed by the same letter are not significantly different at p < 0.05.➢ NA: not available ➢ IEMZ: inner estuarine mixing zone; OEMZ: outer estuarine mixing zone.