3.4 Biomarkers that determined site-specific fish communities
The OTU-based LEfSe selected 21 families, 34 genera, and 37 species as biomarkers (Fig. 4A). The number- and biomass-based LEfSe selected 15 families, 24 genera, and 27 species (Fig. 4B) as well as 22 families, 34 genera, and 37 species (Fig. 4C). No order-level biomarker was selected, indicating that the spatial variation in fish communities at the order level was not significant. The common biomarkers selected by LEfSe from eDNA and electrofishing (see Table 1) were Barbinae|Acrossocheilus |A. beijiangensis , Nemacheilidae|Schistura |S. fasciolata , Cyprinidae|Nicholsicypris|N. normalis , Danioninae|Zacco |Z. platypus , Siluridae|Silurus|S. asotus , Oxudercidae|Rhinogobius |R. giurinusi andR. cliffordpopei , Acheilognathinae|Rhodeus in zone I; Culter , Rhodeus |R. ocellatus ,Hemiculter |H. leucisculus ,Opsariichthys |O. bidens ,Paramisgurnus |P. dabryanus , Clarias fuscusin zone II; Gobioninae|Squalidus |S. argentatus , Coptodon |C. zillii in zone III;Carassius |C. auratus ,Pseudorasbora |P. parva , Gastromyzontidae|Vanmanenia |V. pingchowensis in zone IV; Osteochilus |O. salsburyi in zone V; Hypophthalmichthyinae|Hypophthalmichthys |H. nobilis and H. molitrix , Mugilidae|Liza |L. subviridis , Cichlidae|Oreochromis |O. aureus , Scaridae|Hipposcarus |H. harid , Salmonidae|Salmo |S . salar ,Squaliobarbus |S. curriculus in zone VII; Gobiidae|Glossogobius ,Konosirus , Mugil |M. cephalus , Liza carinata in zone VIII. Notably, there were no common biomarkers observed in zone VI, indicating a great difference in the composition of fish communities detected by eDNA and electrofishing.
An interesting finding was that the eDNA-based biomarkers were similar to the number-based biomarkers but greatly differed in biomass-based biomarkers. Generally, the biomass-based biomarkers that were not detected by eDNA were bottom-dwelling species with large body sizes, such as Xenocyprinae|Xenocypris |X. argentea , Leuciscinae|Squaliobarbus |S. curriculus , Loricariidae|Pterygoplichthys |P. anisitsi in zone IV, and Ictaluridae|Ictalurus |I. punctatus , Sparidae|Rhabdosargus |R. haffara in zone VII. Another finding was that the order-level biomarkers appeared more in headwater zone I and downstream zones VII−VIII than in other zones, indicating a habitat-specific distribution of these order-level biomarkers. For example, in zone I, Barbinae|Acrossocheilus , Danioninae|Zacco , Siluridae|Silurus , and Oxudercidae|Rhinogo biuswere typical rheophilic fish living in rapids and riffles with widespread cobble substrates. In zone VII, Hypophthalmichthyinae|Hypophthalmichthys , Mugilidae|Liza , Cichlidae|Oreochromis , Scaridae|Hipposcarus , and Salmonidae|Salmo preferred slow-flowing and open water bodies. In zone VIII, the appearance of Serrasalmidae|Piaractus , Clupeidae|Konosirus , Gobiidae|Glossogobius , and Mugilidae|Mugil indicated brackish waters near the estuary. Moreover, Coptodon zillii and Labeo rohitain zone III, Pterygoplichthys pardalis in zone V,Oreochromis aureus in zone VII, and Piaractus brachypomusin zone VIII were typical invasive species that could be selected as biomarkers, indicating the sensitivity of eDNA in detecting invasive species.