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.