Potential quality indicators are present in all three domains of
life
Ecological indices for quality assessment rely on indicator organisms
associated to the criteria described in the individual methods. To
explore potential indicator organisms across the three domains analysed
in the present study, three different types of relationships were
investigated. The whole biome and individual domain data were both
subjected to same criteria to extract ZOTUs of interest as potential
indicators. The results from the whole biome dataset were comparable to
the combined results of the individual domains (data not shown). The
individual domains were therefore selected for detailed analysis to
provide the highest taxonomic resolution possible. A selection of the
best potential indicators identified across the three domains of life is
shown in Figure 3, the full result is displayed in Figure S5-S7.
The first type of indicators was assumed to be associated to a single
ecological status category, and extracted by selecting all ZOTUs that
were observed in one third of samples in a single category (with a
minimum of n = 2). This yielded 54, 2, and 0 ZOTUs for Bacteria ,Archaea and Eukaryota , respectively. ZOTUs representingRhodobacteraceae , Flavobacterium andFerruginibacter were associated to streams of bad and poor
ecological status, while ZOTUs representing Pirellulaceae ,Comamonadaceae and Pseudonocardia were associated to those
of good and high ecological status (Figure 3a).
The second type of indicators was assumed to be associated to either low
(bad-moderate, n = 12) or high (good-high, n = 38) quality ecosystems,
under the definition of the WFD which states that all ecosystems must
achieve an ecological status of good or higher. ZOTUs were extracted by
selecting those that occurred in at least one third of samples in either
group. This yielded 60, 0 and 3 ZOTUs for Bacteria ,Archaea and Eukaryota , respectively. Representatives ofFerribacterium and Rhodobacter were found to be associated
to streams of lower ecological status, while ZOTUs representingSolibacillus , Sphingomonadaceae , Continenticola and
the insect order Diptera were associated with high quality
ecosystems (Figure 3b).
The final type of indicator was assumed to have a strong correlation to
ecological status across all categories. ZOTUs that were observed in at
least half of the samples in the dataset (n = 50) were extracted and a
Spearman’s correlation analysis was performed. A total of 546 ZOTUs met
the criteria for Bacteria , and additional filtering for -0.5
< rho > 0.5 reduced this to 34 ZOTUs with strong
correlation to ecological status. The Archaea andEukaryota did not yield ZOTUs with a strong correlation, but
yielded a total of 6 and 14 ZOTUs, respectively. Strong negative
correlation between occurrence and ecological status was observed for
ZOTUs representing OM60(NOR5) clade (r = -0.61), Rhodobacteraceae(r = -0.51) and Caenogastropoda (r = -0.47), while a strong
positive correlatin was observed for ZOTUs representing Calothrix(r = 0.7), Limnohabitans (r = 0.78), Nitrospira (r = 0.71)
and Nitrosomonadaceae (r = 0.65) (Figure 3c).