Table 1.

OTUs identified at species level with its corresponding clade, proportion of reads, and occurrence

Phytophthora species	Clade	% of total readsa	Number of sites presentb
Aquatic Phytophthora spp. (Clade 6 spp.)
P. bilorbang	6	12	88
P. chlamydospora	6	0.01	5
P. gonapodyides	6	24.4	92
P. gregata	6	0.7	11
P. lacustris	6	50.4	95
P. megasperma	6	0.07	6
P. pinifolia	6	0.06	4
P. riparia	6	0.2	19
P. rosacearum	6	0.1	5
Terrestrial Phytophthora spp. (Non-clade 6 spp.)
P. alni	7	1.9	44
P. brassicae	8	0.02	5
P. cactorum	1	1.3	29
P. cambivora	7	0.04	9
P. capensis	2	0.007	1
P. cichorii	8	0.006	2
P. cryptogea	8	0.07	4
P. drechsleri	8	0.02	5
P. europaea	7	0.5	18
P. fragariae	7	0.3	21
P. fragariaefolia	7	0.01	4
P. gallica	10	6.5	73
P. iranica	1	0.03	8
P. niederhauserii	7	0.004	1
P. pisi	7	0.06	7
P. plurivora	2	0.01	5
P. porri	8	0.009	3
P. primulae	8	0.002	1
P. pseudosyringae	3	0.5	32
P. psychrophila	3	0.006	1
P. quercina	4	0.04	1
P. ramorum	8	0.01	1
P. sansomeana	8	0.1	9
P. sojae	7	0.02	2
P. syringae	8	0.4	32
P. trifolii	8	0.1	9
P. uliginosa	7	0.02	2

^aThe total number of reads correspond to those belonging to OTUs that were identified at species level

^bNumber of sites where a species was found over the 2 years of the survey. Number of total sites = 96