Marine Oomycetes of the Genus Halophytophthora Harbor Viruses Related to Bunyaviruses

Abstract

We investigated the incidence of RNA viruses in a collection of Halophytophthora spp. from estuarine ecosystems in southern Portugal. The first approach to detect the presence of viruses was based on the occurrence of dsRNA, typically considered as a viral molecule in plants and fungi. Two dsRNA-banding patterns (∼7 and 9 kb) were observed in seven of 73 Halophytophthora isolates tested (9.6%). Consequently, two dsRNA-hosting isolates were chosen to perform stranded RNA sequencing for de novo virus sequence assembly. A total of eight putative novel virus species with genomic affinities to members of the order Bunyavirales were detected and their full-length RdRp gene characterized by RACE. Based on the direct partial amplification of their RdRp gene by RT-PCR multiple viral infections occur in both isolates selected. Likewise, the screening of those viruses in the whole collection of Halophytophthora isolates showed that their occurrence is limited to one single Halophytophthora species. To our knowledge, this is the first report demonstrating the presence of negative (−) ssRNA viruses in marine oomycetes.

Multiple Viral Infections Detected in Phytophthora condilina by Total and Small RNA Sequencing

“…Interestingly, many of the viruses of this cluster were previously reported in three isolates of Halophytophthora sp. 04 collected like P. condilina isolate BD661 from estuarine waters in the Portuguese Parque Natural da Ria Formosa but from a different site close to Faro [ 21 ]. This result confirms the high bunya-like virus abundance in oomycetes living in these estuarine ecosystems.…”

“…in China and Halophytophthora RNA virus 8 (MT277357), identified in three isolates of Halophytophthora sp. 04 in Santa Luzia, Portugal [ 21 ], previously designated as members of a novel unofficial family Epsilonmycobunyaviridae [ 21 ]. However, this name was previously assigned to a separated cluster in Nerva et al 2019, so this possible virus family (including PcoNSRV1 and HRV8) should be named different.…”

“…Double-stranded RNA (dsRNA) ( Figure 1 a) was extracted as previously explained [ 21 ]. DsRNA bands were cut and purified from the gel with Zymoclean Gel RNA Recovery Kit (Zimo research, Irvine, CA, USA).…”

“…In order to confirm the length of the putative totivirus-like genomes we used the SMARTer RACE 5′/3′ KIT (TAKARA BIO USA, Inc., Mountain View, CA, USA) as described in Botella et al [ 21 ] and following the producer’s instructions.…”

“…Virus-like particles and/or dsRNA have been observed in Pythium irregular [ 18 ], an unclassified gammapartitivirus was reported in Pythium nuun [ 19 ], a toti-like virus was also described from two strains of Globisporangium splendens (formerly Pythium splendes ) and three virus-like sequences, Pythium polare RNA virus 1 (PpRV1), Pythium polare RNA virus 2 (PpRV2) and Pythium polare bunya-like RNA virus 1 (PpBRV1) were identified in Pythium polare infecting mosses in the Arctic [ 20 ]. Finally, multiple co-occurring bunyaviruses have also been described in marine oomycetes from the genus Halophytophthora [ 21 ].…”