Arbuscular mycorrhizal fungal diversity associated with Eleocharis obtusa and Panicum capillare growing in an extreme petroleum hydrocarbon-polluted sedimentation basin.

Arbuscular mycorrhizal fungi (AMF) have been extensively studied in natural and agricultural ecosystems, but little is known about their diversity and community structure in highly petroleum-polluted soils. In this study, we described an unexpected diversity of AMF in a sedimentation basin of a former petrochemical plant, in which petroleum hydrocarbon (PH) wastes were dumped for many decades. We used high-throughput PCR, cloning and sequencing of 18S rDNA to assess the molecular diversity of AMF associated with Eleocharis obtusa and Panicum capillare spontaneously inhabiting extremely PH-contaminated sediments. The analyses of rhizosphere and root samples over two years showed a remarkable AMF richness comparable with that found in temperate natural ecosystems. Twenty-one taxa, encompassing the major families within Glomeromycota, were detected. The most abundant OTUs belong to genera Claroideoglomus, Diversispora, Rhizophagus and Paraglomus. Both plants had very similar overall community structures and OTU abundances; however, AMF community structure differed when comparing the overall OTU distribution across the two years of sampling. This could be likely explained by variations in precipitations between 2011 and 2012. Our study provides the first view of AMF molecular diversity in soils extremely polluted by PH, and demonstrated the ability of AMF to colonize and establish in harsh environments.

Intraisolate mitochondrial genetic polymorphism and gene variants coexpression in arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal fungi (AMF) are multinucleated and coenocytic organisms, in which the extent of the intraisolate nuclear genetic variation has been a source of debate. Conversely, their mitochondrial genomes (mtDNAs) have appeared to be homogeneous within isolates in all next generation sequencing (NGS)-based studies. Although several lines of evidence have challenged mtDNA homogeneity in AMF, extensive survey to investigate intraisolate allelic diversity has not previously been undertaken. In this study, we used a conventional polymerase chain reaction -based approach on selected mitochondrial regions with a high-fidelity DNA polymerase, followed by cloning and Sanger sequencing. Two isolates of Rhizophagus irregularis were used, one cultivated in vitro for several generations (DAOM-197198) and the other recently isolated from the field (DAOM-242422). At different loci in both isolates, we found intraisolate allelic variation within the mtDNA and in a single copy nuclear marker, which highlighted the presence of several nonsynonymous mutations in protein coding genes. We confirmed that some of this variation persisted in the transcriptome, giving rise to at least four distinct nad4 transcripts in DAOM-197198. We also detected the presence of numerous mitochondrial DNA copies within nuclear genomes (numts), providing insights to understand this important evolutionary process in AMF. Our study reveals that genetic variation in Glomeromycota is higher than what had been previously assumed and also suggests that it could have been grossly underestimated in most NGS-based AMF studies, both in mitochondrial and nuclear genomes, due to the presence of low-level mutations.