Oomycete Communities Associated with Reed Die-Back Syndrome

Abstract

Phragmites australis (Cav.) Trin. ex Steud. die-back is a widely-studied phenomenon that was first discovered in northern Europe and that, until recently, was almost unknown in the Mediterranean basin. It has been described as a complex syndrome affecting reed populations leading to their retreat and decline, with significant impacts on valuable ecosystem services. Among the factors that cause the decline, soil-living microorganisms can be crucial. The aims of this study were to analyze the diversity of oomycetes communities associated with reed stands, and to understand whether they could play a key role in the decline. Variations in the structure of oomycetes communities were studied by metabarcoding of the internal transcribed spacer (ITS) 1 region of ribosomal DNA, from the sediments of five Italian freshwater ecosystems. They were chosen to cover a large variability in terms of surface area, water depth, microclimate, and presence of documented reed retreat. From 96 samples collected from reed roots, rhizosphere, and bulk soil, we assembled 207661 ITS1 reads into 523 OTUs. We demonstrated that oomycete communities were structured by several factors, among which the most important was die-back occurrence. Our study also indicates that Pythiogeton spp. could be potentially involved in the development of die-back. The role of heavy metals in the soil was also explored, and cadmium concentration was shown to affect oomycetes distribution. This study represents a significant step forward for the characterization of microbial communities associated with reed die-back syndrome and helps to gain knowledge of the complexity of these important wet ecosystems.

Comparison and validation of Oomycetes metabarcoding primers for Phytophthora high throughput sequencing

“…The two nested PCR approaches, DC6/ITS7 x Oom18S / ITS7 (PERO_ITS) and Oom18S/ITS7 × 5.8S1R/18ph2F (PHYTO_ITS), proved reliable for qualitative characterisation of mock Phytophthora communities without other Oomycete species. However, the second PCR strategy was much more effective for environmental samples, usually containing a much higher abundance of other Peronosporaceans such as Pythium (Cerri et al 2017). Moreover, the number of amplified Phytophthora species corresponded to the order of magnitude of Phytophthora diversity in temperate forests, which is of about 2 to 8 species (Jung et al 2010;Hansen and Delatour 1999).…”

Differences in rhizosphere microbial communities between native and non‐native Phragmites australis may depend on stand density

“…The microorganisms associated with Phragmites populations have been implicated in its performance in a variety of settings worldwide. For instance, in native European populations, bacterial and oomycete communities in the rhizosphere correlated with stages of decline in populations affected by reed die‐back syndrome (Bacci et al., 2018; Cerri et al., 2017). Likewise, several authors have suggested the key to understanding the invasive nature of non‐native Phragmites in North America may lie in microbial associations (Clay et al., 2016; Kowalski et al., 2015; Shearin et al., 2018).…”

Unraveling the Composition of the Root-Associated Bacterial Microbiota of Phragmites australis and Typha latifolia

“…Advances in sequencing technologies and computational analysis have revealed how plants host a myriad of microorganisms, collectively referred to as the microbiota, whose interactions at given plant sites define the plant microbiome ( Schlaeppi and Bulgarelli, 2015 ). The characterization of the microbiota of land plants has been gaining momentum both in basic and translational science ( Hacquard et al, 2015 ), yet elucidating the functional significance of the wetland plants microbiota is a research field in its infancy ( Bowen et al, 2017 ; Cerri et al, 2017 ). For instance, roots of wetland plants offer a unique site of colonization with access to oxygen and organic resources for microorganisms otherwise thriving in water.…”