Managed and Unmanaged Pinus sylvestris Forest Stands Harbour Similar Diversity and Composition of the Phyllosphere and Soil Fungi

Abstract

The aim was to assess fungal communities associated with living needles and soil of Pinus sylvestris in managed and unmanaged forest stands to get a better understanding of whether and how different intensities of forest management affects fungal diversity and community composition under the north temperate forest zone conditions. The study was carried out in three national parks in Lithuania. Each included five study sites in managed stands and five in unmanaged stands. At each site, three random soil cores and five random last-year needle samples were collected. Following DNA isolation, a DNA fragment of the ITS2 rRNA gene region of each sample was individually amplified and subjected to high-throughput sequencing. Analysis of 195,808 high-quality reads showed the presence of 1909 fungal taxa. Richness and composition of fungal taxa were similar in each substrate (needles and soil) in managed vs. unmanaged sites. The most common fungi in needles were Coleosporium campanulae (12.4% of all fungal sequences), Unidentified sp. 3980_1 (12.4%), Unidentified sp. 3980_4 (4.1%) and Sydowia polyspora (3.1%). In soil: Unidentified sp. 3980_21 (8.6%), Umbelopsis nana (8.2%), Archaeorhizomyces sp. 3980_5 (8.1%) and Penicillium spinulosum (6.3%). The results demonstrated that managed and unmanaged P. sylvestris stands support similar diversity and composition of fungal communities associated with living needles and soil.

Seasonal Dynamics of Fungi Associated with Healthy and Diseased Pinus sylvestris Needles in Northern Europe

“…Different epiphytes and endophytes have distinct sporulation regimes and possibly prefer tissues with different age indicating temporal complementarity in niche recruitment. Similar to findings from needles of larch [ 14 ] and first-year needles of spruce [ 14 , 15 ], some fungal species obviously depend on colonizing first-year needles of P. sylvestris , such as species in the rust genus Coleosporium [ 65 ]. As with D. septosporum , L. conigenum was more abundant ( p < 0.05) on lower part of the canopy compared to the upper part where the needles are exposed to harsher environmental conditions, e.g., the frequent, repeated, rapid shifts in humidity, temperature and UV radiation.…”

Comparative analyses of sooty mould communities from Brazil and Central Europe

“…The colour scale illustrates the dominance (%) within the sites. The dendrogram on top illustrates the similarity of the sites; the one on the left represents the similarity in the pattern of occurrence of the individual fungal OTUs and Corlett 2019; Egidi et al 2019;Epstein et al 2019;Li et al 2019;Lynikiene et al 2020;Morales-Rodriguez et al 2019;Nerva et al 2019;Qian et al 2020;Ricks and Koide 2019;Saravesi et al 2019;Wilkinson et al 2019;Würth et al 2019;Yao et al 2019;Zhang et al 2019), others strongly recommended the use of ITS1 (Mbareche et al 2020), as it had already been implemented in many studies (Beule et al 2019;Checinska Sielaff et al 2019;Del Frari et al 2019;Schiro et al 2019). Few studies are based on both ITS regions (Janakiev et al 2019).…”

“…The use of operational taxonomic units (OTUs) versus the recent use of amplicon sequence variants (ASVs) is also inconsistent. Although there are recommendations to use only ASVs (Callahan et al 2017), resulting in a reduction in the number of dominant species (Egidi et al 2019), many of the current studies are still based on OTUs (Bao et al 2019;Beng and Corlett 2019;Beule et al 2019;Checinska Sielaff et al 2019;Epstein et al 2019;Janakiev et al 2019;Lynikiene et al 2020;Morales-Rodriguez et al 2019;Nerva et al 2019;Pan et al 2019;Qian et al 2020;Ricks and Koide 2019;Saravesi et al 2019;Wilkinson et al 2019;Würth et al 2019;Yao et al 2019;Zhang et al 2019), but others rely on ASVs (Del Frari et al 2019;Egidi et al 2019;Li et al 2019), or OTUs generated from ASVs (Ezeokoli et al 2020), and even OTUs from cultivationbased Sanger sequencing are still in use (Janowsky et al 2019). With the availability of the VSEARCH tool within the QIIME2 pipeline, allowing the easy aggregation of OTUs from ASVs, the Illumina sequencing datasets in this Fig.…”

“…Most current studies do not distinguish between epiphytic and endophytic fungal communities, as the complete microbiome is usually extracted from whole leaves (Lynikiene et al 2020;Qian et al 2020;Würth et al 2019). This is problematic in that endophytic fungi are more hostdependent than epiphytic fungi (Fonseca-García et al 2016;Lau et al 2013;Peršoh 2013).…”

Patterns of Fungal Diversity in Needles, Rootlets and Soil of Endemic Pinus Peuce

“…Principles of bioinformatics followed Lynikienė et al (2020). The sequences obtained were subjected to quality control and clustering in the SCATA NGS sequencing pipeline.…”