Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe.

Leho Tedersoo,Elisabeth Rähn,Hardi Tullus,Sergei Põlme,Raul Rosenvald,Rasmus Puusepp,Inge Varik,Indrek Hiiesalu,Ivar Sibul,Katrin Jürimaa,Franz Buegger,Mohammad Bahram,Tiia Drenkhan,Marek Metslaid,Karin Pritsch,Daniyal Gohar,Kalev Adamson,Rein Drenkhan,Kaire Loit,Ahto Agan,Reimo Lutter,Vladimir Mikryukov,Sten Anslan,Kessy Abarenkov,Eveli Otsing,Allar Padari,Urmas Kõljalg,Rasekh Amiri,Niloufar Hagh‐Doust

doi:10.3389/fmicb.2020.01953

Abstract

Soil microbiome has a pivotal role in ecosystem functioning, yet little is known about its build-up from local to regional scales. In a multi-year regional-scale survey involving 1251 plots and long-read third-generation sequencing, we found that soil pH has the strongest effect on the diversity of fungi and its multiple taxonomic and functional groups. The pH effects were typically unimodal, usually both direct and indirect through tree species, soil nutrients or mold abundance. Individual tree species, particularly Pinus sylvestris, Picea abies, and Populus x wettsteinii, and overall ectomycorrhizal plant proportion had relatively stronger effects on the diversity of biotrophic fungi than saprotrophic fungi. We found strong temporal sampling and investigator biases for the abundance of molds, but generally all spatial, temporal and microclimatic effects were weak. Richness of fungi and several functional groups was highest in woodlands and around ruins of buildings but lowest in bogs, with marked group-specific trends. In contrast to our expectations, diversity of soil fungi tended to be higher in forest island habitats potentially due to the edge effect, but fungal richness declined with island distance and in response to forest fragmentation. Virgin forests supported somewhat higher fungal diversity than old non-pristine forests, but there were no differences in richness between natural and anthropogenic habitats such as parks and coppiced gardens. Diversity of most fungal groups suffered from management of seminatural woodlands and parks and thinning of forests, but especially for forests the results depended on fungal group and time since partial harvesting. We conclude that the positive effects of tree diversity on overall fungal richness represent a combined niche effect of soil properties and intimate associations.

Highlights

Soil microorganisms such as bacteria, archaea and fungi play integral roles in soil ecosystem functioning
258 putative fungal operational taxonomic units (OTUs) (1.7%) representing 0.2% of sequences remained unidentified at the phylum level
We addressed the effects of selective harvesting and time since harvesting on soil microbiome by subsampling forest plots dominated by Picea abies, Pinus sylvestris, Betula pendula and Quercus robur aged 9–100 years

Summary

Introduction

Soil microorganisms such as bacteria, archaea and fungi play integral roles in soil ecosystem functioning. It has been argued that the diversity of soil organisms is of particular importance for ecosystem services and resilience to disturbances, with a potential to ameliorate stress caused by global change (Langenheder et al, 2010; Bardgett and van der Putten, 2014). Many of these soil organisms are vulnerable to shifts in land use, changing climate and ecosystem management (Van der Putten, 2013; George et al, 2019; Makiola et al, 2019; Sterkenburg et al, 2019); some of the most conspicuous rare species are protected (Dahlberg et al, 2010). Advances in the socalled environmental DNA (eDNA) analyses have enormously improved our understanding about the diversity and distribution of small soil organisms including fungi (Taberlet et al, 2018; Nilsson et al, 2019)

Methods

Results

Conclusion