Rock Surface Fungi in Deep Continental Biosphere-Exploration of Microbial Community Formation with Subsurface In Situ Biofilm Trap.

Maija Nuppunen-Puputti,Riikka Kietäväinen,Pauliina Rajala,Lotta Purkamo,Malin Bomberg,Merja Itävaara,Ilmo Kukkonen

doi:10.3390/microorganisms9010064

Maija Nuppunen-Puputti, Riikka Kietäväinen + Show 5 more

Open Access

https://doi.org/10.3390/microorganisms9010064

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Abstract

Fungi have an important role in nutrient cycling in most ecosystems on Earth, yet their ecology and functionality in deep continental subsurface remain unknown. Here, we report the first observations of active fungal colonization of mica schist in the deep continental biosphere and the ability of deep subsurface fungi to attach to rock surfaces under in situ conditions in groundwater at 500 and 967 m depth in Precambrian bedrock. We present an in situ subsurface biofilm trap, designed to reveal sessile microbial communities on rock surface in deep continental groundwater, using Outokumpu Deep Drill Hole, in eastern Finland, as a test site. The observed fungal phyla in Outokumpu subsurface were Basidiomycota, Ascomycota, and Mortierellomycota. In addition, significant proportion of the community represented unclassified Fungi. Sessile fungal communities on mica schist surfaces differed from the planktic fungal communities. The main bacterial phyla were Firmicutes, Proteobacteria, and Actinobacteriota. Biofilm formation on rock surfaces is a slow process and our results indicate that fungal and bacterial communities dominate the early surface attachment process, when pristine mineral surfaces are exposed to deep subsurface ecosystems. Various fungi showed statistically significant cross-kingdom correlation with both thiosulfate and sulfate reducing bacteria, e.g., SRB2 with fungi Debaryomyces hansenii.

Highlights

The deep continental subsurface supports diverse microbial life, comprising up to 20%of Earth’s biomass [1,2]
We retrieved samples from two different trap models from 500 and 967 m depths for molecular biology, scanning electron microscopy (SEM), and cell counting purposes. These samples had been incubated for 6 months under in situ conditions
Our methods provide the possibility for long-term in situ incubation, which may reveal how the biofilm develops over time, and that the deep subsurface fungi should not be left out of the equation in the future

Summary

Introduction

The deep continental subsurface supports diverse microbial life, comprising up to 20%of Earth’s biomass [1,2]. The deep continental subsurface supports diverse microbial life, comprising up to 20%. The anoxic deep continental bedrock environment is a hostile and challenging, oligotrophic habitat for microorganisms. The formation of biofilms and microcolonies on fracture zone rock surfaces has been demonstrated in various deep subsurface settings, e.g., gold mines and deep subseafloor crust [10,11,12,13,14,15,16]. Drake et al (2017, 2018) recently revealed fossil fungal cryptoendolithic communities with hyphae-like structures from deep drill core rock surfaces, linking fungi to deep subsurface biofilms [17,18]. Small fossilized yeast-like structures have been visualized in association with bacterial biofilms in Triberg granite, Germany [19]

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