Microbiome composition and geochemical characteristics of deep subsurface high-pressure environment, Pyhäsalmi mine Finland

Abstract

Pyhäsalmi mine in central Finland provides an excellent opportunity to study microbial and geochemical processes in a deep subsurface crystalline rock environment through near-vertical drill holes that reach to a depth of more than two kilometers below the surface. However, microbial sampling was challenging in this high-pressure environment. Nucleic acid yields obtained were extremely low when compared to the cell counts detected (1.4 × 104 cells mL−1) in water. The water for nucleic acid analysis went through high decompression (60–130 bar) during sampling, whereas water samples for detection of cell counts by microscopy could be collected with slow decompression. No clear cells could be identified in water that went through high decompression. The high-pressure decompression may have damaged part of the cells and the nucleic acids escaped through the filter. The microbial diversity was analyzed from two drill holes by pyrosequencing amplicons of the bacterial and archaeal 16S rRNA genes and from the fungal ITS regions from both DNA and RNA fractions. The identified prokaryotic diversity was low, dominated by Firmicute, Beta- and Gammaproteobacteria species that are common in deep subsurface environments. The archaeal diversity consisted mainly of Methanobacteriales. Ascomycota dominated the fungal diversity and fungi were discovered to be active and to produce ribosomes in the deep oligotrophic biosphere. The deep fluids from the Pyhäsalmi mine shared several features with other deep Precambrian continental subsurface environments including saline, Ca-dominated water and stable isotope compositions positioning left from the meteoric water line. The dissolved gas phase was dominated by nitrogen but the gas composition clearly differed from that of atmospheric air. Despite carbon-poor conditions indicated by the lack of carbon-rich fracture fillings and only minor amounts of dissolved carbon detected in formation waters, some methane was found in the drill holes. No dramatic differences in gas compositions were observed between different gas sampling methods tested. For simple characterization of gas composition the most convenient way to collect samples is from free flowing fluid. However, compared to a pressurized method a relative decrease in the least soluble gases may appear.

Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study

“…This fact is in good correlation with repeated PCR-DGGE results. Regarding bacterial part of the community, these results are in contrast with some studies of deep subsurface bedrock-related terrestrial environments where the representatives of Comamonadaceae and Acholeplasmataceae (Nyyssönen et al, 2014) or Alicyclobacillaceae (Miettinen et al, 2015) dominated. However the representatives of the family Methanobacteraceae are fairly common for deep subsurface microbial communities in oil and gas bearing environments formed in sedimentary sequences (Ng et al, 1989; Nazina et al, 1995, 2006; Bonch-Osmolovskaya et al, 2003; Mochimaru et al, 2007; Yamane et al, 2011; Frank et al, 2016).…”

“…It could be assumed that bacteria of this genus are present in the attached part of the microbial community growing organotrophically with minerals as the electron acceptors and are spread in the water at favorable conditions, as in August 2009, when an easily accessible electron acceptor nitrate was abundant. Noteworthily, sequences related to Delftia comprised the majority of RNA library from a borehole in Pyhäsalmi mine (Finland) representing the main active part of the microbial community (Miettinen et al, 2015). Similar sequences have been recovered from saline hydrothermal water in a Mexican mine (Ragon et al, 2013).…”

“…Many authors consider Firmicutes an important component of subsurface microbial communities (Davidson et al, 2011; Itävaara et al, 2011; Miettinen et al, 2015; Frank et al, 2016). Enrichments with microcrystalline cellulose and sulfate at 47°C contained three types of anaerobic organisms: (i) unidentified Clostridia (90% similarity with Thermoanaerobacterium thermosaccharolyticum ), (ii) unidentified Aquificae (89% similarity with Sulfurihydrogenibium azorense ), and (iii) Bellilinea caldifistulae (99%).…”

Fungi diversity in PM<sub>2. 5</sub> and PM<sub>1</sub> at the summit of Mt. Tai: abundance, size distribution, and seasonal variation

“…The taxonomy of ITS sequences was analyzed by RDP Classifier against the UNITE database (release 7.0, http://unite.ut.ee/index.php; Koljalg et al, 2013) using a confidence threshold of 70 %. RDP Classifier was used to determine the taxonomic composition at the phylum, class, order, family, genus, and species levels (Koiv et al, 2015;Miettinen et al, 2015). The raw reads were deposited into the NCBI Sequence Read Archive database under accession number SRR5146156.…”

acp-2017-204-RC1-Response to Reviewer #1

“…Glomerella was widely found on the surface of leaves, suggesting that leaf senescence is an important source of fungi in PM 2.5 in autumn . Some crucial environmental factors having a potential influence on fungal release and growth, such as temperature; NO 2 ; PM 10 ; SO 2 ; CO; relative humidity (Yan et al, 2016) (Moreau et al, 2016); urbanization; and accidental events, e.g., dust storms (Prospero et al, 2005), rainfall (Zhang et al, 2015), hurricanes (DeLeon-Rodriguez et al, 2013), and haze (Yan et al, 2016), have been identified. Herein Spearman's rank coefficient analysis indicated that Ca 2+ , a typical water-soluble inorganic ion from dust, was negatively related to the prevalence of Glomerella and Zasmidium in autumn (Fig.…”