Microbial Life in the Terrestrial Subsurface of Southeastern Coastal Plain Sediments

From individual response to population ecology: Environmental factors restricting survival of vegetative bacteria at solid-air interfaces

Combating microbial survival on dry surfaces contributes to improving public health in indoor environments (clinical and industrial settings) and extends to the natural environment. For vegetative bacteria at solid-air interfaces, lack of water impacts cellular response, and acclimation depends on community support in response to ecological processes. Gaining insights about important ecological processes leading to inhibition of microbial survival under extreme conditions, such as vicinity of highly radioactive nuclear waste, is key for improving engineering designs. Canada plans to store used nuclear fuel and radioactive waste in a deep geological repository (DGR) with a multiple-barrier system constructed at an approximate depth of 500 m. Microorganisms in highly compacted bentonite surrounding used fuel containers will be challenged by high pressure, temperature, and radiation, as well as limited water and nutrients. Thus, it is difficult to estimate microbial activities, given that the prime concern for a microbial community is survival, and energy expenditure is regulated. To enable preventive measures and for risk evaluation, a deeper understanding of community-based survival strategies of bacterial cells exposed to air (gaseous phase) during prolonged periods of desiccation is required. An in-depth review of collective studies that assess microbial survival and persistence during desiccation is presented here to augment and direct our prior knowledge about tactics used by bacteria for survival at interfaces in hostile natural environments including and similar to a DGR.

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

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.

Fungi in Deep Subsurface Environments

The igneous crust of the oceans and the continents represents the major part of Earth's lithosphere and has recently been recognized as a substantial, yet underexplored, microbial habitat. While prokaryotes have been the focus of most investigations, microeukaryotes have been surprisingly neglected. However, recent work acknowledges eukaryotes, and in particular fungi, as common inhabitants of the deep biosphere, including the deep igneous provinces. The fossil record of the subseafloor igneous crust, and to some extent the continental bedrock, establishes fungi or fungus-like organisms as inhabitants of deep rock since at least the Paleoproterozoic, which challenges the present notion of early fungal evolution. Additionally, deep fungi have been shown to play an important ecological role engaging in symbiosis-like relationships with prokaryotes, decomposing organic matter, and being responsible for mineral weathering and formation, thus mediating mobilization of biogeochemically important elements. In this review, we aim at covering the abundance and diversity of fungi in the various igneous rock provinces on Earth as well as describing the ecological impact of deep fungi. We further discuss what consequences recent findings might have for the understanding of the fungal distribution in extensive anoxic environments and for early fungal evolution.

Characterisation of yeasts isolated from deep igneous rock aquifers of the Fennoscandian Shield

The diversity of prokaryotes in the groundwater deep below the surface of the Baltic Sea at the Aspö Hard Rock Laboratory (HRL) in southeast Sweden is well documented. In addition, there is some evidence that eukaryotes, too, are present in the deep groundwater at this site, although their origins are uncertain. To extend the knowledge of eukaryotic life in this environment, five yeast, three yeastlike, and 17 mold strains were isolated from Aspö HRL groundwater between 201 and 444 m below sea level. Phenotypic testing and phylogenetic analysis of 18S rDNA sequences of the five yeast isolates revealed their relationships to Rhodotorula minuta and Cryptococcus spp. Scanning and transmission electron microscopy demonstrated that the strains possessed morphological characteristics typical for yeast, although they were relatively small, with an average length of 3 micro m. Enumeration through direct counting and most probable number methods showed low numbers of fungi, between 0.01 and 1 cells mL(-1), at some sites. Five of the strains were characterized physiologically to determine whether they were adapted to life in the deep biosphere. These studies revealed that the strains grew within a pH range of 4-10, between temperatures of 4 degrees C and 25-30 degrees C, and in NaCl concentrations from 0 to 70 g L(-1). These growth parameters suggest a degree of adaptation to the groundwater at Aspö HRL. Despite the fact that these eukaryotic microorganisms may be transient members of the deep biosphere microbial community, many of the observations of this study suggest that they are capable of growing in this extreme environment.

Comparison of bacteria from deep subsurface sediment and adjacent groundwater

Samples of groundwater and the enclosing sediments were compared for densities of bacteria using direct (acridine orange direct staining) and viable (growth on 1% PTYG medium) count methodology. Sediments to a depth of 550 m were collected from boreholes at three sites on the Savannah River Site near Aiken, South Carolina, using techniques to insure a minimum of surface contamination. Clusters of wells screened at discreet intervals were established at each site. Bacterial densities in sediment were higher, by both direct and viable count, than in groundwater samples. Differences between direct and viable counts were much greater for groundwater samples than for sediment samples. Densities of bacteria in sediment ranged from less than 1.00×10(6) bacteria/g dry weight (gdw) up to 5.01 ×10(8) bacteria/gdw for direct counts, while viable counts were less than 1.00×10(3) CFU/gdw to 4.07×10(7) CFU/gdw. Bacteria densities in groundwater were 1.00×10(3)-6.31×10(4) bacteria/ml and 5.75-4.57×10(2) CFU/ml for direct and viable counts, respectively. Isolates from sediment were also found to assimilate a wider variety of carbon compounds than groundwater bacteria. The data suggest that oligotrophic aquifer sediments have unique and dense bacterial communities that are attached and not reflected in groundwater found in the strata. Effective in situ bioremediation of contaimination in these aquifers may require sampling and characterization of sediment communities.

Microbial transformation of heterocyclic molecules in deep subsurface sediments

Recently attempts have been made to establish the presence and to determine the metabolic versatility of microorganisms in the terrestrial deep subsurface at the Savannah River Plant, Aiken, SC, USA. Sediment samples obtained at 20 different depths of up to 526 m were examined to determine carbon mineralization under aerobic, sulfate-reducing, and methanogenic conditions. The evolution of(14)CO2 from radiolabelled glucose was observed under aerobic conditions in all sediments, whereas pyridine was transformed in 50% of the 20 sediments and indole was metabolized in 85% of the sediments. Glucose mineralization in certain sediments was comparable to that in the surface environment. Sulfate was reduced in only five sediments, and two were carbon limited. Methane production was detected in ten sediments amended with formate only after long-term incubations. The transformation of indole and pyridine was only rarely observed under sulfate-reducing conditions and was never detected in methanogenic incubations. This study provides information concerning the metabolic capability of both aerobic and anaerobic microorganisms in the deep subsurface and may prove useful in determining the feasibility of microbial decontamination of such environments.