E. van Heerden

Nematoda from the terrestrial deep subsurface of South Africa

Since its discovery over two decades ago, the deep subsurface biosphere has been considered to be the realm of single-cell organisms, extending over three kilometres into the Earth’s crust and comprising a significant fraction of the global biosphere. The constraints of temperature, energy, dioxygen and space seemed to preclude the possibility of more-complex, multicellular organisms from surviving at these depths. Here we report species of the phylum Nematoda that have been detected in or recovered from 0.9–3.6-kilometre-deep fracture water in the deep mines of South Africa but have not been detected in the mining water. These subsurface nematodes, including a new species, Halicephalobus mephisto, tolerate high temperature, reproduce asexually and preferentially feed upon subsurface bacteria. Carbon-14 data indicate that the fracture water in which the nematodes reside is 3,000–12,000-year-old palaeometeoric water. Our data suggest that nematodes should be found in other deep hypoxic settings where temperature permits, and that they may control the microbial population density by grazing on fracture surface biofilm patches. Our results expand the known metazoan biosphere and demonstrate that deep ecosystems are more complex than previously accepted. The discovery of multicellular life in the deep subsurface of the Earth also has important implications for the search for subsurface life on other planets in our Solar System.

Aerobic Cr(VI) reduction by Thermus scotoductus strain SA‐01

Aim:  To evaluate Thermus scotoductus SA‐01’s ability to reduce Cr(VI) aerobically.

Oxylipins and ascospore morphology in the ascomycetous yeast genus Dipodascus

Immunofluorescence microscopy was used to assess members of the yeast genus Dipodascus for the presence of 3-hydroxy oxylipins. Fluorescence was associated with the aggregating ascospores in all species tested, thus suggesting the association of 3-hydroxy oxylipins with these cells, especially the surrounding slime sheaths. An ultrastructural study of the ascospores revealed sheaths with indentations, probably caused by the close packing of the ascospores to form clusters. In addition, an increase in the neutral and glycolipid fractions as well as a decrease in the phospholipid fraction during ascosporogenesis in D. ambrosiae was found.

Discovery of a novel carboxylesterase through functional screening of a pre-enriched environmental library

Aims:  The aim of this study was to demonstrate the application of environmental sample pre‐enrichment to access novel carboxylesterases from environmental genomes, along with subsequent heterologous expression and characterization of the discovered enzyme(s).

Eukaryotic opportunists dominate the deep-subsurface biosphere in South Africa.

Following the discovery of the first Eukarya in the deep subsurface, intense interest has developed to understand the diversity of eukaryotes living in these extreme environments. We identified that Platyhelminthes, Rotifera, Annelida and Arthropoda are thriving at 1.4 km depths in palaeometeoric fissure water up to 12,300 yr old in South African mines. Protozoa and Fungi have also been identified; however, they are present in low numbers. Characterization of the different species reveals that many are opportunistic organisms with an origin due to recharge from surface waters rather than soil leaching. This is the first known study to demonstrate the in situ distribution of biofilms on fissure rock faces using video documentation. Calculations suggest that food, not dissolved oxygen is the limiting factor for eukaryal population growth. The discovery of a group of Eukarya underground has important implications for the search for life on other planets in our solar system.

Metabolic promiscuity from the deep subsurface: a story of survival or superiority

The Witwatersrand Supergroup is a 2.9-billion-year-old formation of low permeability sandstone and shale with minor volcanic units and conglomerates with an ambient rock temperature of approximately 60°C. Thermus scotoductus SA-01 was isolated from fissure water at a depth of 3.2 kmbls in a South African gold mine and it shows the ability to reduce a variety of heavy metals under anaerobic conditions. It has been postulated that such microorganisms could play an important role in nutrient and metal cycling within the subsurface. Recently, our studies indicate that the cycling of metals could also occur under aerobic conditions and not only by the action of redox active enzymes, but other diverse metabolic proteins as well. In this study the capability of specific proteins to interact with metals is elucidated. Using Thermus SA-01 and its now completed genome sequence, metal reduction is studied through classic proteomic- and genomic methods. Finally we identify thermostable enzymes responsible for the transformation of various metals (Iron, Chrome, Uranium, Gold, etc) and discuss that reduction occurs via the serendipitous action of enzymes with other primary physiological functions, some of which are classical catabolic enzymes and anabolic proteins. This paper discusses the use of a ubiquitous enzyme/protein performing more than one function, possibly detoxifying the environment and using moonlighting as resource to decrease cellular energy requirements rather than elaborate metabolism in the subsurface.

Fluctuations in populations of subsurface methane oxidizers in coordination with changes in electron acceptor availability

ABSTRACT The concentrations of electron donors and acceptors in the terrestrial subsurface biosphere fluctuate due to migration and mixing of subsurface fluids, but the mechanisms and rates at which microbial communities respond to these changes are largely unknown. Subsurface microbial communities exhibit long cellular turnover times and are often considered relatively static—generating just enough ATP for cellular maintenance. Here, we investigated how subsurface populations of CH4 oxidizers respond to changes in electron acceptor availability by monitoring the biological and geochemical composition in a 1339 m‐below‐land‐surface (mbls) fluid‐filled fracture over the course of both longer (2.5 year) and shorter (2‐week) time scales. Using a combination of metagenomic, metatranscriptomic, and metaproteomic analyses, we observe that the CH4 oxidizers within the subsurface microbial community change in coordination with electron acceptor availability over time. We then validate these findings through a series of 13C‐CH4 laboratory incubation experiments, highlighting a connection between composition of subsurface CH4 oxidizing communities and electron acceptor availability.

The biomass and biodiversity of the continental subsurface

Despite accounting for a significant portion of the Earth’s prokaryotic biomass, controls on the abundance and biodiversity of microorganisms residing in the continental subsurface are poorly understood. To redress this, we compiled cell concentration and microbial diversity data from continental subsurface localities around the globe. Based on considerations of global heat flow, surface temperature, depth and lithology, we estimated that the continental subsurface hosts 2 to 6 × 1029 cells and found that other variables such as total organic carbon and groundwater cellular abundances do not appear to be predictive of cell concentrations in the continental subsurface. Although we were unable to identify a reliable predictor of species richness in the continental subsurface, we found that bacteria are more abundant than archaea and that their community composition was correlated to sample lithology. Using our updated continental subsurface cellular estimate and existing literature, we estimate that the total global prokaryotic biomass is approximately 23 to 31 Pg of carbon C (PgC), roughly 4 to 10 times less than previous estimates.The abundance of microorganisms in the continental subsurface may have been overestimated, according to a review compilation of data from subsurface localities around the globe.