New ecosystems in the deep subsurface follow the flow of water driven by geological activity.

Eukarya have been discovered in the deep subsurface at several locations in South Africa, but how organisms reach the subsurface remains unknown. We studied river-subsurface fissure water systems and identified Eukarya from a river that are genetically identical for 18S rDNA. To further confirm that these are identical species one metazoan species recovered from the overlying river interbred successfully with specimen recovered from an underlying mine at -1.4 km. In situ seismic simulation experiments were carried out and show seismic activity to be a major force increasing the hydraulic conductivity in faults allowing organisms to create ecosystems in the deep subsurface. As seismic activity is a non-selective force we recovered specimen of algae and Insecta that defy any obvious other explanation at a depth of -3.4 km. Our results show there is a steady flow of surface organisms to the deep subsurface where some survive and adapt and others perish. As seismic activity is also present on other planets and moons in our solar system the mechanism elucidated here may be relevant for future search and selection of landing sites in planetary exploration.

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

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.

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.

Divergent effects of RIP1 or RIP3 blockade in murine models of acute liver injury.

Necroptosis is a recently described Caspase 8-independent method of cell death that denotes organized cellular necrosis. The roles of RIP1 and RIP3 in mediating hepatocyte death from acute liver injury are incompletely defined. Effects of necroptosis blockade were studied by separately targeting RIP1 and RIP3 in diverse murine models of acute liver injury. Blockade of necroptosis had disparate effects on disease outcome depending on the precise etiology of liver injury and component of the necrosome targeted. In ConA-induced autoimmune hepatitis, RIP3 deletion was protective, whereas RIP1 inhibition exacerbated disease, accelerated animal death, and was associated with increased hepatocyte apoptosis. Conversely, in acetaminophen-mediated liver injury, blockade of either RIP1 or RIP3 was protective and was associated with lower NLRP3 inflammasome activation. Our work highlights the fact that diverse modes of acute liver injury have differing requirements for RIP1 and RIP3; moreover, within a single injury model, RIP1 and RIP3 blockade can have diametrically opposite effects on tissue damage, suggesting that interference with distinct components of the necrosome must be considered separately.

Does aspartic acid racemization constrain the depth limit of the subsurface biosphere?

Previous studies of the subsurface biosphere have deduced average cellular doubling times of hundreds to thousands of years based upon geochemical models. We have directly constrained the in situ average cellular protein turnover or doubling times for metabolically active micro-organisms based on cellular amino acid abundances, D/L values of cellular aspartic acid, and the in vivo aspartic acid racemization rate. Application of this method to planktonic microbial communities collected from deep fractures in South Africa yielded maximum cellular amino acid turnover times of ~89 years for 1 km depth and 27 °C and 1-2 years for 3 km depth and 54 °C. The latter turnover times are much shorter than previously estimated cellular turnover times based upon geochemical arguments. The aspartic acid racemization rate at higher temperatures yields cellular protein doubling times that are consistent with the survival times of hyperthermophilic strains and predicts that at temperatures of 85 °C, cells must replace proteins every couple of days to maintain enzymatic activity. Such a high maintenance requirement may be the principal limit on the abundance of living micro-organisms in the deep, hot subsurface biosphere, as well as a potential limit on their activity. The measurement of the D/L of aspartic acid in biological samples is a potentially powerful tool for deep, fractured continental and oceanic crustal settings where geochemical models of carbon turnover times are poorly constrained. Experimental observations on the racemization rates of aspartic acid in living thermophiles and hyperthermophiles could test this hypothesis. The development of corrections for cell wall peptides and spores will be required, however, to improve the accuracy of these estimates for environmental samples.

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.

Trace element concentrations from lichen transplants in Pretoria, South Africa.

PURPOSE: The purpose of this study was to assess the level and possible sources of trace elements in Tshwane metropolis using transplanted lichen thallus of Parmelia sulcata with a view to evaluating the ability of this lichen species to monitor air pollutants from a perceived polluted environment. METHODS: Samples of the lichen thalli were transplanted into ten different sites and covered with a net. Samples were exposed for 3 months. Concentrations of ten trace elements were determined with the use of inductively coupled plasma mass spectrometry. RESULTS: A significant difference was observed in the values of elemental concentration in lichen from unpolluted area and those transplanted to all the sites (p < 0.01). Variations in values of trace elements recorded in lichen transplant from different sites were also statistically significant (p < 0.01). The high traffic sites showed significantly higher elemental concentrations, particularly for Pb, Zn, and Cu than the industrial and residential areas (p < 0.05). CONCLUSION: Trends in the trace element values from different sites suggested that the elements might have come from anthropogenic sources.

Investigating Jacaranda mimosifolia tree as biomonitor of atmospheric trace metals.

Studies on the use of tree bark as biomonitors for environmental pollutants are still very scarce. We evaluated the reliability of using Jacaranda mimosifolia, a common tree in Tshwane City of South Africa, as a suitable biomonitor of atmospheric trace metals. Bark samples were collected from ten different locations during two sampling periods. The concentrations of the metals were determined by inductively coupled plasma mass spectrometry. The concentrations of the metals were 33.2-1,795 microg/g (Pb), 21.4-210 microg/g (Cu), 68.4-490 microg/g (Zn), 30.6-2,916 microg/g (Cr), 0.12-1.34 microg/g (Cd), and 6.04-68.0 microg/g (V), respectively. The differences obtained for the results from different sites were significant (p < 0.05). A significant difference was also observed between the two sampling periods. The trace metals concentrations suggested that automobile emissions are a major source of these metals. The study also confirms the suitability of J. mimosifolia as a biomonitor of atmospheric deposition of these metals.

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). METHODS AND RESULTS: A positive recombinant clone (UVCL29), conferring an esterase phenotype was identified from a shotgun gene library. The complete sequence of the 3.0 kb DNA insert from the pUVCL29 recombinant plasmid was obtained using primer-walking strategies. Nucleotide sequence analysis revealed a complete 945 bp open reading frame (ORF1). Translational analysis of the ORF1 showed a protein of 314 amino acids (named EstAM) with a predicted molecular weight of 34 kDa. EstAM's primary structure showed a classical (-G-D-S-A-G-) motif, corresponding with the generally conserved (G-x-S-x-G) esterase signature motif. Identity searches indicated that EstAM has high sequence similarity with esterases from family IV. EstAM was successfully expressed in Escherichia coli in a biologically active form. Partial purification was achieved using a one-step Pro-PurTM IMAC column. Biochemical characterization revealed that EstAM has a temperature optimum of 40 degrees C. CONCLUSION: Based on its substrate profile, EstAM was classified as a carboxylesterase because of its preference for short p-nitrophenyl ester substrates. SIGNIFICANCE AND IMPACT OF THE STUDY: This study is a demonstration of the successful application of environmental sample pre-enrichment technology in accessing novel esterases from a mining environment.

Haemophilus paragallinarum haemagglutinin: role in adhesion, serotyping and pathogenicity.

It is suggested that Haemophilus paragallinarum requires at least three haemagglutinins for adhesion during infection. This paper reports the partial purification and characterization of the HA-L haemagglutinin from H. paragallinarum strain 46-C3, a heat sensitive, trypsin sensitive haemagglutinin that has been shown to be the serovar specific haemagglutinin in this organism. Using the pl and molecular mass obtained, it was shown that this protein shares similarities with other types of adhesins found in Gram-negative bacteria. The haemagglutination assay conditions were optimized at pH 7.5 at 37 degrees C. It was also shown that activity is enhanced by the addition of Ca2+ and Mn2+ ions.

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

AIM: To evaluate Thermus scotoductus SA-01's ability to reduce Cr(VI) aerobically. METHODS AND RESULTS: T. scotoductus SA-01 is able to reduce Cr(VI) aerobically when grown in a complex organic medium containing Cr(VI) concentrations up to 0.5 mmol l(-1). Suspension of T. scotoductus SA-01 cells also reduced Cr(VI) aerobically under nongrowth conditions using a variety of electron donors as well as in the absence of an exogenous electron donor. The optimum temperature and pH for Cr(VI) reduction under nongrowth conditions were found to be 80 degrees C and 7, respectively. It was also found that the Cr(VI) reduction was catalysed by a cytoplasmic, constitutively expressed enzyme. CONCLUSIONS: Apart from SA-01's ability to reduce Cr(VI) through a strictly anaerobic membrane-bound mechanism (unpublished data), it also has a second enzyme localized in the cytoplasm that can reduce Cr(VI) aerobically. As this enzyme is constitutively expressed and not induced by Cr(VI), it remains to be determined whether it has any other physiological functions. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report of a Thermus species able to reduce Cr(VI) aerobically and extends the knowledge of parameters associated with Cr(VI) reduction. Employing thermophiles in bioremediation using industrial bioreactors would cancel the need for expensive cooling systems.

Isolation and characterization of a Geobacillus thermoleovorans strain from an ultra-deep South African gold mine.

A thermophilic facultative bacterial isolate was recovered from 3.2km depth in a gold mine in South Africa. This isolate, designated GE-7, was cultivated from pH 8.0, 50 degrees C water from a dripping fracture near the top of an exploration tunnel. GE-7 grows optimally at 65 degrees C and pH 6.5 on a wide range of carbon substrates including cellobiose, hydrocarbons and lactate. In addition to O(2), GE-7 also utilizes nitrate as an electron acceptor. GE-7 is a long rod-shaped bacterium (4-6microm longx0.5microm wide) with terminal endospores and flagella. Phylogenetic analysis of GE-7 16S rDNA sequence revealed high sequence similarity with G. thermoleovorans DSM 5366(T) (99.6%), however, certain phenotypic characteristics of GE-7 were distinct from this and other previously described strains of G. thermoleovorans.

The testing and modification of a commercially available transport medium for the transportation of pure cultures of Haemophilus paragallinarum for serotyping.

Haemophilus paragallinarum, the causative agent of infectious coryza in poultry, is an extremely fastidious organism requiring specific growth conditions for isolation. For complete control of the disease in regions where more that one of the serovars of the different serogroups occurs, it is essential that the bacterium causing the problem be isolated and serotyped. This work describes the modification and testing of transport media, which will ensure the survival of the causative agents in suspected infectious coryza cases for transport to a laboratory where the bacterium can be isolated and serotyped. The various transport media used are based on commercially available Amies Transport Medium supplemented with the different supplements used for the growth of H. paragallinarum. It was established that the bacterium remains viable for up to 18 days in Amies Transport Medium containing all the supplements when stored at 4 degrees C or 37 degrees C. At room temperature or 25 degrees C, there was no difference in the survival of H. paragallinarum in commercial Amies Transport Medium (without charcoal) and Amies Transport Medium with supplements.

Genetic organisation of the capsule transport gene region from Haemophilus paragallinarum.

The region involved in export of the capsule polysaccharides to the cell surface of Haemophilus paragallinarum was cloned and the genetic organisation determined. Degenerate primers designed from sequence alignment of the capsule transport genes of Haemophilus influenzae, Pasteurella multocida and Actinobacillus pleuropneumoniae were used to amplify a 2.6 kb fragment containing a segment of the H. paragallinarum capsule transport gene locus. This fragment was used as a digoxigenin labelled probe to isolate the complete H. paragallinarum capsule transport gene locus from genomic DNA. The sequence of the cloned DNA was determined and analysis revealed the presence of four genes, each showing high homology with known capsule transport genes. The four genes were designated hctA, B, C and D (for H. paragallinarum capsule transport genes) and the predicted products of these genes likely encode an ATP-dependent export system responsible for transport of the capsule polysaccharides to the cell surface, possibly a member of a super family designated ABC (ATP-binding cassette) transporters.

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.

Virulence of South African isolates of Haemophilus paragallinarum. Part 3: experimentally produced NAD-independent isolate.

A NAD-dependent isolate 46 (C-3) of Haemophilus paragallinarum, which was previously demonstrated to be of high virulence, was transformed to NAD independence using a plasmid isolated from a naturally occurring NAD-independent isolate of H. paragallinarum. The transformation was performed by two different methods and the identity of all of the isolates, before and after transformation was confirmed using a H. paragallinarum-specific PCR test. The transformed NAD-independent serovar C-3 isolate and the wild-type serovar C-3 isolate were used to experimentally infect vaccinated layer chickens. It was shown that the transformation to NAD independence significantly altered the virulence of the serovar C-3 isolate that was used in the transformation experiment. The mechanisms responsible for a decrease in virulence are not clear, but may be related to the pathology of the transformed isolate in the sinus of the chickens.

Bioconcentration of atrazine, zinc and iron in the blood of Tilapia sparrmanii (Cichlidae).

1. The bioconcentration of atrazine, zinc and iron in the blood of Tilapia sparrmanii has been determined separately in each of six exposure groups. 2. An increased bioconcentration of atrazine in the blood occurred with an increased exposure concentration. 3. With exposure to zinc, there was a gradual decrease in bioconcentration of zinc in the blood of T. sparrmanii with an increased concentration in the water. 4. A similar tendency was observed during iron exposure, except that the decrease in bioconcentration was not significant.