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Intraterrestrials : discovering the strangest life on Earth
Life thrives in the deepest, darkest recesses of Earth's crust - from methane seeps in the ocean floor to the highest reaches of Arctic permafrost - and it is unlike anything seen on the surface. Intraterrestrials shares what scientists are learning about these strange types of microbial life - and how research expeditions to some of the most extreme locales on the planet are broadening our understanding of what life is and how its earliest forms may have evolved. Drawing on her experiences and those of her fellow scientists working in challenging and often dangerous conditions, Karen Lloyd takes readers on an adventure from the bottom of the ocean through the jungles of Central America to the high-altitude volcanoes of the Andes.
BOOK
Molecular basis for inhibition of methane clathrate growth by a deep subsurface bacterial protein
Abstract
Methane clathrates on continental margins contain the largest stores of hydrocarbons on Earth, yet the role of biomolecules in clathrate formation and stability remains almost completely unknown. Here, we report new methane clathrate-binding proteins (CbpAs) of bacterial origin discovered in metagenomes from gas clathrate-bearing ocean sediments. CbpAs show similar suppression of methane clathrate growth as the commercial gas clathrate inhibitor polyvinylpyrrolidone and inhibit clathrate growth at lower concentrations than antifreeze proteins (AFPs) previously tested. Unlike AFPs, CbpAs are selective for clathrate over ice. CbpA3 adopts a nonglobular, extended structure with an exposed hydrophobic surface, and, unexpectedly, its TxxxAxxxAxx motif common to AFPs is buried and not involved in clathrate binding. Instead, simulations and mutagenesis suggest a bipartite interaction of CbpAs with methane clathrate, with the pyrrolidine ring of a highly conserved proline residue mediating binding by filling empty clathrate cages. The discovery that CbpAs exert such potent control on methane clathrate properties implies that biomolecules from native sediment bacteria may be important for clathrate stability and habitability.
Journal Article
Movement of contaminants in the unsaturated zone of the subsurface from a low flush on-site sanitation system in Ivory Park, Johannesburg
This study measured the movement of contaminants in the unsaturated zone of the subsurface from a low-flush on-site sanitation system (also known as an aqua-privy) at three sites in Ivory Park, which at the time that the fieldwork was done was a newly-established informal settlement in Johannesburg. The aim of the study was to provide field data on the movement of contaminants from this sanitation system in a low-income area, in these climatic and subsurface conditions, and to counter a perception that on-site sanitation will inevitably cause pollution. Subsurface conditions consisted nominally of a 1 m thick layer of silty sand with denser gravel at the bottom of it, underlain by a stiff sandy clay (residual granite), with the natural water table more than 15 m below ground surface. In summary, it can be deduced that movement in the unsaturated zone of bacterial indicators, nitrogen and phosphorus from low-flush on-site sanitation systems in low-income areas is very limited, as long as the effluent remains in the subsurface. More specifically, the impact in terms of COD appears to be negligible, with substantial treatment apparently taking place within the soakaway or within the immediate vicinity thereof. With respect to (i) bacteriological indicators, (ii) nitrogen (in the form of ammonium, nitrite and nitrate) and (iii) phosphorus (in the form of Total Phosphorus), using the distilled water washout technique, there is a very rapid drop-off of contamination with distance from the soakaway. At horizontal distances of 3 m from the soakaway, levels of the measured contaminants had dropped to values consistent with the background levels. The results of this study are not confined to this particular sanitation system. By virtue of the higher hydraulic loading, these results provide an upper bound for contaminant movement from dry on-site systems under similar conditions.
Journal Article
Antibiotic- and heavy-metal resistance in bacteria isolated from deep subsurface in El Callao region, Venezuela
The effect of contamination with mercury (Hg) in the deep subsurface bacterial communities in the region of El Callao (Bolívar State, Venezuela) was investigated. Bacterial communities from two deep levels (-288 m and -388 m) in a gold mine were studied with the aim of describe the most relevant features of their colonizing indigenous culturable bacteria. Antibiotic and heavy metals resistance patterns, presence of the merA gene and plasmids in resistant isolates were evaluated. A high frequency of resistant indigenous bacteria to Hg and other heavy metals was found. From 76 Hg-resistant isolates tested 73.7 % were, in addition, resistant to ampicillin, 86.8% to chloramphenicol, 67.1 % for tetracycline, 56.6 % streptomycin, and 51.3 % kanamycin. Furthermore, it was found that 40.74 % (-328 mm) and 26.53 % (-388 m) of Hg-resistant bacteria were simultaneously resistant to both four and five of these antibiotics. The presence of low and high molecular weight plasmids was detected and, despite that isolated showed resistance to mercurial compounds, the presence of the gene merA was detected only in 71.05 % of strains. These results suggest that exposure to Hg could be a selective pressure on the proliferation of antibiotic-resistant bacteria and promote the preservation and propagation of these resistance genes. However, the existence of such resistances to these depths could also support the idea that antibiotic resistance in these bacteria is natural and has a more ancient origin than their exposure to Hg.
Journal Article
Phylogenetic characterization of bacteria in the subsurface microbial culture collection
The Subsurface Microbial Culture Collection (SMCC) was established by the U.S. Dept. of Energy (DOE) and contains nearly 10,000 strains of microorganisms (mostly bacteria) isolated from terrestrial subsurface environments. Selected groups of bacterial isolates from three sample sites situated above geochemically and hydrologically different subsurface environments have been characterized by phylogenetic analysis of 16S ribosomal RNA (rRNA) gene nucleotide sequences. Among these isolates were members of six major phylogenetic groups of bacteria: the high-G+C and low-G+C Gram-positive bacteria; the
α-,
β-, and
γ-subdivisions of the
Proteobacteria; and the
Flexibacter/Cytophaga/Bacteroides group. A small number of the SMCC strains may be members of new bacterial genera, but most of them could be placed with reasonable confidence into more than 35 previously described genera. The majority of the Gram-positive isolates were species of
Arthrobacter, Bacillus, or
Streptococcus, whereas
Acinetobacter, Comamonas, Pseudomonas, Sphingomonas, and
Variovorax were among the most frequently encountered Gram-negative genera. A high proportion of the strains were placed in fewer than 10 genera, implying that there is substantial duplication within the SMCC at the genus level. When groups of isolates assigned to
Acinetobacter, Arthrobacter, or
Sphingomonas were analyzed in more detail, however, it was found that each group consisted of subgroups of strains that probably differed at the species level. Restriction endonuclease analysis (applied to the strains from one sample site) indicated that additional diversity was present at the strain level. Most of the SMCC isolates assigned to some genera (e.g.,
Acinetobacter) were very closely related to previously described species in those genera, but most of the isolates assigned to other genera (e.g.,
Arthrobacter and
Sphingomonas) appeared (or were shown) to be new species, thereby indicating that a reasonable amount of novelty is present within the SMCC at the species level.
Journal Article
Screening for microbial markers in Miocene sediment exposed during open-cast brown coal mining
Viable microorganisms were found in Miocene lacustrine clays of the cypris formation excavated from 200-m below the surface as spoil during open-cast brown coal mining (Sokolov Brown Coal Basin, North-Western Bohemia, Czech Republic). Both saprotrophic microfungi of the genera Penicillium, Verticillium, Cladosporium and Aspergillus as well as heterotrophic bacteria were isolated from an intact sediment cores. Heterotrophic bacteria were classified by the MIS Sherlock System as representatives of genera Nocardiopsis, Arthrobacter, Micrococcus, Kocuria, Rothia, Clavibacter, Bacillus, Paenibacillus, Brevibacillus, Microbacterium, Acinetobacter and Pseudomonas. A bacterium found among the strains had an atypical fatty acids profile enriched by branched fatty acids and polyunsaturated fatty acid (18:3 omega 6) and gave no MIS Sherlock match. Phospholipid fatty acids analysis indicates a relatively high (535 pmol g(-1)) but inhomogeneously distributed viable microbial biomass. Fatty acids analyses of non-fractioned lipids (representing viable, storage and dead biomass; 8390 pmol g(-1)) detected rich and homogenous profiles with fungal, bacterial and actinomycetal markers but no protozoan and algal fatty acids markers.
Journal Article
Phylogenetic characterization of bacteria in the subsurface microbial culture collection
Abstract
The Subsurface Microbial Culture Collection (SMCC) was established by the U.S. Dept. of Energy (DOE) and contains nearly 10,000 strains of microorganisms (mostly bacteria) isolated from terrestrial subsurface environments. Selected groups of bacterial isolates from three sample sites situated above geochemically and hydrologically different subsurface environments have been characterized by phylogenetic analysis of 16S ribosomal RNA (rRNA) gene nucleotide sequences. Among these isolates were members of six major phylogenetic groups of bacteria: the high-G+C and low-G+C Gram-positive bacteria; the α-, β-, and γ-subdivisions of the Proteobacteria; and the Flexibacter/Cytophaga/Bacteroides group. A small number of the SMCC strains may be members of new bacterial genera, but most of them could be placed with reasonable confidence into more than 35 previously described genera. The majority of the Gram-positive isolates were species of Arthrobacter, Bacillus, or Streptococcus, whereas Acinetobacter, Comamonas, Pseudomonas, Sphingomonas, and Variovorax were among the most frequently encountered Gram-negative genera. A high proportion of the strains were placed in fewer than 10 genera, implying that there is substantial duplication within the SMCC at the genus level. When groups of isolates assigned to Acinetobacter, Arthrobacter, or Sphingomonas were analyzed in more detail, however, it was found that each group consisted of subgroups of strains that probably differed at the species level. Restriction endonuclease analysis (applied to the strains from one sample site) indicated that additional diversity was present at the strain level. Most of the SMCC isolates assigned to some genera (e.g., Acinetobacter) were very closely related to previously described species in those genera, but most of the isolates assigned to other genera (e.g., Arthrobacter and Sphingomonas) appeared (or were shown) to be new species, thereby indicating that a reasonable amount of novelty is present within the SMCC at the species level.
Journal Article
Biodegradation of polycyclic aromatic hydrocarbons by Sphingomonas strains isolated from the terrestrial subsurface
Several strains of Sphingomonas isolated from deep Atlantic coastal plain aquifers at the US Department of Energy Savannah River Site (SRS) near Aiken, SC were shown to degrade a variety of aromatic hydrocarbons in a liquid culture medium. Sphingomonas aromaticivorans strain B0695 was the most versatile of the five strains examined. This strain was able to degrade acenaphthene, anthracene, phenanthrene, 2,3-benzofluorene, 2-methylnaphthalene, 2,3-dimethylnaphthalene, and fluoranthene in the presence of 400 mg l−1 Tween 80. Studies involving microcosms composed of aquifer sediments showed that S. aromaticivorans B0695 could degrade phenanthrene effectively in sterile sediment and could enhance the rate at which this compound was degraded in nonsterile sediment. These findings indicate that it may be feasible to carry out (or, at least, to enhance) in situ bioremediation of phenanthrene-contaminated soils and subsurface environments with S. aromaticivorans B0695. In contrast, strain B0695 was unable to degrade fluoranthene in microcosms containing aquifer sediments, even though it readily degraded this polynuclear aromatic hydrocarbon (PAH) in a defined liquid growth medium. Journal of Industrial Microbiology & Biotechnology (2001) 26, 283–289.
Journal Article
Antibiotic- and heavy-metal resistance in bacteria isolated from deep subsurface in El Callao region, Venezuela
Se investigó el efecto de la contaminación con mercurio (Hg) en las comunidades bacterianas del subsuelo profundo en la región de El Callao (Estado Bolívar, Venezuela). Se estudiaron comunidades bacterianas de dos niveles de profundidad (-288 m y -388 m) en una mina de oro con el propósito de describir las características más relevantes de las bacterias indígenas cultivables que colonizaban esta mina. Se evaluaron los patrones de resistencia a antibióticos y metales pesados, presencia del gen merA y plásmidos en aislados resistentes. Se encontró una elevada frecuencia de bacterias indígenas resistentes al Hg y otros metales pesados. De 76 aislados Hg-resistentes probados 73.7 % fueron adicionalmente resistentes a ampicilina; 86.8 % a cloranfenicol; 67.1 % a tetraciclina; 56.6 % a estreptomicina y 51.3 % a kanamicina. Además, se encontró que 40.74 % (-328 m) y 26.53 % (-388 m) de las bacterias Hg-resistentes fueron simultáneamente resistentes tanto a cuatro como a cinco de estos antibióticos. Se detectó la presencia de plásmidos de alto y bajo peso molecular y, a pesar de que los aislados mostraban resistencia a compuestos mercuriales, la presencia del gen merA fue detectada solo en 71.05 % de los cepas. Estos resultados sugieren que la exposición a Hg podría ser una presión selectiva en la proliferación de bacterias resistentes a antibióticos y promover el mantenimiento y propagación de estos genes de resistencia. Sin embargo, la existencia de tales resistencias a estas profundidades podría también apoyar la idea de que la resistencia a antibióticos en estas bacterias es natural y tiene un origen más antiguo que su exposición al Hg.
Journal Article
Microbial ecology of the deep terrestrial subsurface
The terrestrial subsurface hosts microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, deep subsurface microbial communities are supported by chemolithoautotrophic primary production, with hydrogen serving as an important source of electrons. Despite recent progress, relatively little is known about the deep terrestrial subsurface compared to more commonly studied environments. Understanding the composition of deep terrestrial subsurface microbial communities and the factors that influence them is of importance because of human-associated activities including long-term storage of used nuclear fuel, carbon capture, and storage of hydrogen for use as an energy vector. In addition to identifying deep subsurface microorganisms, recent research focuses on identifying the roles of microorganisms in subsurface communities, as well as elucidating myriad interactions—syntrophic, episymbiotic, and viral—that occur among community members. In recent years, entirely new groups of microorganisms (i.e. candidate phyla radiation bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoloarchaeota, Nanoarchaeota archaea) have been discovered in deep terrestrial subsurface environments, suggesting that much remains unknown about this biosphere. This review explores the historical context for deep terrestrial subsurface microbial ecology and highlights recent discoveries that shape current ecological understanding of this poorly explored microbial habitat. Additionally, we highlight the need for multifaceted experimental approaches to observe phenomena such as cryptic cycles, complex interactions, and episymbiosis, which may not be apparent when using single approaches in isolation, but are nonetheless critical to advancing our understanding of this deep biosphere.
Journal Article