Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile

Indexación: Web of Science; PubMedLeptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod- shaped bacterium, isolated from an industrial bioleaching operation in northern Chile, where chalcocite is the major copper mineral and copper hydroxychloride atacamite is present in variable proportions in the ore. This strain has unique features as compared to the other members of the species, namely resistance to elevated concentrations of chloride, sulfate and metals. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 2,475,669 bp draft genome is arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834 protein coding genes were predicted from its annotation; 55 % of these were assigned a putative function. Release of the genome sequence of this strain will provide further understanding of the mechanisms used by acidophilic bacteria to endure high osmotic stress and high chloride levels and of the role of chloride-tolerant iron-oxidizers in industrial bioleaching operations.https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0142-

Surface Morphologies in a Mars-Analog Ca-Sulfate Salar, High Andes, Northern Chile

Salar de Pajonales, a Ca-sulfate salt flat in the Chilean High Andes, showcases the type of polyextreme environment recognized as one of the best terrestrial analogs for early Mars because of its aridity, high solar irradiance, salinity, and oxidation. The surface of the salar represents a natural climate-transition experiment where contemporary lagoons transition into infrequently inundated areas, salt crusts, and lastly dry exposed paleoterraces. These surface features represent different evolutionary stages in the transition from previously wetter climatic conditions to much drier conditions today. These same stages closely mirror the climate transition on Mars from a wetter early Noachian to the Noachian/Hesperian. Salar de Pajonales thus provides a unique window into what the last near-surface oases for microbial life on Mars could have been like in hypersaline environments as the climate changed and water disappeared from the surface. Here we open that climatological window by evaluating the narrative recorded in the salar surface morphology and microenvironments and extrapolating to similar paleosettings on Mars. Our observations suggest a strong inter-dependence between small and large scale features that we interpret to be controlled by extrabasinal changes in environmental conditions, such as precipitation-evaporation-balance changes and thermal cycles, and most importantly, by internal processes, such as hydration/dehydration, efflorescence/deliquescence, and recrystallization brought about by physical and chemical processes related to changes in groundwater recharge and volcanic processes. Surface structures and textures record a history of hydrological changes that impact the mineralogy and volume of Ca-sulfate layers comprising most of the salar surface. Similar surface features on Mars, interpreted as products of freeze-thaw cycles, could, instead, be products of water-driven, volume changes in salt deposits. On Mars, surface manifestations of such salt-related processes would point to potential water sources. Because hygroscopic salts have been invoked as sources of localized, transient water sufficient to support terrestrial life, such structures might be good targets for biosignature exploration on Mars

Microbiology and Nitrogen Cycle in the Benthic Sediments of a Glacial Oligotrophic Deep Andean Lake as Analog of Ancient Martian Lake-Beds

Potential benthic habitats of early Mars lakes, probably oligotrophic, could range from hydrothermal to cold sediments. Dynamic processes in the water column (such as turbidity or UV penetration) as well as in the benthic bed (temperature gradients, turbation, or sedimentation rate) contribute to supply nutrients to a potential microbial ecosystem. High altitude, oligotrophic, and deep Andean lakes with active deglaciation processes and recent or past volcanic activity are natural models to assess the feasibility of life in other planetary lake/ocean environments and to develop technology for their exploration. We sampled the benthic sediments (down to 269 m depth) of the oligotrophic lake Laguna Negra (Central Andes, Chile) to investigate its ecosystem through geochemical, biomarker profiling, and molecular ecology studies. The chemistry of the benthic water was similar to the rest of the water column, except for variable amounts of ammonium (up to 2.8 ppm) and nitrate (up to 0.13 ppm). A life detector chip with a 300-antibody microarray revealed the presence of biomass in the form of exopolysaccharides and other microbial markers associated to several phylogenetic groups and potential microaerobic and anaerobic metabolisms such as nitrate reduction. DNA analyses showed that 27% of the Archaea sequences corresponded to a group of ammonia-oxidizing archaea (AOA) similar (97%) to Nitrosopumilus spp. and Nitrosoarchaeum spp. (Thaumarchaeota), and 4% of Bacteria sequences to nitrite-oxidizing bacteria from the Nitrospira genus, suggesting a coupling between ammonia and nitrite oxidation. Mesocosm experiments with the specific AOA inhibitor 2-Phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) demonstrated an AOA-associated ammonia oxidation activity with the simultaneous accumulation of nitrate and sulfate. The results showed a rich benthic microbial community dominated by microaerobic and anaerobic metabolisms thriving under aphotic, low temperature (4°C), and relatively high pressure, that might be a suitable terrestrial analog of other planetary settings

Distribution of Microbial Arsenic Reduction, Oxidation and Extrusion Genes along a Wide Range of Environmental Arsenic Concentrations

14 páginas, 5 figuras, 2 tablas.The presence of the arsenic oxidation, reduction, and extrusion genes arsC, arrA, aioA, and acr3 was explored in a range of natural environments in northern Chile, with arsenic concentrations spanning six orders of magnitude. A combination of primers from the literature and newly designed primers were used to explore the presence of the arsC gene, coding for the reduction of As (V) to As (III) in one of the most common detoxification mechanisms. Enterobacterial related arsC genes appeared only in the environments with the lowest As concentration, while Firmicutes-like genes were present throughout the range of As concentrations. The arrA gene, involved in anaerobic respiration using As (V) as electron acceptor, was found in all the systems studied. The As (III) oxidation gene aioA and the As (III) transport gene acr3 were tracked with two primer sets each and they were also found to be spread through the As concentration gradient. Sediment samples had a higher number of arsenic related genes than water samples. Considering the results of the bacterial community composition available for these samples, the higher microbial phylogenetic diversity of microbes inhabiting the sediments may explain the increased number of genetic resources found to cope with arsenic. Overall, the environmental distribution of arsenic related genes suggests that the occurrence of different ArsC families provides different degrees of protection against arsenic as previously described in laboratory strains, and that the glutaredoxin (Grx)-linked arsenate reductases related to Enterobacteria do not confer enough arsenic resistance to live above certain levels of As concentrations.Peer reviewe

Microbial Precipitation of Arsenic Sulfides in Andean Salt Flats

13 pages, 7 figures, 2 tablesAn abiotic origin has traditionally been assumed for the arsenic minerals realgar and orpiment associated with thermal springs. Microbial precipitation of arsenic, however, has been studied in pure cultures and the isotopic composition of arsenic sulfides associated with some borate deposits suggests a biotic origin for those minerals. The aim of the present study is to demonstrate the role of bacterial arsenic precipitation in the biogeochemical cycle of arsenic in such borate deposits. For this purpose both enrichment and pure cultures were obtained from the natural arsenic minerals and the composition and isotopic signatures of the arsenic sulfide minerals precipitated by the cultures and those associated with boron deposits from an Andean salt flat in northern Chile were compared. Based on the microbiological and chemical evidence gathered, it is concluded that bacteria contributed to the formation of the arsenic minerals. This interpretation is based on the consistent association of a variety of features that strongly indicate microbial involvement in the precipitation process. These include: (1) enrichment and isolation of cultures with arsenic precipitation capacity from arsenic mineral samples, (2) high numbers of arsenic-precipitating bacteria in the Andean minerals and brines, (3) chemical and mineralogical properties of precipitates experimentally formed under biotic and abiotic conditions, (4) similarities in stoichiometry between natural and laboratory obtained minerals, and (5) the consistent depletion in δ34S values for natural versus laboratory obtained sulfides. Thus, microbial precipitation of arsenic sulfides is a geochemically relevant metabolismThis work was supported by funds provided by the Chilean Government through FONDECYT Project 1030441, FONDEF Project D99I1026 from the Science and Technology Chilean Commission (CONICYT), CICYT BTE2001-3225 project of the Spanish Government and BBVA Foundation project BIOARSENICOPeer reviewe

Enrichment of arsenic transforming and resistant heterotrophic bacteria from sediments of two salt lakes in Northern Chile

18 pages, 5 figures, 2 tablesMicrobial populations are involved in the arsenic biogeochemical cycle in catalyzing arsenic transformations and playing indirect roles. To investigate which ecotypes among the diverse microbial communities could have a role in cycling arsenic in salt lakes in Northern Chile and to obtain clues to facilitate their isolation in pure culture, sediment samples from Salar de Ascotán and Salar de Atacama were cultured in diluted LB medium amended with NaCl and arsenic, at different incubation conditions. The samples and the cultures were analyzed by nucleic acid extraction, fingerprinting analysis, and sequencing. Microbial reduction of As was evidenced in all the enrichments carried out in anaerobiosis. The results revealed that the incubation factors were more important for determining the microbial community structure than arsenic species and concentrations. The predominant microorganisms in enrichments from both sediments belonged to the Firmicutes and Proteobacteria phyla, but most of the bacterial ecotypes were confined to only one system. The occurrence of an active arsenic biogeochemical cycle was suggested in the system with the highest arsenic content that included populations compatible with microorganisms able to transform arsenic for energy conservation, accumulate arsenic, produce H2, H2S and acetic acid (potential sources of electrons for arsenic reduction) and tolerate high arsenic levelsThis work was supported by funds provided by the BBVA Foundation project BIOARSENICO and the Chilean Government through FONDECYT Project 1100795 from the Science and Technology Chilean Commission (CONICYT). We also would like to thank the A. v. Humboldt Stiftung for the donation of part of the equipment used in this project, as well as V. Iturriaga, M. J. Demergasso and M.V. Coalova for their collaborationPeer reviewe

Novelty and spatio-temporal heterogeneity in the bacterial diversity of hypersaline Lake Tebenquiche (Salar de Atacama)

14 pages, 7 figures, 3 tablesLake Tebenquiche is one of the largest saline water bodies in the Salar de Atacama at 2,500 m above sea level in northeastern Chile. Bacteria inhabiting there have to deal with extreme changes in salinity, temperature and UV dose (i.e., high environmental dissimilarity in the physical landscape). We analyzed the bacterioplankton structure of this lake by 16S rRNA gene analyses along a spatio–temporal survey. The bacterial assemblage within the lake was quite heterogeneous both in space and time. Salinity changed both in space and time ranging between 1 and 30% (w/v), and total abundances of planktonic prokaryotes in the different sampling points within the lake ranged between two and nine times 106 cells mL−1. Community composition changed accordingly to the particular salinity of each point as depicted by genetic fingerprinting analyses (denaturing gradient gel electrophoresis), showing a high level of variation in species composition from place to place (beta-diversity). Three selected sites were analyzed in more detail by clone libraries. We observed a predominance of Bacteroidetes (about one third of the clones) and Gammaproteobacteria (another third) with respect to all the other bacterial groups. The diversity of Bacteroidetes sequences was large and showed a remarkable degree of novelty. Bacteroidetes formed at least four clusters with no cultured relatives in databases and rather distantly related to any known 16S rRNA sequence. Within this phylum, a rich and diverse presence of Salinibacter relatives was found in the saltiest part of the lake. Lake Tebenquiche included several novel microorganisms of environmental importance and appeared as a large unexplored reservoir of unknown bacteriaSampling and measurements carried out in Chile were funded by grants FONDECYT 1030441 and FONDEF D99I1026. Measurements carried out in Barcelona were funded by grant "ATACAMA-2002" (CICYT, BOS2002-10258-E). Grant "BIOARSENICO" from Fundación BBVA funds current workPeer reviewe