Modestobacter excelsi sp. nov., a novel actinobacterium isolated from a high altitude Atacama Desert soil

A polyphasic study was undertaken to establish the taxonomic status of three Modestobacter strains isolated from a high altitude Atacama Desert soil. The isolates, strains 1G6^T, 1G14 and 1G50, showed chemotaxonomic and morphological properties characteristic of members of the genus Modestobacter. The peptidoglycan contained meso-diaminopimelic acid, the whole cell sugars were glucose and ribose (diagnostic sugars) and arabinose, the predominant menaquinone was MK-9(H₄), polar lipid patterns contained diphosphatidylglycerol, glycophosphatidylinositol, phosphatidylethanolamine (diagnostic component), phosphatidylglycerol and phosphatidylinositol while whole cellular fatty acid profiles consisted of complex mixtures of saturated, unsaturated iso- and anteiso-components. The isolates were shown to have different BOX-PCR fingerprint and physiological profiles. They formed a distinct phyletic line in Modestobacter 16S rRNA gene trees, were most closely related to the type strain of Modestobacter italicus (99.9 % similarity) but were distinguished from this and other closely related Modestobacter type strains using a combination of phenotypic properties. Average nucleotide identity and digital DNA:DNA hybridization similarities between the draft genome sequences of isolate 1G6^T and M. italicus BC 501^T were 90.9 % and 42.3 %, respectively, indicating that they belong to different species. Based on these phenotypic and genotypic data it is proposed that the isolates be assigned to a novel species in the genus Modestobacter, namely as Modestobacter excelsi with isolate 1G6^T (=DSM 107535^T =PCM 3004^T) as the type strain. Analysis of the whole genome sequence of M. excelsi 1G6^T (genome size of 5.26 Mb) showed the presence of genes and gene clusters that encode for properties that are in tune with its adaptation to extreme environmental conditions that prevail in the Atacama Desert biome.

Amycolatopsis vastitatis sp. nov., an isolate from a high altitude subsurface soil on Cerro Chajnantor, northern Chile

The taxonomic position of a novel Amycolatopsis strain isolated from a high altitude Atacama Desert subsurface soil was established using a polyphasic approach. The strain, isolate H5^T, was shown to have chemical properties typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diamino acid in the cell wall peptidoglycan, arabinose and galactose as diagnostic sugars and MK-9(H₄) as the predominant isoprenologue. It also has cultural and morphological properties consistent with its classification in the genus, notably the formation of branching substrate hyphae which fragment into rod-like elements. 16S rRNA gene sequence analyses showed that the strain is closely related to the type strain of Amycolatopsis mediterranei but could be distinguished from this and other related Amycolatopsis strains using a broad range of phenotypic properties. It was separated readily from the type strain of Amycolatopsis balhymycina, its near phylogenetic neighbour, based on multi-locus sequence data, by low average nucleotide identity (92.9%) and in silico DNA/DNA relatedness values (51.3%) calculated from draft genome assemblies. Consequently, the strain is considered to represent a novel species of Amycolatopsis for which the name Amycolatopsis vastitatis sp. nov. is proposed. The type strain is H5^T (= NCIMB 14970^T = NRRL B-65279^T).

Influence of hydraulic retention time and plant species on performance of mesocosm subsurface constructed wetlands during municipal wastewater treatment in super-arid areas

A constructed wetland (CW) in arid areas requires special knowledge given the particular climatic conditions. Among other aspects, the Hydraulic Retention Time (HRT) and plant species may be two important design parameters in hyper- and super-arid areas. Therefore, the study aimed to evaluate the influence of both variables in the application of CW in super-arid areas. Two HRT, 3.5 d and 7 d, and plant species classified by their origin: (a) native, Festuca Orthopylla, Cortaderia atacamensis and Schoenoplectus americanus, and (b) foreign, Cyperus papyrus, were evaluated in four Mesocosm Constructed Wetlands (MCW) operated in a super-arid area. The results showed that the HRT significantly increased (α < 0.05) in more than 10% the removal efficiency of nitrogen and phosphorus forms (TN, NH₄⁺-N, TP, PO₄^-3-P). These results were the same for the two groups of plants assessed. Moreover, Cyperus papyrus significantly increased (α < 0.05) above 30% the removal efficiency, but only for nitrogen and phosphorus forms. MCW with this plant species showed a water loss above 25% and significantly increased (α < 0.05) the Electrical Conductivity (EC) of effluents. MCW planted with Schoenoplectus americanus showed water losses of around 25% for the both HRT evaluated, and its influence was not significant (α > 0.05) on the EC of the effluents. These results suggest that Schoenoplectus americanus would be an ideal candidate species for use in CW with subsurface flow in super-arid areas, with HRT varying between 3.5 d and 7 d.

Pre-Columbian transregional captive rearing of Amazonian parrots in the Atacama Desert

The feathers of tropical birds were one of the most significant symbols of economic, social, and sacred status in the pre-Columbian Americas. In the Andes, finely produced clothing and textiles containing multicolored feathers of tropical parrots materialized power, prestige, and distinction and were particularly prized by political and religious elites. Here we report 27 complete or partial remains of macaws and amazon parrots from five archaeological sites in the Atacama Desert of northern Chile to improve our understanding of their taxonomic identity, chronology, cultural context, and mechanisms of acquisition. We conducted a multiproxy archaeometric study that included zooarchaeological analysis, isotopic dietary reconstruction, accelerated mass spectrometry radiocarbon dating, and paleogenomic analysis. The results reveal that during the Late Intermediate Period (1100 to 1450 CE), Atacama oasis communities acquired scarlet macaws (Ara macao) and at least five additional translocated parrot species through vast exchange networks that extended more than 500 km toward the eastern Amazonian tropics. Carbon and nitrogen stable isotopes indicate that Atacama aviculturalists sustained these birds on diets rich in marine bird guano-fertilized maize-based foods. The captive rearing of these colorful, exotic, and charismatic birds served to unambiguously signal relational wealth in a context of emergent intercommunity competition.

The Bulimulidae (Mollusca: Pulmonata) from the Región de Atacama, northern Chile

The bulimulid genus BostryxTroschel, 1847 is the most species-rich genus of land snails found in Chile, with the majority of its species found only in the northern part of the country, usually in arid coastal zones. This genus has been sparsely studied in Chile and there is little information on their distribution, diversity or ecology. Here, for the first time, a formal analysis of the diversity of bulimulids in the Región de Atacama, northern Chile, is reported. Of the seventeen species recorded for the area, most of them were efectively found in the field collections and one record was based on literature. Five taxa are described as new: Bostryx ancavilorum sp. nov., Bostryx breurei sp. nov., Bostryx calderaensis sp. nov., Bostryx ireneae sp. nov. and Bostryx valdovinosi sp. nov., and the known geographic distribution of seven species is extended. Results reveal that the Región de Atacama is the richest region in terrestrial snails in Chile, after the Juan Fernández Archipelago. All of the terrestrial molluscan species occurring in the area are endemic to Chile, most of them with restricted geographic distributions along the coastal zones, and none of them are currently protected by law. Further sampling in northern Chile will probably reveal more snail species to be discovered and described.

New genus-specific primers for PCR identification of Rubrobacter strains

A set of oligonucleotide primers, Rubro223f and Rubro454r, were found to amplify a 267 nucleotide sequence of 16S rRNA genes of Rubrobacter type strains. The primers distinguished members of this genus from other deeply-rooted actinobacterial lineages corresponding to the genera Conexibacter, Gaiella, Parviterribacter, Patulibacter, Solirubrobacter and Thermoleophilum of the class Thermoleophilia. Amplification of DNA bands of about 267 nucleotides were generated from environmental DNA extracted from soil samples taken from two locations in the Atacama Desert. Sequencing of a DNA library prepared from the bands showed that all of the clones fell within the evolutionary radiation occupied by the genus Rubrobacter. Most of the clones were assigned to two lineages that were well separated from phyletic lines composed of Rubrobacter type strains. It can be concluded that primers Rubro223f and Rubro454r are specific for the genus Rubrobacter and can be used to detect the presence and abundance of members of this genus in the Atacama Desert and other biomes.

Purification and characterization of two thermostable xylanases from a halotolerant Bacillus sp. Asc6BA isolated from Salar de Ascotán, Atacama Desert

Two extracellular xylanases, denominated X2 and X3, were purified and characterized from the halotolerant bacterium Bacillus sp. Asc6BA isolated from "Salar de Ascotán" in the Atacama Desert. Xylanases were purified by anion exchange, cation exchange and size exclusion liquid chromatography. Xylanase X2 and X3 were purified ~ 690-fold and ~ 629-fold, respectively, compared to the concentrated extracellular fraction with a final specific activity of 169 and 154 u mg^-1, respectively. Optimal conditions of pH and temperature of xylanolytic activity were 6.0 and 60 °C for X2 and 7.0 and 60 °C for X3. Half-life of X2 xylanase was 30 min at 50 °C, while X3 xylanase was remarkably more thermostable, retaining more than 70% of its activity after 32 h of incubation at 50 °C. X2 exhibited K_m, V_max and k_cat values of 7.17 mg mL^-1, 1.28 mM min^-1 mg^-1 and 425.33 s^-1, respectively. X3 exhibited K_m, V_max and k_cat values of 6.00 mg mL^-1, 19.25 mM min^-1 mg^-1 and 82,515 s^-1, respectively. In addition to their thermal stabilities, these enzymes were shown to be resistant to freeze-drying. These stability properties, in addition to the ability of these enzymes to be active in a wide range of temperatures and pHs, make these xylanases good candidates for industrial applications.

Museum-archived and recent acquisition nitrates from the Atacama Desert, Chile, South America: refinement of the dual isotopic compositions (δ15N vs. δ18O)

Sodium nitrate ores from the Atacama Desert in South America were economically important as they represented huge natural resources for the fertilizer and explosives industries during the early nineteenth to early twentieth centuries. Nitrogen and oxygen isotope ratios (δ¹⁵N and δ¹⁸O) of these desert nitrates generally show unique compositions (from close to 0 and up to ca. +50 ‰, respectively). The nitrates indicate the provenance as atmospheric in origin due to the mass-independent photochemical reaction of nitric oxide (NO) with ozone (O₃) in the atmosphere to produce nitrate (NO₃^-). This paper examines the previously existing isotope data for specimens acquired from the Atacama Desert. It then reports new data from dual isotope analysis of historic nitrate specimens archived in museums in the UK. In the stable isotope signatures for nitrates from two areas of the Atacama Desert, Tarapacá in the north and Antofagasta in the south, were examined, and this analysis enabled a more detailed definition of their isotopic compositional ranges. This improved database is useful for tracing the provenance of the historic nitrates used in gunpowder and saltpetre, and also the cause of nitrate pollution in natural environments for which routine chemistry alone cannot provide the definite evidence for the origin.

Corrosion of bare carbon steel as a passive sensor to assess moisture availability for biological activity in Atacama Desert soils

Here we consider that the corrosion of polished bared metal coupons can be used as a passive sensor to detect or identify the lower limit of water availability suitable for biological activity in Atacama Desert soils or solid substrates. For this purpose, carbon steel coupons were deposited at selected sites along a west-east transect and removed at predetermined times for morphological inspection. The advantage of this procedure is that the attributes of the oxide layer (corrosion extent, morphology and oxide phases) can be considered as a fingerprint of the atmospheric moisture history at a given time interval. Two types of coupons were used, long rectangular shaped ones that were half-buried in a vertical position, and square shaped ones that were deposited on the soil surface. The morphological attributes observed by SEM inspection were found to correlate to the so-called humectation time which is determined from local meteorological parameters. The main finding was that the decreasing trend of atmospheric moisture along the transect was closely related to corrosion behaviour and water soil penetration. For instance, at the coastal site oxide phases formed on the coupon surface rapidly evolve into well-crystallized species, while at the driest inland site Lomas Bayas only amorphous oxide was observed on the coupons.

Evolution of gene networks underlying adaptation to drought stress in the wild tomato Solanum chilense

Drought stress is a key limitation for plant growth and colonization of arid habitats. We study the evolution of gene expression response to drought stress in a wild tomato, Solanum chilense, naturally occurring in dry habitats in South America. We conduct a transcriptome analysis under standard and drought experimental conditions to identify drought-responsive gene networks and estimate the age of the involved genes. We identify two main regulatory networks corresponding to two typical drought-responsive strategies: cell cycle and fundamental metabolic processes. The metabolic network exhibits a more recent evolutionary origin and a more variable transcriptome response than the cell cycle network (with ancestral origin and higher conservation of the transcriptional response). We also integrate population genomics analyses to reveal positive selection signals acting at the genes of both networks, revealing that genes exhibiting selective sweeps of older age also exhibit greater connectivity in the networks. These findings suggest that adaptive changes first occur at core genes of drought response networks, driving significant network re-wiring, which likely underpins species divergence and further spread into drier habitats. Combining transcriptomics and population genomics approaches, we decipher the timing of gene network evolution for drought stress response in arid habitats.

Extreme human-induced pocket beach growth on a rocky coast

A large human-induced sediment supply (~ 400 Mt) took place on the Atacama Desert rocky coast (~ 26° S) as a result of the dumping of copper mine tailings between 1938 and 1990. We show that the input of this large sediment load has affected the natural sediment dynamics in this coastal area. The coastal system counterbalanced this abrupt increase in sediment supply with rapid accretion while the dumping was active. A different accretion pattern is observed in each of the two bays that received tailings. In one of them, the tailings input occurred in its center, resulting in a radial-to-rectilinear pattern that caused the growth of an existing pocket beach. In the other bay, where the alongshore transport is hindered by a small central rocky headland, the sediment input occurred on a lateral headland, resulting in a lateral-to-bypassed pattern that triggered the formation of two artificial beaches. Once the dumping of tailings ceased, the artificial beaches have been in a period of strong erosion, although the most recently formed beach still experiences northward accretion. This work contributes to assessing the impact of large human-induced sediment supplies on rocky coasts, providing valuable data for investigating current and future coastal changes according to both natural forces and human activities and their consequences.

Water Vapor Adsorption Provides Daily, Sustainable Water to Soils of the Hyperarid Atacama Desert

Water is necessary for all life on Earth. Water is so critical that organisms have developed strategies to survive in hyperarid environments. These regions with extremely low water availability are also unique analogs in which to study the physico-chemical conditions of extraterrestrial environments such as Mars. We have identified a daily, sustainable cycle of water vapor adsorption (WVA) and desorption that measurably affects soil water content (SWC) in the hyperarid region of the Atacama Desert in southern Perú. We pair field-based soil temperature and relative humidity soil profiles with laboratory simulations to provide evidence for a daily WVA cycle. Using our WVA model, we estimate that one adsorptive period-one night-increases SWC by 0.2-0.3 mg/g of soil (∼30 μm rainfall). We can plausibly rule out other water inputs during our field campaign that could account for this water input, and we provide evidence that this WVA cycle is driven by solar heating and maintained by atmospheric water vapor. The WVA may also serve to retain water from infrequent rain events in these soils. If the water provided by WVA in these soils is bioavailable, it could have significant implications for the microorganisms that are endemic to hyperarid environments.

A case of enlarged parietal foramina or foramina parietalia permagna in an individual from the Chinchorro Culture of northern Chile (4000 BP)

OBJECTIVE

The goal of this study was to analyze and differentially diagnose the presence of two large holes noted in the parietal bones of an individual and the presence of traumatic lesions.

MATERIALS

A partially mummified young adult female associated with the Chinchorro culture, 4000 BP, from the coast of the Atacama Desert (northern Chile).

METHODS

The bone lesions were evaluated macroscopically and radiologically. In addition, Sr isotopic analyses were performed on 62 individuals from eight sites associated with the Chinchorro culture.

RESULTS

The parietal orifices are compatible with a rare anomaly of genetic origin known as foramina parietalia permagna (FPP). In addition, the cranial fracture pattern appear compatible with perimortem trauma, and Sr isotopes indicate a marine signal for Chinchorro populations.

CONCLUSIONS

This case serves as evidence that FPP was present in the early Andean populations and that endogamy and mutagenic factors might have contributed to its presence.

SIGNIFICANCE

This paper expands our knowledge of the genetic anomalies that affected past populations and may contribute to our understanding of the etiologies of the condition.

LIMITATIONS

The absence of comparative FPP data inhibits comparative studies (with the exception of cases from California, USA).

SUGGESTIONS FOR FUTURE RESEARCH

To explore in depth the genetic component of this condition in the Chinchorro populations.