Virginia Helena Albarracín

Amycolatopsis tucumanensis sp. nov., a copper-resistant actinobacterium isolated from polluted sediments.

A novel actinomycete strain, ABO(T), isolated from copper-polluted sediments showed remarkable copper resistance as well as high bioaccumulation abilities. Classical taxonomic methods, including chemotaxonomy and molecular techniques, were used to characterize the isolate. Strain ABO(T) developed a honey-yellow substrate mycelium on all ISP media tested. Abundant, white, aerial mycelium was only formed on ISP 2, 5 and 7 and MM agar. Both types of hyphae fragmented into squarish rod-shaped elements. The aerial mycelium displayed spore-like structures with smooth surfaces in long, straight to flexuous chains. The organism has a type-IV cell wall lacking mycolic acids and type-A whole-cell sugar pattern (meso-diaminopimelic acid, arabinose and galactose) in addition to a phospholipid type-II profile. 16S rRNA gene sequence studies indicated that this organism is a member of the family Pseudonocardiaceae and that it forms a monophyletic clade with Amycolatopsis eurytherma NT202(T). The DNA-DNA relatedness of strain ABO(T) to A. eurytherma DSM 44348(T) was 39.5 %. It is evident from these genotypic and phenotypic data that strain ABO(T) represents a novel species in the genus Amycolatopsis, for which the name proposed is Amycolatopsis tucumanensis sp. nov. The type strain is ABO(T) (=DSM 45259(T) =LMG 24814(T)).

Bioaugmentation of copper polluted soil microcosms with Amycolatopsis tucumanensis to diminish phytoavailable copper for Zea mays plants

Amycolatopsis tucumanensis DSM 45259, the strain of a recently recognized novel species of the genus Amycolatopsis with remarkable copper resistance, was used to bioaugment soil microcosms experimentally polluted with copper and for studying the ability of this strain to effectively diminish phytoavailable copper from soils. Our results demonstrated that A. tucumanensis was capable of profusely colonizing both, copper polluted and non-polluted soil. Copper bioimmobilization ability of A. tucumanensis on soil was assessed measuring the bioavailable copper in the soil solution extracted from polluted soil by using chemical and physical methods and, in this way, 31% lower amounts of the metal were found in soil solution as compared to non-bioaugmented soil. The results obtained when using Zea mays as bioindicator correlated well with the values obtained by the chemical and physical procedures: 20% and 17% lower tissue contents of copper were measured in roots and leaves, respectively. These data confirmed the efficiency of the bioremediation process using A. tucumanensis and at the same time proved that chemical, physical and biological methods for assessing copper bioavailability in soils were correlated. These results suggest a potential use of this strain at large scale in copper soil bioremediation strategies. To our knowledge, this work is the first to apply and to probe the colonization ability of an Amycolatopsis strain in soil microcosms and constitutes the first application of an Amycolatopsis strain on bioremediation of polluted soils.

High-Up: A Remote Reservoir of Microbial Extremophiles in Central Andean Wetlands.

The Central Andes region displays unexplored ecosystems of shallow lakes and salt flats at mean altitudes of 3700 m. Being isolated and hostile, these so-called “High-Altitude Andean Lakes” (HAAL) are pristine and have been exposed to little human influence. HAAL proved to be a rich source of microbes showing interesting adaptations to life in extreme settings (poly-extremophiles) such as alkalinity, high concentrations of arsenic and dissolved salts, intense dryness, large daily ambient thermal amplitude, and extreme solar radiation levels. This work reviews HAAL microbiodiversity, taking into account different microbial niches, such as plankton, benthos, microbial mats and microbialites. The modern stromatolites and other microbialites discovered recently at HAAL are highlighted, as they provide unique modern—though quite imperfect—analogs of environments proxy for an earlier time in Earths history (volcanic setting and profuse hydrothermal activity, low atmospheric O2 pressure, thin ozone layer and high UV exposure). Likewise, we stress the importance of HAAL microbes as model poly-extremophiles in the study of the molecular mechanisms underlying their resistance ability against UV and toxic or deleterious chemicals using genome mining and functional genomics. In future research directions, it will be necessary to exploit the full potential of HAAL poly-extremophiles in terms of their biotechnological applications. Current projects heading this way have yielded detailed molecular information and functional proof on novel extremoenzymes: i.e., DNA repair enzymes and arsenic efflux pumps for which medical and bioremediation applications, respectively, are envisaged. But still, much effort is required to unravel novel functions for this and other molecules that dwell in a unique biological treasure despite its being hidden high up, in the remote Andes.

Forged Under the Sun: Life and Art of Extremophiles from Andean Lakes

High‐altitude Andean lakes (HAAL) are a treasure chest for microbiological research in South America. Their indigenous microbial communities are exposed to extremely high UV irradiation and to multiple chemical extremes (Arsenic, high salt content, alkalinity). Microbes are found both, free‐living or associated into microbial mats with different degrees of mineralization and lithification, including unique modern stromatolites located at 3570 m above sea level. Characterization of these polyextremophilic microbes began only recently, employing morphological and phylogenetic methods as well as high‐throughput sequencing and proteomics approach. Aside from providing a general overview on microbial communities, special attention is given to various survival strategies; HAALs microbes present a complex system of shared genetic and physiological mechanisms (UV‐resistome) based on UV photoreceptors and stress sensors with their corresponding response regulators, UV avoidance and protection strategies, damage tolerance and UV damage repair. Molecular information will be provided for what is, so far the most studied HAAL molecule, a CPD‐Class I photolyase from Acinetobacter Ver3 (Laguna Verde, 4400 m). This work further proposes some strategies that make an appeal for the preservation of HAAL, a highly fragile environment that offers promising and ample research possibilities.

Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis

Modern stromatolites thrive only in selected locations in the world. Socompa Lake, located in the Andean plateau at 3570 masl, is one of the numerous extreme Andean microbial ecosystems described over recent years. Extreme environmental conditions include hypersalinity, high UV incidence, and high arsenic content, among others. After Socompa’s stromatolite microbial communities were analysed by metagenomic DNA sequencing, taxonomic classification showed dominance of Proteobacteria, Bacteroidetes and Firmicutes, and a remarkably high number of unclassified sequences. A functional analysis indicated that carbon fixation might occur not only by the Calvin-Benson cycle, but also through alternative pathways such as the reverse TCA cycle, and the reductive acetyl-CoA pathway. Deltaproteobacteria were involved both in sulfate reduction and nitrogen fixation. Significant differences were found when comparing the Socompa stromatolite metagenome to the Shark Bay (Australia) smooth mat metagenome: namely, those involving stress related processes, particularly, arsenic resistance. An in-depth analysis revealed a surprisingly diverse metabolism comprising all known types of As resistance and energy generating pathways. While the ars operon was the main mechanism, an important abundance of arsM genes was observed in selected phyla. The data resulting from this work will prove a cornerstone for further studies on this rare microbial community.

Modern Stromatolite Ecosystems at Alkaline and Hypersaline High-Altitude Lakes in the Argentinean Puna

High-altitude Lakes at the northwest of Argentina in the Puna and Andean regions (HAAL) are considered extreme environments of biotechnological interest (Fig. 1; Seufferheld et al., 2008). The HAAL ecosystems are almost unexplored systems of shallow lakes formed during the tertiary geological period, distributed in the geographical area called the Puna at altitudes from 3,000 to 6,000 m above sea level. Most of these wetlands are completely isolated, experience a wide daily range in temperatures (40°C), are slight saline to hypersaline, and are subject to low phosphate availability and high intensity of solar ultraviolet-B (UV-B) radiation. The HAAL ecosystems are unique not only for their geographical characteristics and broad range of extreme environments but also for their abundant biodiversity. The microbial communities that have evolved within these high-altitude aquatic ecosystems tolerate chemical and physical stresses such as wide fluctuations in daily temperatures, hypersalinity, and variable pH and have proved to be adapted to high levels of UV radiation, a low level of nutrient availability, and high concentrations of heavy metals, especially arsenic (Demergasso et al., 2004; Ferrero et al., 2004; Escudero et al., 2007; Fernandez Zenoff et al., 2006; Zenoff et al., 2006; Dib et al., 2008, 2010a, b; Ordonez et al., 2009; Flores et al., 2009; Farias et al., 2009). The high altitude and low latitude geographical position of the HAAL expose the indigenous extremophilic communities to high solar irradiance (i.e., 165% higher than at sea level) with instantaneous UV-B flux reaching 17 Wm−2; UV-flux is twice the amount of present-day equatorial Mars, while UV-B is half the amount on Mars. Hence, these environments have been proposed for future studies on astrobiology (Farias et al., 2009).

Functional Green-Tuned Proteorhodopsin from Modern Stromatolites

The sequenced genome of the poly-extremophile Exiguobacterium sp. S17, isolated from modern stromatolites at Laguna Socompa (3,570 m), a High-Altitude Andean Lake (HAAL) in Argentinean Puna revealed a putative proteorhodopsin-encoding gene. The HAAL area is exposed to the highest UV irradiation on Earth, making the microbial community living in the stromatolites test cases for survival strategies under extreme conditions. The heterologous expressed protein E17R from Exiguobacterium (248 amino acids, 85% sequence identity to its ortholog ESR from E. sibiricum) was assembled with retinal displaying an absorbance maximum at 524 nm, which makes it a member of the green-absorbing PR-subfamily. Titration down to low pH values (eventually causing partial protein denaturation) indicated a pK value between two and three. Global fitting of data from laser flash-induced absorption changes gave evidence for an early red-shifted intermediate (its formation being below the experimental resolution) that decayed (τ1 = 3.5 μs) into another red-shifted intermediate. This species decayed in a two-step process (τ2 = 84 μs, τ3 = 11 ms), to which the initial state of E17-PR was reformed with a kinetics of 2 ms. Proton transport capability of the HAAL protein was determined by BLM measurements. Additional blue light irradiation reduced the proton current, clearly identifying a blue light absorbing, M-like intermediate. The apparent absence of this intermediate is explained by closely matching formation and decay kinetics.

UV-Resistant Actinobacteria from High-Altitude Andean Lakes: Isolation, Characterization and Antagonistic Activities†

Polyextremophiles are present in a wide variety of extreme environments in which they must overcome various hostile conditions simultaneously such as high UVB radiation, extreme pHs and temperatures, elevated salt and heavy‐metal concentration, low‐oxygen pressure and scarce nutrients. High‐altitude Andean lakes (HAALs; between 2000 and 4000 m) are one example of these kinds of ecosystems suffering from the highest total solar and UVB radiation on Earth where an abundant and diverse polyextremophilic microbiota was reported. In this work, we performed the first extensive isolation of UV‐resistant actinobacteria from soils, water, sediments and modern stromatolites at HAALs. Based on the 16S rRNA sequence, the strains were identified as members of the genera Streptomyces, Micrococcus, Nesterenkonia, Rhodococcus, Microbacterium, Kocuria, Arthrobacter, Micromonospora, Blastococcus, Citrococcus and Brevibacterium. Most isolates displayed resistance to multiple environmental stress factors confirming their polyextremophilic nature and were able to produce effective antimicrobial compounds. HAALs constitute a largely unexplored repository of UV‐resistant actinobacteria, with high potential for the biodiscovery of novel natural products.

Bioremediation Potential of Heavy Metal–Resistant Actinobacteria and Maize Plants in Polluted Soil

The screening and characterization of metal resistant microorganisms and plants are important for developing novel bioremediation processes. Considering these, we assessed the potential of copper- and chromium-resistant actinomycetes for bioremediation activity in polluted soils. Also, we assessed the effects of copper concentrations on roots, shoots, and leaf growth of maize and the copper uptake and accumulation by the maize plants. Four chromium resistant Streptomyces strains reduced hexavalent chromium up to 85–95% after 21 days. The novel copper-resistant actinobacterium Amycolatopsis tucumanensis efficiently immobilized copper when inoculated into copper-polluted soil microcosms: bioavailable Cu was 31% lower in soil compared to non-bioaugmented soil. Maize plant was found interesting both as biomarker and bioremediation tool. The bioremediation activity of A. tucumanensis inoculated maize plants grown in polluted soil microcosms correlated well with the values obtained with chemical and physical methods: 20% and 17% lower tissue contents of copper were measured in roots and leaves, respectively. The roots, shoots, and leaves of maize plants also showed a great ability to accumulate copper, which however increased with metal concentration. The metal concentrations were 382 times more in roots, 157 in shoots, and only 16 in leaves, compared to the control (without CuSO4).