Omar Federico Ordoñez

Isolation of Bacteria from Remote High Altitude Andean Lakes Able to Grow in the Presence of Antibiotics

High altitude Andean lakes are placed in Puna desert over 4400 above sea level. Completely isolated, they are exposed to extreme environmental factors like high levels of salinity, UV radiation and heavy metals and low concentrations of phosphorus. Nevertheless, they are the habitat of enormous populations of three flamingo species that migrate among these Lakes. Previous reports have determined that bacteria isolated from these environments present high levels of resistance to antibiotics. The aim of this work was to determine the diversity of antibiotic resistant bacteria in water from Andean Lakes and their connection with flamingo enteric biota. Bacteria from water and birds faeces from high altitude Lakes: Laguna (L.) Aparejos, L. Negra, L. Vilama and L. Azul (all are located between 4,200 and 4,600 m altitude) were isolated by plating in five different Antibiotics (ampicillin, 100 microg ml(-1); chloramphenicol, 170 microg ml(-1); colistin , 20 microg ml(-1); erythromycin, 50 microg ml(-1) and tetracycline 50 microg ml(-1)). 56 bacteria were isolated and identified by 16 S rDNA sequencing. Antibiotic resistance profiles of isolated bacteria were determined for 22 different antibiotics. All identified bacteria were able to growth in multiple ATBs. Colistin, ceftazidime, ampicillin/sulbactam, cefotaxime, cefepime, cefalotin, ampicillin and erythromycin were the most distributed resistances among the 56 tested bacteria. The current results demonstrated that antibiotic resistance was abundant and diverse in high altitude Lakes. Also the present article indicates some useful patents regarding the isolation of bacteria able to grow in the present of antibiotics.

Genome Sequence of Sphingomonas sp. S17, Isolated from an Alkaline, Hyperarsenic, and Hypersaline Volcano-Associated Lake at High Altitude in the Argentinean Puna

The high-altitude Andean lakes (HAAL) in the Argentinean Puna-high Andes region represent an almost unexplored ecosystem exposed to extreme conditions (high UV irradiation, hypersalinity, drastic temperature changes, desiccation, and high pH). Here we present the first genome sequence, a Sphingomonas sp., isolated from this extreme environment.

Draft Genome Sequence of the Polyextremophilic Exiguobacterium sp. Strain S17, Isolated from Hyperarsenic Lakes in the Argentinian Puna

ABSTRACT Exiguobacterium sp. strain S17 is a moderately halotolerant, arsenic-resistant bacterium that was isolated from Laguna Socompa stromatolites in the Argentinian Puna. The draft genome sequence suggests potent enzyme candidates that are essential for survival under multiple environmental extreme conditions, such as high levels of UV radiation, elevated salinity, and the presence of critical arsenic concentrations.

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.

Genome comparison of two Exiguobacterium strains from high altitude andean lakes with different arsenic resistance: identification and 3D modeling of the Acr3 efflux pump

Arsenic exists in natural systems in a variety of chemical forms, including inorganic arsenite (As [III]) and arsenate (As [V]). The majority of living organisms have evolved various mechanisms to avoid occurrence of arsenic inside the cell due to its toxicity. Common core genes include a transcriptional repressor ArsR, an arsenate reductase ArsC, and arsenite efflux pumps ArsB and Acr3. To understand arsenic resistance we have performed arsenic tolerance studies, genomic and bioinformatic analysis of two Exiguobacterium strains, S17 and N139, from the high-altitude Andean Lakes. In these environments high concentrations of arsenic were described in the water due to a natural geochemical phenomenon, therefore, these strains represent an attractive model system for the study of environmental stress and can be readily cultivated. Our experiments show that S17 has a greater tolerance to arsenite (10nM) than N139, but similar growth in arsenate (150nM). We sequenced the genome of the two Exiguobacterium and identified an acr3 gene in S17 as the only difference between both species regarding known arsenic resistance genes. To further understand the Acr3 we modeled the 3D structure and identified the location of relevant residues of this protein. Our model is in agreement with previous experiments and allowed us to identify a region where a relevant cysteine lies. This Acr3 membrane efflux pump, present only in S17, may explain its increased tolerance to As(III) and is the first Acr3-family protein described in Exiguobacterium genus.

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.

Haloarchaea from the Andean Puna: Biological Role in the Energy Metabolism of Arsenic

Biofilms, microbial mats, and microbialites dwell under highly limiting conditions (high salinity, extreme aridity, pH, and elevated arsenic concentration) in the Andean Puna. Only recent pioneering studies have described the microbial diversity of different Altiplano lakes and revealed their unexpectedly diverse microbial communities. Arsenic metabolism is proposed to be an ancient mechanism to obtain energy by microorganisms. Members of Bacteria and Archaea are able to exploit arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite. Only six aioAB sequences coding for arsenite oxidase and three arrA sequences coding for arsenate reductase from haloarchaea were previously deposited in the NCBI database. However, no experimental data on their expression and function has been reported. Recently, our working group revealed the prevalence of haloarchaea in a red biofilm from Diamante Lake and microbial mat from Tebenquiche Lake using a metagenomics approach. Also, a surprisingly high abundance of genes used for anaerobic arsenate respiration (arr) and arsenite oxidation (aio) was detected in the Diamante’s metagenome. In order to study in depth the role of arsenic in these haloarchaeal communities, in this work, we obtained 18 haloarchaea belonging to the Halorubrum genus, tolerant to arsenic. Furthermore, the identification and expression analysis of genes involved in obtaining energy from arsenic compounds (aio and arr) showed that aio and arr partial genes were detected in 11 isolates, and their expression was verified in two selected strains. Better growth of two isolates was obtained in presence of arsenic compared to control. Moreover, one of the isolates was able to oxidize As[III]. The confirmation of the oxidation of arsenic and the transcriptional expression of these genes by RT-PCR strongly support the hypothesis that the arsenic can be used in bioenergetics processes by the microorganisms flourishing in these environments.

The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions

We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. ‘Chiri qhucha’ in Quechua means ‘cold lake’, which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. chiriqhucha str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina.