About
422
Publications
24,285
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
4,060
Citations
Introduction
Skills and Expertise
Publications
Publications (422)
Drylands’ poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African d...
In the nutrient-limited Antarctic terrestrial habitat, penguins transfer a significant amount of nutrients from the marine to the terrestrial ecosystem through their depositions (i.e., guano). This guano influences soil physicochemical properties, leading to the formation of ornithogenic soil rich in nutrients and organic matter. We hypothesize tha...
Mobile genetic elements (MGEs), collectively referred to as the “mobilome”, can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhib...
Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is ‘Igneacidithiobacillus’, a novel genus-level taxon, represented by ‘Igneacidithiobacillus copahuensis’ VAN18-1T as its type species,...
Temperature, pH, and hydrochemistry of terrestrial hot springs play a critical role in shaping thermal microbial communities. However, the interactions of biotic and abiotic factors at this terrestrial-aquatic interface are still not well understood on a global scale, and the question of how underground events influence microbial communities remain...
Several hydrolases have been described to degrade polyethylene terephthalate (PET) at moderate temperatures ranging from 25°C to 40°C. These mesophilic PET hydrolases (PETases) are less efficient in degrading this plastic polymer than their thermophilic homologs and have, therefore, been the subject of many protein engineering campaigns. However, e...
In terrestrial hot springs, some members of the microbial mat community utilize sulfur chemical species for reduction and oxidization metabolism. In this study, the diversity and activity of sulfur-metabolizing bacteria were evaluated along a temperature gradient (48–69 °C) in non-acidic phototrophic mats of the Porcelana hot spring (Northern Patag...
Microbes play an important role in coastal and estuarine waters. We present 93 metagenomes and 677 metagenome-assembled genomes (MAGs) from Comau Fjord, Patagonia (42°S), to further understand the microbial dynamics and their response to anthropogenic disturbances. These data represent a spatially (35-km transect) and temporally (2016 to 2019) expl...
While progress has been made in surveying the oceans to understand microbial and viral communities, the coastal ocean and, specifically, estuarine waters, where the effects of anthropogenic activity are greatest, remain partially understudied. The coastal waters of Northern Patagonia are of interest since this region experiences high-density salmon...
Viruses are key players in marine environments, affecting food webs and biogeochemical cycles. We present 48 viral metagenomes and 5,656 viral operational taxonomic units (vOTUs) from Comau Fjord, Patagonia (42°S), to understand viral-mediated processes in coastal and estuarine waters. These data represent a spatial (35-km transect, two depths) and...
Fresh water supply is critical along the Andes, where drought conditions over the past decade are projected to persist. At high Andean headwater catchments, frozen ground conditions are assumed to modulate groundwater flow paths and their hydrological signals at different timescales. However, knowledge of hydrological connections in subtropical And...
Key organisms in the environment, such as oxygenic photosynthetic primary producers (photosynthetic eukaryotes and cyanobacteria), are responsible for fixing most of the carbon globally. However, they are affected by environmental conditions, such as temperature, which in turn affect their distribution. Globally, the cyanobacterium Fischerella ther...
The Cas1 protein is essential for the functioning of CRISPR-Cas adaptive systems. However, despite the high prevalence of CRISPR-Cas systems in thermophilic microorganisms, few studies have investigated the occurrence and diversity of Cas1 across hot spring microbial communities. Phylogenomic analysis of 2,150 Cas1 sequences recovered from 48 metag...
At present, there is no simple, first principles–based, and general model for quantitatively describing the full range of observed biological temperature responses. Here we derive a general theory for temperature dependence in biology based on Eyring–Evans–Polanyi’s theory for chemical reaction rates. Assuming only that the conformational entropy o...
Drylands play a significant role in the global biogeochemical cycling of nutrients (carbon, nitrogen, and phosphorus) through abiotic (geological, atmospheric, and hydrological) and biotic (animals, insects, plants, and microorganisms) pathways. They act as important carbon reservoirs and are estimated to store over 30% of the global soil organic c...
Although crucial for the addition of new nitrogen in marine ecosystems, dinitrogen (N2) fixation remains an understudied process, especially under dark conditions and in polar coastal areas, such as the West Antarctic Peninsula (WAP). New measurements of light and dark N2 fixation rates in parallel with carbon (C) fixation rates, as well as analysi...
Marine ammonia oxidizers that oxidize ammonium to nitrite are abundant in polar waters, especially during the winter in the deeper mixed-layer of West Antarctic Peninsula (WAP) waters. However, the activity and abundance of ammonia-oxidizers during the summer in surface coastal Antarctic waters remain unclear. In this study, the ammonia-oxidation r...
Polyethylene terephthalate (PET) is one of the most widely used synthetic plastics in the packaging industry, and consequently has become one of the main components of plastic waste found in the environment. However, several microorganisms have been described to encode enzymes that catalyze the depolymerization of PET. While most known PET hydrolas...
Viruses exert diverse ecosystem impacts by controlling their host community through lytic predator-prey dynamics. However, the mechanisms by which lysogenic viruses influence their host-microbial community are less clear. In hot springs, lysogeny is considered an active lifestyle, yet it has not been systematically studied in all habitats, with pho...
Proteorhodopsin-bearing microorganisms in the Southern Ocean have been overlooked since their discovery in 2000. The present study identify taxonomy and quantify the relative abundance of proteorhodopsin-bearing bacteria and proteorhodopsin gene transcription in the West Antarctic Peninsula’s coastal waters.
The Southern Ocean (SO) represents up to one-fifth of the total carbon drawdown worldwide. Intense selective pressures (low temperature, high UV radiation, and strong seasonality) and physical isolation characterize the SO, serving as a “natural” laboratory for the study of ecogenomics and unique adaptations of endemic viral populations. Here, we r...
Volatile organic silicon compounds (VOSiC) are harmful pollutants to the biota and ecological dynamics as well as biogas-based energy conversion systems. However, there is a lack of understanding regarding the source of VOSiCs in biogas, especially arising from the biochemical conversion of siloxane polymers such as polydimethylsiloxanes (PDMS). Th...
Fjords are sensitive areas affected by climate change and can act as a natural laboratory to study microbial ecological processes. The Chilean Patagonian fjords (41–56°S), belonging to the Subantarctic ecosystem (46–60°S), make up one of the world’s largest fjord systems. In this region, Estuarine Water (EW) strongly influences oceanographic condit...
At present, there is no simple, complete, and first principles-based model for quantitatively describing the full range of observed biological temperature responses. Here, we derive a theory exhibiting these features based on the Eyring-Evans-Polanyi theory governing chemical reaction rates, and which is applicable across all scales from the micro...
Current warming in the Western Antarctic Peninsula (WAP) has multiple effects on the marine ecosystem, modifying the trophic web and the nutrient regime. In this study, the effect of decreased surface salinity on the marine microbial community as a consequence of freshening from nearby glaciers was investigated in Chile Bay, Greenwich Island, WAP....
Several cyanobacterial species are dominant primary producers in hot spring microbial mats. To date, hot spring cyanobacterial taxonomy, as well as the evolution of their genomic adaptations to high temperatures, are poorly understood, with genomic information currently available for only a few dominant genera, including Fischerella and Synechococc...
Sewage-associated viruses can cause several human and animal diseases, such as gastroenteritis, hepatitis, and respiratory infections. Therefore, their detection in wastewater can reflect current infections within the source population. To date, no viral study has been performed using the sewage of any large South American city. In this study, we u...
The detection of viruses in sewage is a method of environmental surveillance, which allows evaluating the circulation of different viruses in a community. This study presents the first results of sewage surveillance to detect the circulation of SARS-CoV-2 virus in Santiago, Chile. Using ultracentrifugation associated with RT-qPCR, we detected SARS-...
Deficient disinfection systems enable bacteria to form in drinking water; these can invade plumbing systems even if the pipes are composed of antibacterial materials such as copper. Severe copper corrosion by microorganisms and their subsequent release into the water system are evidenced by the blue water phenomenon. Proper monitoring and control c...
The true-branching cyanobacterium Fischerella thermalis (also known as Mastigocladus laminosus) is widely distributed in hot springs around the world. Morphologically, it has been described as early as 1837. However, its taxonomic placement remains controversial. F. thermalis belongs to the same genus as mesophilic Fischerella species but forms a m...
Mangroves in the Northwest Coast of South America are contaminated with heavy metals due to wastewater discharges from industries, affecting the biota from this environment. However, bacteria proliferate in these harsh environmental conditions becoming possible sentinel of these contaminations. In this study, bacterial community composition was ana...
We used the 16S rRNA gene pyrosequencing approach to investigate the microbial diversity and community composition in several Costa Rican hot springs alongside the latitudinal axis of the country, with a range of temperatures (37–63°C), pH (6–7.5) and other geochemical conditions. A principal component analyses of the physicochemical parameters sho...
In Antarctic coastal waters where nutrient limitations are low, viruses are expected to play a major role in the regulation of bloom events. Despite this, research in viral identification and dynamics is scarce, with limited information available for the Southern Ocean (SO). This study presents an integrative-omics approach, comparing variation in...
For tolerating extreme desiccation, cyanobacteria are known to produce both compatible solutes at intracellular level and a copious amount of exopolysaccharides as a protective coat. However, these molecules make cyanobacterial cells refractory to a broad spectrum of cell disruption methods, hindering genome sequencing, and molecular studies. In fa...
Phytoplankton blooms taking place during the warm season drive high productivity in Antarctic coastal seawaters. Important temporal and spatial variations exist in productivity patterns, indicating local constraints influencing the phototrophic community. Surface water in Chile Bay (Greenwich Island, South Shetlands) is influenced by freshwater fro...
Composition, carbon and nitrogen uptake, and gene transcription of microbial mat communities in Porcelana neutral hot spring (Northern Chilean Patagonia) were analyzed using metagenomics, metatranscriptomics and isotopically labeled carbon (H¹³CO3) and nitrogen (¹⁵NH4Cl and K¹⁵NO3) assimilation rates. The microbial mat community included 31 phyla,...
Total transcripts (cDNA) assigned to phototrophic processes. (a) Transcripts associated with photosystems PSI (psaA gene) and PSII (psbA gene) in oxygenic photosynthesis. (b) Transcripts (pufM, fmoA, pscA and bchC genes) associated with anoxygenic photosynthesis. Each bar represents a different temperature and daily period. Transcripts were normali...
Diurnal carbon and nitrogen assimilation rates recorded at 58 and 48°C in Porcelana microbial mats. Nitrogen fixation data from Alcamán et al. (2015). The black bars represent the C or N assimilation rates in the dark.
Process and pathways analyzed with principal genes associated and encoding protein. All this was used as diagnostic for phototrophy, autotrophy, and nitrogen cycle transformations.
Taxonomic assignment of Chloroflexi by metagenomic (DNA; white bars) and metatranscriptomic reads (cDNA day: gray bars; cDNA night: black bars) at the Order (a) and genus (b) levels at the three temperatures studied.
Total transcripts (cDNA) associated with the autotrophic carbon fixation pathways. CC, Calvin–Benson–Basham cycle (rbcL gene); 3HP, 3-hydroxypropionate bi-cycle (mcr gene); HH, hydroxypropionate-hydroxybutyrate cycle (atoB gene). Transcripts were normalized by RPKM.
Total transcripts (cDNA) associated with specific carbon fixation pathways. (a) 3-Hydroxypropionate bi-cycle (mcr, prpE, and mcl genes) and (b) hydroxypropionate-hydroxybutyrate atoB, crt, abfD, sucD genes) cycle. Transcripts were normalized by RPKM.
Results of high throughput sequencing: raw reads, quality reads, percentage of reads corresponding to ribosomal RNA, non-ribosomal genes, non-redundant (NR) hits and percentage of the latter that could be taxonomically assigned. Numbers of sequences are shown in millions.
Taxonomic assignment of Cyanobacteria by metagenomic (DNA; white bars) and metatranscriptomic reads (cDNA day: gray bars; cDNA night: black bars) at the three temperatures studied. (a) Proportion of cyanobacterial reads in different Orders. (b) Proportion of Stigonematales reads in different genera.
Total reads assigned to Proteobacteria by 16S rRNA sequences recovered from metagenomes. Rhodospirillales (alphaproteobacteria) and Burkholderiales (betaproteobacteria) were the most abundant orders at the lowest temperature. Note that the vertical scale is logarithmic.
Total transcripts (cDNA) assigned to nitrogen cycle pathways: ammonia transporter (amt gene), nitrate assimilation (narB gene), ammonia assimilation (glnA gene), ammonia oxidation (amoA gene), N2 fixation (nifH gene), DNRA (nrfA gene), and denitrification (nosZ gene). Transcripts were normalized by RPKM.
Total percentage of Bacteria and Archaea phyla present in the entire temperature gradient of Porcelana hot spring at noon and night (N) periods.
Best hits and % similarity in the SILVA database of the most relevant organisms found in Porcelana mat.
Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed o...
Cyanophages are viruses with a wide distribution in aquatic ecosystems, that specifically infect Cyanobacteria. These viruses can be readily isolated from marine and fresh waters environments; however, their presence in cosmopolitan thermophilic phototrophic mats remains largely unknown. This study investigates the morphological diversity (TEM), ta...
In the Porcelana Hot Spring (Northern Patagonia), true-branching cyanobacteria are the dominant primary producers in microbial mats, and they are mainly responsible for carbon and nitrogen fixation. However, little is known about their metabolic and genomic adaptations at high temperatures. Therefore, in this study, a total of 81 Fischerella therma...
Phytoplankton biomass during the austral summer is influenced by freezing and melting cycles as well as oceanographic processes that enable nutrient redistribution in the West Antarctic Peninsula (WAP). Microbial functional capabilities, metagenomic and metatranscriptomic activities as well as inorganic 13C- and 15N-assimilation rates were studied...
Porcelana Geysers are located on the slopes of Barranco Colorado volcano, southern Chile, and is characterized by having a lateral hydrothermal fluid transport and an important CO2 content, having high gas exsolution rates on the surface at temperatures above 80°C. But it does not seem to be enough to explain the genesis of columnar travertines mor...
Lake Big Momela, one of the East African soda lakes in Northern Tanzania characterised by highly saline-alkaline conditions, making them inhospitable to a range of organisms, although supporting massive growths of some adapted planktonic microorganisms that serve as food for birds, such as Lesser Flamingo. The temporal dynamics of plankton, with an...