Astrobiology and Cuatro Ciénegas Basin as an Analog of Early Earth, 2020
Deep hydrothermal systems result from the magmatic and tectonic activity of the ocean floor. This... more Deep hydrothermal systems result from the magmatic and tectonic activity of the ocean floor. This deep extreme biosphere represents a unique oasis of life driven by sulfur-based chemosynthesis instead of photosynthesis. The organisms inhabiting these systems are adapted to cope with harsh environmental conditions such as the absence of sunlight, high temperatures and hydrostatic pressures, and elevated concentrations of hydrogen sulfide, as well as high concentrations of heavy metals. Therefore, this biome is different from any other environment on modern Earth. As expected from such conditions, chemoautotrophic prokaryotes are the leading primary producers at the base of the food web considered as an analog to the oldest signs of life on Earth. Herein, we discuss prokaryotic diversity and community structure from the newly discovered hydrothermal systems in the Alarcon Rise (AR), the Pescadero Basin (PB), and the Pescadero Transform Fault (PTF) at the mouth of the Gulf of California, Mexico, using 16S rRNA gene amplicon Illumina sequencing. Despite the spatial proximity of the studied vent systems (<100 km), they differ considerably in their physical, chemical, geological settings, and biotic characteristics. Our results indicated that beta prokaryotic diversity is associated to the sampling source, suggesting a strong effect of environmental conditions in shaping microbial distribution. The most abundant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, Chloroflexi, and Epsilonbacteraeota. Also, we found evidence on the oxidation of methane as a prevalent process in PB and PTF, since methylotrophic bacteria and Atribacteria were abundant, in contrast to AR basalt-hosted system. Bacteria associated with the sulfur cycle, in particular sulfur compounds reducing and sulfur compounds oxidizing bacteria predominated in all samples, confirming the importance of sulfur supporting vent communities. It is possible that vent systems played a significant role in the origins of life on Earth. Hence, they represent useful models when searching for life elsewhere in the universe.
Cuatro Ciénegas Basin: An Endangered Hyperdiverse Oasis, 2018
The Cuatro Cienegas Basin (CCB) is considered an important biodiversity hot spot despite its arid... more The Cuatro Cienegas Basin (CCB) is considered an important biodiversity hot spot despite its arid climate conditions. The valley is located in the southern part of the Chihuahuan desert at 26° 50′ 41″ N and is strongly affected by a divergent wind zone with high pressure at 30° N. The average annual solar radiation is 5.28 kWh m−2 day−1, exhibiting a seasonal pattern with the highest values occurring in the summer months. The annual mean temperature is 21.9 °C. The average temperatures of the coldest month (January) is 12.9 °C while the hottest month (July) is 28.8 °C, resulting in a seasonal monthly pattern similar to that of solar radiation. The temperatures show a variation over the years with an apparent increase in the frequency of extreme cold events during the winter and extreme hot events during the summer. These results suggest that the winters are becoming colder while the summer months are becoming warmer. This annual variability is associated with the North Atlantic Oscillation (NAO). The annual averages of potential evapotranspiration and annual precipitation are 2602 mm year−1 and 211 mm year−1, respectively, suggesting that the average annual rainfall only represents only 8% of the annual water for evapotranspiration demand. The annual precipitation also shows high variability over the years as a consequence of El Nino, NAO, and tropical cyclones. The models under global climate change predict that the climate of CCB has a trend of becoming drier and warmer with a high frequency of extreme climatic events, resulting in a more extreme climate.
Barriers to microbial migrations can lead adaptive radiations and increased endemism. We propose ... more Barriers to microbial migrations can lead adaptive radiations and increased endemism. We propose that extreme unbalanced nutrient stoichiometry of essential nutrients can be a barrier to microbial immigration over geological timescales. At the oasis in the Cuatro Ciénegas Basin in Mexico, nutrient stoichiometric proportions are skewed given the low phosphorus availability in the ecosystem. We show that this endangered oasis can be a model for a lost world. The ancient niche of extreme unbalanced nutrient stoichiometry favoured survival of ancestral microorganisms. This extreme nutrient imbalance persisted due to environmental stability and low extinction rates, generating a diverse and unique bacterial community. Several endemic clades of Bacillus invaded the Cuatro Cienegas region in two geological times, the late Precambrian and the Jurassic. Other lineages of Bacillus, Clostridium and Bacteroidetes migrated into the basin in isolated events. Cuatro Ciénegas Basin conservation is ...
TIP Revista Especializada en Ciencias Químico-Biológicas, 2018
La domesticación de plantas y animales permite estudiar diferentes procesos evolutivos, como la s... more La domesticación de plantas y animales permite estudiar diferentes procesos evolutivos, como la selección, adaptación y especiación. En este artículo se describen avances recientes en el estudio de las calabazas, las cuales constituyen el género Cucurbita (Cucurbitaceae) siendo un grupo de plantas herbáceas americanas que incluyen entre 12 y 15 especies. Cucurbita ha tenido seis eventos de domesticación, de los cuales cuatro sucedieron en México. Este es un género relativamente reciente, que surgió en Norte América hace 16 millones de años y sus especies cultivadas mantienen una alta variación genética; Cucurbita pepo es la especie que presenta mayor variación genética,variación asociada a dos domesticaciones independientes, una en el norte de México, y otra en el Sureste de los Estados Unidos. En otra especie, Cucurbita argyrosperma, sus poblaciones de la Península de Yucatán, representan una poza genética diferenciada del resto de la especie. El estudio del genoma de C. argyrosper...
Proceedings of the National Academy of Sciences, 1992
Many bacterial species exhibit strong linkage disequilibrium of their chromosomal genes, which ap... more Many bacterial species exhibit strong linkage disequilibrium of their chromosomal genes, which apparently indicates restricted recombination between alleles at different loci. The extent to which restricted recombination reflects limited migration between geographically isolated populations versus infrequent mixis of genotypes within populations is more difficult to determine. We examined the genetic structure of Rhizobium leguminosarum biovar phaseoli populations associated with wild and cultivated beans (Phaseolus spp.) over several spatial scales, ranging from individual host plants to throughout the Western Hemisphere. We observed significant linkage disequilibrium at scales at least as small as a cultivated plot. However, the amount of disequilibrium was much greater among isolates collected throughout the Western Hemisphere than among isolates from one area of Mexico, even when disequilibrium was quantified using an index that scales for allelic diversity. This finding suggest...
ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is pred... more ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to theRoseobacterlineage and other marineAlphaproteobacteriavia DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution betweenRoseobacterand the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution betweenRoseobacterand the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior toRoseobacterorigin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution betweenRoseobacterand phytoplankton. Our data suggest...
Cuatro Ciénegas Basin: An Endangered Hyperdiverse Oasis
Due to its chemical properties and several stable redox states, microbial transformations of sulf... more Due to its chemical properties and several stable redox states, microbial transformations of sulfur compounds have been affecting the geochemical features of the Earth’s biosphere since the Archaean. However, despite the great importance of sulfur cycling, reconciling the geologic record with genomic data has been challenging. Here we first review current state-of-the-art evidence about the emergence of life on Earth in sulfur-rich environments, providing a conceptual framework that closely connects these two largely separated disciplines. Then, we summarize the current astonishing diversity of prokaryotes responsible for driving the sulfur cycle, suggesting that, due to their ancient origin, sulfur-associated taxa perhaps hold the greatest diversity of any group of microorganisms to metabolize a single element on Earth. Finally, because the guilds of sulfur metabolizing microbes co-occur at millimeter scales within microbial mats, we use the taxonomic and metabolic information derived from these primordial communities as ecological models to highlight sulfur as the guiding axis of these complex intersections, recapitulating a gear of the clock of life.
With more than 200 species, the genus Agave is one of the most interesting and complex groups of ... more With more than 200 species, the genus Agave is one of the most interesting and complex groups of plants in the world, considering for instance its great diversity and adaptations. The adaptations include the production of a single, massive inflorescence (the largest among plants) where after growing for many years, sometimes more than 30, the rosette dies shortly afterward, and the remarkable coevolution with their main pollinators, nectarivorous bats, in particular of the genus Leptonycteris. The physiological adaptations of Agave species include a photosynthetic metabolism that allows efficient use of water and a large degree of succulence, helping to store water and resources for their massive flowering event. Ecologically, the agaves are keystone species on which numerous animal species depend for their subsistence due to the large amounts of pollen and nectar they produce, that support many pollinators, including bats, perching birds, hummingbirds, moths, and bees. Moreover, in...
We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated from a high-al... more We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated from a high-altitude Andean lake. The 2,952,588-bp genome contains one chromosome and three megaplasmids. The genome analysis suggests the presence of enzymes that confer E. pavilionensis str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals and high ultraviolet B radiation. 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 .
Herein we describe the Archaea diversity in a shallow pond in the Cuatro Ciénegas Basin (CCB), No... more Herein we describe the Archaea diversity in a shallow pond in the Cuatro Ciénegas Basin (CCB), Northeast Mexico, with fluctuating hypersaline conditions containing elastic microbial mats that can form small domes where their anoxic inside reminds us of the characteristics of the Archaean Eon, rich in methane and sulfur gases; thus, we named this site the Archaean Domes (AD). These domes only form after heavy rains that are rare in the Chihuahuan desert. CCB is a unique oasis with hundreds of ponds, containing endemic species of animals, plants and highly diverse and unique microbial communities, despite its very biased stoichiometry, due mostly to extreme low phosphorus content (soils, water columns and sediments). This extreme oligotrophy has favored survival of ancestral microorganisms. Whole metagenome sequencing approach was performed for this unusual site in three different seasons to assess the extent of the Archaea biodiversity, with a focus on extremophiles, since members of...
La familia Agavaceae abarca ocho géneros con biologías reproductivas contrastantes, ya que pueden... more La familia Agavaceae abarca ocho géneros con biologías reproductivas contrastantes, ya que pueden ser iteróparos (se pueden reproducir varias veces) o semélparos (producen una sola inflorescencia en su vida, para después morir) y tienen una notable diversidad de morfologías florales y de polinizadores (desde abejas a murciélagos, pasando por colibríes y polillas). Revisamos la biología reproductiva de cada género ( Yucca, Hesperalë, Furcraea, Beschorneria, Agave, Manfreda, Polianthes y Prochnyanthes) e intentamos una síntesis de lo que se conoce de su genética de poblaciones y evolución. Para ello reconstruimos su filogenia a partir de datos de los ITS l e ITS 2 y calibramos un reloj molecular. Para fin es comparativos utilizamos a Hosta, aunque revisarnos otros géneros que se han considerado cercanos a la familia. Por último, discutimos los patrones evolutivos en la familia, analizando los diferentes caracteres en la filogenia.
Astrobiology and Cuatro Ciénegas Basin as an Analog of Early Earth, 2020
Deep hydrothermal systems result from the magmatic and tectonic activity of the ocean floor. This... more Deep hydrothermal systems result from the magmatic and tectonic activity of the ocean floor. This deep extreme biosphere represents a unique oasis of life driven by sulfur-based chemosynthesis instead of photosynthesis. The organisms inhabiting these systems are adapted to cope with harsh environmental conditions such as the absence of sunlight, high temperatures and hydrostatic pressures, and elevated concentrations of hydrogen sulfide, as well as high concentrations of heavy metals. Therefore, this biome is different from any other environment on modern Earth. As expected from such conditions, chemoautotrophic prokaryotes are the leading primary producers at the base of the food web considered as an analog to the oldest signs of life on Earth. Herein, we discuss prokaryotic diversity and community structure from the newly discovered hydrothermal systems in the Alarcon Rise (AR), the Pescadero Basin (PB), and the Pescadero Transform Fault (PTF) at the mouth of the Gulf of California, Mexico, using 16S rRNA gene amplicon Illumina sequencing. Despite the spatial proximity of the studied vent systems (<100 km), they differ considerably in their physical, chemical, geological settings, and biotic characteristics. Our results indicated that beta prokaryotic diversity is associated to the sampling source, suggesting a strong effect of environmental conditions in shaping microbial distribution. The most abundant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, Chloroflexi, and Epsilonbacteraeota. Also, we found evidence on the oxidation of methane as a prevalent process in PB and PTF, since methylotrophic bacteria and Atribacteria were abundant, in contrast to AR basalt-hosted system. Bacteria associated with the sulfur cycle, in particular sulfur compounds reducing and sulfur compounds oxidizing bacteria predominated in all samples, confirming the importance of sulfur supporting vent communities. It is possible that vent systems played a significant role in the origins of life on Earth. Hence, they represent useful models when searching for life elsewhere in the universe.
Cuatro Ciénegas Basin: An Endangered Hyperdiverse Oasis, 2018
The Cuatro Cienegas Basin (CCB) is considered an important biodiversity hot spot despite its arid... more The Cuatro Cienegas Basin (CCB) is considered an important biodiversity hot spot despite its arid climate conditions. The valley is located in the southern part of the Chihuahuan desert at 26° 50′ 41″ N and is strongly affected by a divergent wind zone with high pressure at 30° N. The average annual solar radiation is 5.28 kWh m−2 day−1, exhibiting a seasonal pattern with the highest values occurring in the summer months. The annual mean temperature is 21.9 °C. The average temperatures of the coldest month (January) is 12.9 °C while the hottest month (July) is 28.8 °C, resulting in a seasonal monthly pattern similar to that of solar radiation. The temperatures show a variation over the years with an apparent increase in the frequency of extreme cold events during the winter and extreme hot events during the summer. These results suggest that the winters are becoming colder while the summer months are becoming warmer. This annual variability is associated with the North Atlantic Oscillation (NAO). The annual averages of potential evapotranspiration and annual precipitation are 2602 mm year−1 and 211 mm year−1, respectively, suggesting that the average annual rainfall only represents only 8% of the annual water for evapotranspiration demand. The annual precipitation also shows high variability over the years as a consequence of El Nino, NAO, and tropical cyclones. The models under global climate change predict that the climate of CCB has a trend of becoming drier and warmer with a high frequency of extreme climatic events, resulting in a more extreme climate.
Barriers to microbial migrations can lead adaptive radiations and increased endemism. We propose ... more Barriers to microbial migrations can lead adaptive radiations and increased endemism. We propose that extreme unbalanced nutrient stoichiometry of essential nutrients can be a barrier to microbial immigration over geological timescales. At the oasis in the Cuatro Ciénegas Basin in Mexico, nutrient stoichiometric proportions are skewed given the low phosphorus availability in the ecosystem. We show that this endangered oasis can be a model for a lost world. The ancient niche of extreme unbalanced nutrient stoichiometry favoured survival of ancestral microorganisms. This extreme nutrient imbalance persisted due to environmental stability and low extinction rates, generating a diverse and unique bacterial community. Several endemic clades of Bacillus invaded the Cuatro Cienegas region in two geological times, the late Precambrian and the Jurassic. Other lineages of Bacillus, Clostridium and Bacteroidetes migrated into the basin in isolated events. Cuatro Ciénegas Basin conservation is ...
TIP Revista Especializada en Ciencias Químico-Biológicas, 2018
La domesticación de plantas y animales permite estudiar diferentes procesos evolutivos, como la s... more La domesticación de plantas y animales permite estudiar diferentes procesos evolutivos, como la selección, adaptación y especiación. En este artículo se describen avances recientes en el estudio de las calabazas, las cuales constituyen el género Cucurbita (Cucurbitaceae) siendo un grupo de plantas herbáceas americanas que incluyen entre 12 y 15 especies. Cucurbita ha tenido seis eventos de domesticación, de los cuales cuatro sucedieron en México. Este es un género relativamente reciente, que surgió en Norte América hace 16 millones de años y sus especies cultivadas mantienen una alta variación genética; Cucurbita pepo es la especie que presenta mayor variación genética,variación asociada a dos domesticaciones independientes, una en el norte de México, y otra en el Sureste de los Estados Unidos. En otra especie, Cucurbita argyrosperma, sus poblaciones de la Península de Yucatán, representan una poza genética diferenciada del resto de la especie. El estudio del genoma de C. argyrosper...
Proceedings of the National Academy of Sciences, 1992
Many bacterial species exhibit strong linkage disequilibrium of their chromosomal genes, which ap... more Many bacterial species exhibit strong linkage disequilibrium of their chromosomal genes, which apparently indicates restricted recombination between alleles at different loci. The extent to which restricted recombination reflects limited migration between geographically isolated populations versus infrequent mixis of genotypes within populations is more difficult to determine. We examined the genetic structure of Rhizobium leguminosarum biovar phaseoli populations associated with wild and cultivated beans (Phaseolus spp.) over several spatial scales, ranging from individual host plants to throughout the Western Hemisphere. We observed significant linkage disequilibrium at scales at least as small as a cultivated plot. However, the amount of disequilibrium was much greater among isolates collected throughout the Western Hemisphere than among isolates from one area of Mexico, even when disequilibrium was quantified using an index that scales for allelic diversity. This finding suggest...
ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is pred... more ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to theRoseobacterlineage and other marineAlphaproteobacteriavia DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution betweenRoseobacterand the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution betweenRoseobacterand the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior toRoseobacterorigin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution betweenRoseobacterand phytoplankton. Our data suggest...
Cuatro Ciénegas Basin: An Endangered Hyperdiverse Oasis
Due to its chemical properties and several stable redox states, microbial transformations of sulf... more Due to its chemical properties and several stable redox states, microbial transformations of sulfur compounds have been affecting the geochemical features of the Earth’s biosphere since the Archaean. However, despite the great importance of sulfur cycling, reconciling the geologic record with genomic data has been challenging. Here we first review current state-of-the-art evidence about the emergence of life on Earth in sulfur-rich environments, providing a conceptual framework that closely connects these two largely separated disciplines. Then, we summarize the current astonishing diversity of prokaryotes responsible for driving the sulfur cycle, suggesting that, due to their ancient origin, sulfur-associated taxa perhaps hold the greatest diversity of any group of microorganisms to metabolize a single element on Earth. Finally, because the guilds of sulfur metabolizing microbes co-occur at millimeter scales within microbial mats, we use the taxonomic and metabolic information derived from these primordial communities as ecological models to highlight sulfur as the guiding axis of these complex intersections, recapitulating a gear of the clock of life.
With more than 200 species, the genus Agave is one of the most interesting and complex groups of ... more With more than 200 species, the genus Agave is one of the most interesting and complex groups of plants in the world, considering for instance its great diversity and adaptations. The adaptations include the production of a single, massive inflorescence (the largest among plants) where after growing for many years, sometimes more than 30, the rosette dies shortly afterward, and the remarkable coevolution with their main pollinators, nectarivorous bats, in particular of the genus Leptonycteris. The physiological adaptations of Agave species include a photosynthetic metabolism that allows efficient use of water and a large degree of succulence, helping to store water and resources for their massive flowering event. Ecologically, the agaves are keystone species on which numerous animal species depend for their subsistence due to the large amounts of pollen and nectar they produce, that support many pollinators, including bats, perching birds, hummingbirds, moths, and bees. Moreover, in...
We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated from a high-al... more We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated from a high-altitude Andean lake. The 2,952,588-bp genome contains one chromosome and three megaplasmids. The genome analysis suggests the presence of enzymes that confer E. pavilionensis str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals and high ultraviolet B radiation. 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 .
Herein we describe the Archaea diversity in a shallow pond in the Cuatro Ciénegas Basin (CCB), No... more Herein we describe the Archaea diversity in a shallow pond in the Cuatro Ciénegas Basin (CCB), Northeast Mexico, with fluctuating hypersaline conditions containing elastic microbial mats that can form small domes where their anoxic inside reminds us of the characteristics of the Archaean Eon, rich in methane and sulfur gases; thus, we named this site the Archaean Domes (AD). These domes only form after heavy rains that are rare in the Chihuahuan desert. CCB is a unique oasis with hundreds of ponds, containing endemic species of animals, plants and highly diverse and unique microbial communities, despite its very biased stoichiometry, due mostly to extreme low phosphorus content (soils, water columns and sediments). This extreme oligotrophy has favored survival of ancestral microorganisms. Whole metagenome sequencing approach was performed for this unusual site in three different seasons to assess the extent of the Archaea biodiversity, with a focus on extremophiles, since members of...
La familia Agavaceae abarca ocho géneros con biologías reproductivas contrastantes, ya que pueden... more La familia Agavaceae abarca ocho géneros con biologías reproductivas contrastantes, ya que pueden ser iteróparos (se pueden reproducir varias veces) o semélparos (producen una sola inflorescencia en su vida, para después morir) y tienen una notable diversidad de morfologías florales y de polinizadores (desde abejas a murciélagos, pasando por colibríes y polillas). Revisamos la biología reproductiva de cada género ( Yucca, Hesperalë, Furcraea, Beschorneria, Agave, Manfreda, Polianthes y Prochnyanthes) e intentamos una síntesis de lo que se conoce de su genética de poblaciones y evolución. Para ello reconstruimos su filogenia a partir de datos de los ITS l e ITS 2 y calibramos un reloj molecular. Para fin es comparativos utilizamos a Hosta, aunque revisarnos otros géneros que se han considerado cercanos a la familia. Por último, discutimos los patrones evolutivos en la familia, analizando los diferentes caracteres en la filogenia.
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