Valeria Souza

Valeria Souza
Universidad Nacional Autónoma de México | UNAM · Department of Evolutionary Ecology

About

722
Publications
93,113
Reads
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10,284
Citations
Additional affiliations
January 2000 - present
Instituto de Ecologia, Universidad Nacional Autonoma de México
Position
  • Total biological inventarium of an oasis in Cuatro cienegas Coahuila
May 1993 - present
Universidad Nacional Autónoma de México
Position
  • Professor (Full)
Description
  • I am within the Instituto de Ecología at UNAM
January 1993 - present
Universidad Nacional Autónoma de México
Description
  • I teach undergrad basic biology through microbes and graduate students on evolution, microbial ecology and molecular evolution

Publications

Publications (722)
Preprint
Cuatro cienegas Basin (CCB) is an extraordinary diverse oasis that is dying in front of our eyes. The Churince system disappeared completely in 2016 and the poza named for its amazing diversity, Archaean Domes, disappeared in 2023. However, there could be groundwater water connections between sites, allowing to dispersal of taxa as well as the surv...
Article
Environmental microbes routinely colonize wildlife body surface microbiota. However, animals experience dynamic environmental shifts throughout their daily routine. Yet, the effect of ecological shifts in wildlife body surface microbiota has been poorly explored. Here, we sequenced the hypervariable region V3–V4 of the 16S rRNA gene to characterize...
Article
Full-text available
A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the “Archaean Domes” (AD) site in the CCB, which is characterized by an abundance of hypersaline, non-lithifying microbial mats. In AD, we analyzed...
Article
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Modern microbial mats are relictual communities mostly found in extreme environments worldwide. Despite their significance as representatives of the ancestral Earth and their important roles in biogeochemical cycling, research on microbial mats has largely been localized, focusing on site-specific descriptions and environmental change experiments....
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Full-text available
Due to the enormous diversity of non-culturable viruses, new viruses must be characterized using culture-independent techniques. The associated host is an important phenotypic feature that can be inferred from metagenomic viral contigs thanks to the development of several bioinformatic tools. Here, we compare the performance of recently developed v...
Article
Microbial mats are microbial communities capable of recycling the essential elements of life and considered to be the oldest evidence of microbial communities on Earth. Due to their uniqueness and limited sampling material, analyzing their metabolomic profile in different seasons or conditions is challenging. In this study, microbial mats from a sm...
Preprint
Full-text available
The sheer diversity of unculturable viruses has prompted the need to describe new viruses through culture-independent techniques. The associated host is one important phenotypic feature that can be inferred from metagenomic viral contigs -- thanks to the development of various bioinformatic tools. Here we compare the performance of recently develop...
Article
Full-text available
Microbial mats are complex ecological assemblages that have been present in the rock record since the Precambrian and can still be found in extant marginalized environments. These structures are considered highly stable ecosystems. In this study, we evaluate the ecological stability of dome-forming microbial mats in a modern, water-level fluctuatin...
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Full-text available
In spring 2016, a shallow hypersaline pond (50×25 m) was found in the Cuatro Cienegas Basin (CCB). This pond, known as Archaean Domes (AD) because of its elastic microbial mats that form dome-shaped structures due to the production of reducing gases reminiscent of the Archaean eon, such as methane and hydrogen sulfide, harbour a highly diverse micr...
Article
Microbial mats are biologically diverse communities that are analogs to some of the earliest ecosystems on Earth. In this study, we describe a unique transiently hypersaline microbial mat uncovered in a shallow pond within the Cuatro Cienegas Basin (CCB) in northern México. The CCB is an endemism-rich site that harbors living stromatolites that hav...
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The simplest form of heterotrophy in the carbon cycle is to metabolize C1 compounds, this is a widely spread strategy that includes genus in different phyla inhabiting diverse environments that seem to have acquired the methanol dehydrogenase by horizontal gene transfer (HGT). The objective of this study was to isolate and explore the diversity of...
Article
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Plant genomes contain huge troves of information, and nowadays molecular tools to analyze genomes are less expensive and keep improving. In this review, we aimed to produce a “roadmap” to take advantage of this explosion of molecular methods and opportunities. We explain how to decide which strategies are adequate for a given evolutionary or taxono...
Preprint
Full-text available
Although microbial mats are considered relictual communities that are nowadays mostly constrained in their distribution by predation and phosphorus availability, they are still found in a wide range of environmental conditions. Their ancestral history, geographical isolation, stratified community composition and interspecies dynamics make them an i...
Article
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Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper, we present an open-source python toolbox which consists of two modules: on one hand, we introduce a visualization module that incorpo...
Article
Full-text available
We evaluated the microbial diversity and metabolome profile of an uncommon hypersaline elastic microbial mat from Cuatro Ciénegas Basin (CCB) in the Chihuahuan Desert of Coahuila, México. We collected ten samples on a small scale transect (1.5-m) and described its microbial diversity through NGS-based ITS and 16S rDNA gene sequencing. A very low nu...
Article
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Pozas Rojas is a hydrological system comprising nine isolated shallow ponds and a deep lagoon, which were temporally merged in 2010 by increased rainfall due to a tropical cyclone. In this work, we assess which components, biotic interactions, or environment filtering effects, drive the assembly of microbial communities after a natural perturbation...
Preprint
Full-text available
Microbial mats are complex ecological assemblages that are found in the Precambrian fossil record and in extant extreme environments. Hence, these structures are regarded as highly stable ecosystems. In this work, we assess the ecological stability in a modern, fluctuating, hypersaline pond from the Cuatro Ciénegas Basin. From the 2016 to 2019 meta...
Preprint
Full-text available
We evaluated the microbial diversity and metabolomic signatures of a hypersaline elastic microbial mat from Cuatro Cienegas Basin (CCB) in the Chihuahuan Desert of Coahuila, Mexico. We collected ten samples within a small scale (1.5-meters transect) and found a high microbial diversity through NGS-based ITS and 16S rRNA gene sequencing. A very low...
Article
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 roset...
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Anthropogenic perturbations introduce novel selective pressures to natural environments, impacting the genomic variability of organisms and thus altering the evolutionary trajectory of populations. Water overexploitation for agricultural purposes and defective policies in Cuatro Cienegas, Coahuila, Mexico, have strongly impacted its water reservoir...
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Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common a...
Article
Full-text available
Due to the environmental conditions presented in arid zones, it is expected to have a high influence of deterministic processes over the community assemblages. Symbiotic interactions with microorganisms could increase colonization and survival of plants in difficult conditions, independent of the plants physiological and morphological characteristi...
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Full-text available
Fungal ecological interactions play a key role in structuring community assemblages. These associations may involve both antagonistic and synergistic relationships, which are commonly influenced by abiotic factors such as nutrient conditions. However, information for extreme, oligotrophic systems remain poor. Herein, interactions among key members...
Chapter
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, hi...
Chapter
Let’s travel in our mind eye to either early Earth or Mars: life had already evolved, but it was most probably patchy and hard to find; it was likely rare. We can even imagine the same process in exoplanets or moons, life starting as an organic oddity that eventually starts to evolve by Darwinian evolution, consuming resources to grow and reproduce...
Chapter
The Cuatro Ciénegas Basin (CCB), located in Coahuila, México, is considered a living laboratory for astrobiology. This site is an analogue for the Gale Crater in Mars because of its gypsum-rich soils. Moreover, the “pozas” at the site are extremely oligotrophic, which is characteristic of ancient oceans chemistry. Despite the oligotrophic condition...
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Background: In bacteria, pan-genomes are the result of an evolutionary "tug of war" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (Ne), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduce...
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Full-text available
Trhypochthoniellus comprises nine species, being mostly associated to aquatic vegetation; T. chilensis Ermilov & Weigmann as the only known species from North and South America. This genus is recorded for the first time in Mexico. Herein we present the description, illustrations and SEM photographs of Trhypochthoniellus churincensis sp. nov., which...
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With the purpose of discovering new anticancer molecules that might have fewer side effects or reduce resistance to current antitumor drugs, a bioprospecting study of the microalgae of the Cuatro Cienegas Basin (CCB), an oasis in the Chihuahuan desert in Mexico was conducted. A microalgae was identified as Granulocystopsis sp. through sequencing th...
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Full-text available
Several universal genomic traits affect trade-offs in the capacity, cost, and efficiency of the biochemical information processing that underpins metabolism and reproduction. We analyzed the role of these traits in mediating the responses of a planktonic microbial community to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cua...
Book
Astrobiology not only investigates how early life took hold of our planet but also life on other planets – both in our Solar System and beyond – and their potential for habitability. The book take readers from the scars on planetary surfaces made by space rocks to the history of the Solar System narrated by those space rocks as well as exoplanets i...
Preprint
Full-text available
Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry b...
Preprint
Full-text available
Background In bacteria, pan-genomes are the result of the evolutionary "tug of war" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size, resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by H...
Preprint
Full-text available
Background: In bacteria, pan-genomes are the result of an evolutionary "tug of war" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (Ne), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced...
Preprint
Full-text available
Background: In bacteria, pan-genomes are the result of the evolutionary "tug of war" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size, resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by...
Preprint
Full-text available
Several universal genomic traits affect the capacity, cost, and efficiency of biochemical information processing underpinning metabolism and reproduction. We analyzed their role in mediating planktonic microbial community responses to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Cienegas, Mexico - one of the first who...
Article
Pseudomonas aeruginosa is a widely distributed environmental bacterium, but is also an opportunistic pathogen that represents an important health hazard due to its high intrinsic antibiotic resistance and its production of virulence factors. The genetic structure of P. aeruginosa populations using whole genome sequences shows the existence of three...
Article
The Cuatro Cienegas Basin (CCB) in the Chihuahuan desert is characterized by the presence of over 500 ponds located in an endorheic basin. These ponds are subsaline ecosystems characterized by a low productivity and a particularly high sulfate concentration, comparable to marine environments. This study focused on assessing the main physicochemical...
Chapter
The Cuatro Ciénegas Basin (CCB) is a biologically exceptional place. In general, CCB aquatic systems are extremely oligotrophic, but paradoxically they are extraordinarily biodiverse, and viruses are not an exception. Previous studies had shown that two stable ecosystems within CCB had very different virus; one of them, Pozas Azules, presented dive...
Article
Full-text available
To date, it remains unclear how anthropogenic perturbations influence the dynamics of microbial communities, what general patterns arise in response to disturbance, and whether it is possible to predict them. Here, we suggest the use of microbial mats as a model of study to reveal patterns that can illuminate the ecological processes underlying mic...
Article
Full-text available
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...
Article
Full-text available
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 esp...
Chapter
The Cuatro Cienegas Basin (CCB) encompasses hundreds of aquatic systems that harbor diverse microbialites with different community structure composition and with the highest level of endemism in North America. Thus, CCB represents a desert oasis of high biodiversity. Despite the great importance of this unique site, increasing demand on water for a...
Chapter
Ecological stoichiometry theory helps us to better understand trophic interactions by analyzing the imbalances in the relative supplies of key elements (carbon, nitrogen, and phosphorus) between organisms and their resources. However, the mechanisms that control elemental stoichiometry in different taxonomic groups and the effects of nutrient suppl...
Chapter
To understand the biodiversity of the Cuatro Cienegas Basin (CCB), we realized that some historical context was needed. In this case, the history reaches far back in geological time. This chapter will be a “once upon a time” story—told using the available data in the geological record—that follows the ever-increasing complexity of metabolic life an...
Chapter
Wendell Minckley had just graduated from college in 1957, and his love was aquatic environments and wildlife management. After his first fortuitous trip to Cuatro Cienegas Basin (CCB) in 1958, his life changed and devoted his career to understand this amazing oasis. In 1997 Minckley, by then a well-established professor at Arizona State University,...
Chapter
Full-text available
Given the fragility of the Cuatro Cienegas Basin and the danger of its loss, we started to study the variables affecting the resilience of the microbial community using different experimental approaches. How do microbial communities react to different kinds of perturbations and global change scenarios? We analyzed a series of experimental models th...
Chapter
In this chapter, we describe some genomic studies that have been conducted in the CCB to describe the microdiversity of different microbial taxa. Firstly, we describe the genomic variation in the endemic species B. coahuilensis, for which we analyzed three strains, and the evolutionary mechanism that have shaped their genomes, in particular for the...
Chapter
Full-text available
In this chapter we will explore whether the niche concept is useful to understand microbes, since we believe that this key concept in ecology is particularly useful in the investigation of microbial biodiversity. On the one hand, with microbes we can conduct experiments to analyze in detail all the aspects of the Grinnellian niche, in a way that ca...
Chapter
To understand microbial life and get the full picture, we ought to zoom out in order to grasp its magnitud and diversity and zoom in to dissect their genes and functions. We have obtained a significant amount of data on the great diversity of bacteria in the different environments of the Cuatro Ciénegas Basin (CCB), equivalent to obtaining the cens...
Chapter
The unique and untapped microbiological diversity of the Cuatro Cienegas Basin needs to be saved from the overexploitation of the aquifer by unsustainable agricultural practices. Considering the great value of the biodiversity enclosed in this valley, as a group we decided to change the future of the area, to start evolving from a poor agricultural...
Article
Full-text available
Microbial interactions play a key role in ecosystem functioning, with nutrient availability as an important determinant. Although phylogenetically distant bacteria and fungi commonly co-occur in nature, information on their cross-kingdom interactions under unstable, extreme environments remains poor. Hence, the aims of this work were to evaluate po...
Article
Full-text available
Mite-fungal interactions play a key role in structuring core ecosystem processes such as nutrient dynamics. Despite their ecological relevance, these cross-kingdom interactions remain poorly understood particularly in extreme environments. Herein, we investigated feeding preferences of a novel genetic lineage of aquatic oribatids obtained from an o...
Article
Full-text available
For more than 20 years cotton has been the most widely sown genetically modified (GM) crop in Mexico. Its cultivation has fulfilled all requirements and has gone through the different regulatory stages. During the last 20 years, both research-institutions and biotech-companies have generated scientific and technical information regarding GM cotton...
Article
Full-text available
The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and mi...