The Cuatro Cienegas basin in the Chihuahuan desert is a system of springs, streams, and pools. These ecosystems support >70 endemic species and abundant living stromatolites and other microbial communities, representing a desert oasis of high biodiversity. Here, we combine data from molecular microbiology and geology to document the microbial biodiversity of this unique environment. Ten water samples from locations within the Cuatro Cienegas basin and two neighboring valleys as well as three samples of wet sediments were analyzed. The phylogeny of prokaryotic populations in the samples was determined by characterizing cultured organisms and by PCR amplification and sequencing of 16S rRNA genes from total community DNA. The composition of microbial communities was also assessed by determining profiles of terminal restriction site polymorphisms of 16S rRNA genes in total community DNA. There were 250 different phylotypes among the 350 cultivated strains. Ninety-eight partial 16S rRNA gene sequences were obtained and classified. The clones represented 38 unique phylotypes from ten major lineages of Bacteria and one of Archaea. Unexpectedly, 50% of the phylotypes were most closely related to marine taxa, even though these environments have not been in contact with the ocean for tens of millions of years. Furthermore, terminal restriction site polymorphism profiles and geological data suggest that the aquatic ecosystems of Cuatro Cienegas are hydrologically interconnected with adjacent valleys recently targeted for agricultural intensification. The findings underscore the conservation value of desert aquatic ecosystems and the urgent need for study and preservation of freshwater microbial communities.Cuatro Cienegas ͉ terminal restriction site polymorphism ͉ 16S clone library ͉ water conservation ͉ microbial ecology

1. The effects of phosphorus enrichment and grazing snails on a benthic microbial community that builds stromatolic oncolites were examined in an experiment at Rio Mesquites, Cuatro Ciénegas, Mexico. Chemical analyses of stream water samples indicated that overall atomic ratios of total nitrogen (N) to total phosphorus (P) were approximately 110, indicating a strong potential for P-limitation of microbial growth. 2. Phosphorus enrichment involved addition of 5 lmol Na 2 HPO 4 L )1 to streamside microcosms receiving intermittent inputs of stream water while grazer manipulation involved removal of the dominant grazer, the snail Mexithauma quadripaludium. After 7 weeks, we examined responses in organic matter content, C : N : P ratios, metabolism (P removal, primary production, dark respiration, and calcification), and microbial community structure using molecular fingerprinting of 16S rRNA genes. 3. Manipulation of snails did not affect response variables measured in these treatments (organic matter, C : P ratio, P removal rate). However, P enrichment significantly decreased the C : P and N : P ratios of surficial materials in the oncolites (organic matter content was unchanged), increased net and gross photosynthesis (oxygen consumption in the dark was unchanged), increased rates of calcification, and increased diatoms relative to cyanobacteria. Heterotrophic Eubacteria and Archaea were only modestly affected. Thus, our results indicate weak grazing effects but strong impacts of P in this benthic system. 4. We hypothesise that a state of severe P-limitation is imposed on autotrophic production in this food web due, at least in part, to co-precipitation of phosphate during calcite deposition. This produces severe P-limitation of the benthic algae and cyanobacteria, resulting in high C : P ratio of microbial mats relative to the biomass of photoautotrophs (phytoplankton, terrestrial foliage) in other ecosystems. In turn, this high C : P ratio is likely to generate severe stoichiometric constraints on the herbivores, thus limiting their populations and resulting in weak overall grazing impacts.

Aim To assess the hypothesis that free-living prokaryotes show a pattern of 'no biogeography' by examining the scaling of soil prokaryotic diversity and by comparing it with other groups' biogeographical patterns.Location Two sites in the tropical deciduous forest of Chamela, Jalisco, on the western coast of Mexico. MethodsWe examined the diversity and distribution of soil prokaryotes in two 8 × 8 m quadrats divided in such manner that we could sample at four spatial scales. Restriction fragment length polymorphisms of 16S rRNA genes were used to define operational taxonomic units (OTUs) that we used in lieu of species to assess diversity. ResultsWe found highly structured species assemblages that allowed us to reject multiple predictions of the hypothesis that soil bacteria show 'no biogeography' . The frequency distribution of range size (measured as the occupancy of quadrats) of OTUs followed a hollow curve similar to that of vertebrates on continents. Assemblages showed high levels of beta diversity and a non-random nested pattern of diversity. OTU diversity scaled with area followed a power function with slopes z = 0.42 and 0.47. Main conclusionsWe demonstrate a non-ubiquitous dispersal for soil prokaryotes, which suggests a complex biogeography similar to that found for terrestrial vertebrates.

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The Cuatro Ciénegas Basin (CCB) is a rare oasis in the Chihuahuan Desert in the state of Coahuila, Mexico. It has a biological endemism similar to that of the Galapagos Islands, and its spring-fed ecosystems have very low nutrient content (nitrogen or phosphorous) and are dominated by diverse microbialites. Thus, it has proven to be a distinctive opportunity for the field of astrobiology, as the CCB can be seen as a proxy for an earlier time in Earth's history, in particular the late Precambrian, the biological frontier when prokaryotic life yielded at least partial dominance to eukaryotes and multicellular life. It is a kind of ecological time machine that provides abundant opportunities for collaborative investigations by geochemists, geologists, ecologists, and population biologists in the study of the evolutionary processes that structured Earth-based life, especially in the microbial realm. The CCB is an object of investigation for the identification of biosignatures of past and present biota that can be used in our search for extraterrestrial life. In this review, we summarize CCB research efforts that began with microbial ecology and population biology projects and have since been expanded into broader efforts that involve biogeochemistry, comparative genomics, and assessments of biosignatures. We also propose that, in the future, the CCB is sanctioned as a ''Precambrian Park'' for astrobiology.

The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems.

The Cuatro Cienegas basin (Coahuila, México) is a composite of different water systems in the middle of the desert with unusually high levels of endemism and diversity in different taxa. Although the diversity of macrobiota has been well described, little is known about the diversity and distribution of microorganisms in the oligotrophic ponds. Here we describe the extent and distribution of diversity found in aquatic prokaryotic communities by analysis of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes and phylogenetic analysis of cloned genes. Twelve locations within the basin were sampled. Among all the samples, we found a total of 117 operational taxonomic units (OTUs) using T-RFLPs, which ranged in any single sample from four to 49. OTU richness and Shannon diversity indices for different sites varied, but none were particularly high. 16S rRNA gene sequence data showed 68 different phylotypes among 198 clones. The most abundant phylotypes were Gamma- and Betaproteobacteria, and extreme halophiles. The differences among sites were significant; 45 TRFs were found only once, and 37% of the total diversity was represented by differences between sites, suggesting high beta-diversity. Further studies are needed to test whether this is a direct consequence of environmental heterogeneity in the basin.

Fungi play fundamental ecological roles in terrestrial ecosystems. However, their distribution and diversity remain poorly described in natural communities, particularly in arid and semi-arid ecosystems. In order to identify environmental factors determining fungal community structure in these systems, we assessed their diversity in conjunction with soil physicochemical characteristics in a semi-arid ecosystem in Baja California, Mexico, endemic for Coccidioidomycosis (Valley Fever). Two different microhabitats, burrows (influenced by rodent activity) and topsoil, were compared in winter and summer. Using a metagenomic approach, the ITS1 region of nuclear ribosomal DNA was used as barcode. A total of 1940 Operational Taxonomic Units (OTUs) were identified from 362 332 ITS1 sequences obtained by 454 pyrosequencing. Differences in fungal composition between seasons were clearly identified. Moreover, differences in composition between microhabitats were mainly correlated to significant differences in environmental factors, such as moisture and clay content in topsoil samples, and temperature and electrical conductivity in burrow samples. Overall, the fungal community structure (dominated by Ascomycota and Basidiomycota) was less variable between seasons in burrow than in topsoil samples. Coccidioides spp. went undetected by pyrosequencing. However, a nested PCR approach revealed its higher prevalence in burrows.