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Agave lechuguilla has one of the widest distributions among other agave species in the Chihuahuan Desert. Their capacity to grow in poorly developed soils and harsh conditions has been related to their association with plant growth-promoting rhizobacteria. In this work, we explored how soil properties and plant growth stage influence the composition of the rhizobacterial communities, their interactions, and the enzymatic activity and abundance of nitrogen-fixing bacteria and organic phosphorus-mineralizing bacteria in two subregions of the Chihuahuan Desert. We found that mature plants of lechuguilla stimulated the activity and abundance of nutrient-improvement rhizobacteria, and these soil samples had a higher content of total organic carbon, ammonium (NH4) and nitrite + nitrate (NO2+NO3). Nutrient availability seems to be an essential driver of the bacterial community's structure since the genera with more connections (hubs) were those with known mechanisms related to the availability of nutrients, such as env. OPS17 (Bacteroidetes), Gemmatimonadaceae uncultured, S0134terrestrial group, BD211terrestrial group (Gemmatimonadetes), Chthoniobacteracea and Candidatus Udaeobacter (Verrucomicrobia). This work shows that the late growth stages of lechuguilla recruit beneficial bacteria that favor its establishment and tolerance to harsh conditions of the arid lands.

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 characteristics. In this context, the microbial communities associated to plants that inhabit these types of areas can be a good model to understand the community assembly processes. We investigated the influence of stochastic and deterministic processes in the assemblage of rhizosphere microbial communities of Agave lechuguilla and bulk soil on the Cuatro Cienegas Basin, a site known for its oligotrophic conditions. We hypothesize that rhizospheric microbial communities of A. lechuguilla differ from those of bulk soil as they differ in physicochemical properties of soil and biotic interactions, including not only the plant, but also their microbial co-occurrence networks, it is expected that microbial species usually critical for plant growth and health are more common in the rhizosphere, whereas in the bulk soil microbial species related to the resistance to abiotic stress are more abundant. In order to confirm this hypothesis, 16S rRNA gene was sequenced by Illumina from rhizospheric and bulk soil samples in two seasons, also the physicochemical properties of the soil were determined. Our results showed differences in bacterial diversity, community composition, potential functions, and interaction networks between the rhizosphere samples and the ones from bulk soil. Although community structure arises from a complex interplay between deterministic and stochastic forces, our results suggest that A. lechuguilla recruits specific rhizospheric microbes with functional traits that benefits the plant through growth promotion and nutrition. This selection follows principally a deterministic process that shapes the rhizospheric microbial communities, directed by the plant modifications around the roots but also subjected to the influence of other environmental variables, such as seasonality and soil properties. Interestingly, keystone taxa in the interactions networks, not necessarily belong to the most abundant taxonomic groups, but they have an important role by their functional traits and keeping the connections on the community network.

Identification of microbial processes driving the loss of nitrogen from the oceans is of paramount relevance as these processes affect primary productivity in these ecosystems, which ultimately affects global biogeochemical cycles. Denitrification and anammox (anaerobic ammonium oxidation coupled to nitrite reduction) are the only identified processes so far that lead to nitrogen loss in marine environments. Here we provide stoichiometric and spectroscopic evidence, as well as tracer analysis with [15N]ammonium, revealing that anaerobic ammonium oxidation linked to the microbial reduction of natural organic matter (NOM) fuels nitrogen loss in marine sediments from the eastern tropical North Pacific coast. Tracer analysis revealed that the NOM-dependent anammox process was responsible for producing ∼1.5 μg of 15N2 (g of sediment)−1 day–1 after incubation for 27 days in sediment incubations amended with Pahokee peat, while intrinsic NOM present in the sediment promoted the production of ∼0.4 μg of 15N2 (g o...

One of the riskiest stages in the reproduction of cactus is the germination of seeds. Although evidence indicates the relevance of the seed-associated microbiome during this stage, little is known about its structure and function. In this work, we explore the diversity of the seed-associated microbiome of cactus, their role in the germination and protection of the emerging embryo. We characterized the microbial communities of the internal tissues (endoseminal) and those that colonize the surface of the seeds (episeminal) of four cactus species (Echinocactus platyacanthus, Ferocactus latispinus, Ferocactus pilosus, and Stenocereus queretaroensis). We sequenced by Illumina the 16S rRNA gene for Bacteria and the ITS1/ITS4 region for fungi. We isolated cultivable microorganisms and characterized their plant growth-promoting abilities. We determined that microbial communities associated with cactus seeds have high richness but are dominated by few taxa, and in most cases, there are clear differences between episeminal and endoseminal microbial groups, especially for fungi. The cactus seed microbiota comprises potential pathogens and beneficial microorganisms that could influence the germination percentage and seedling's development. We can highlight bacterial groups such as Kluyvera, Bacillus, Paenibacillus, and Stenotrophomonas; for fungi, the classes Tremellomycetes, Dothideomycetes, Eurotiomycetes, Leotiomycetes, and Sordariomycetes.

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 that represent different ecosystem compartments: bulk soil, soil crusts, water, and sediment. The experiments were performed in mesocosm or microcosm model systems, which we call in general “cosm” experiments. Different questions were addressed. How does water availability affect the recovery of microbial communities in disturbed soil patches? How do changes in temperature affect microbial crusts? How do bacterioplankton and bacterial mat communities respond to changes in temperature and UV radiation? What would happen to an oligotrophic environment if there was a high nutrient input? Our results suggested perturbations that influenced community structure and community cohesion were stronger in less fluctuating environments. Although it had been suggested that there was a functional (ecological) equivalence between microbial communities, our results on N2-fixing microorganisms of two arid ecosystems showed functional differences, even though similar species occur in both systems. Currently, new experiments are being carried out in “cosms” with replicates of the sediment and water interphase. Sadly, in one of the sites we have studied better, the Churince ecosystem, its conditions were dire the last time that sediment and water were sampled there. This ecosystem has now nearly disappeared. Nevertheless, the sediment in these fish tanks seems to be recovering its original structure. While seeming like a white rhino in a zoo, it might be the only ecosystem of this kind left to learn about what we lost.

In terrestrial arid ecosystems, one of the most limiting factors for productivity, following water, is thought to be nitrogen (N) availability. The N cycle can be summarized as an exchange of N forms between the atmosphere and the biosphere, mediated by the biological activity of microorganisms. Arid lands typically have a heterogeneous distribution of resources, with vegetated areas and microbial crusts having greater nutrient concentrations and microbial densities than bare soils. However, the contribution of each compartment to the entire N budget in these arid ecosystems is poorly understood. In this chapter, we summarize studies performed in the terrestrial component of Cuatro Cienegas Basin (CCB) regarding different aspects of the N cycle. We present selected results from two different studies that contrast microbial diversity and specific N transformations in (i) different moisture conditions and (ii) different temperatures. Although microbial crusts are important components of many desert ecosystems, there is very little evidence that the N fixed within them is in turn available to higher plants. Considering this, N fixers in the rhizosphere of plants could also be relevant N suppliers. In the last part of this chapter, we compare the potential composition of the microbial N fixers and denitrifier communities present in bare soils and in the rhizosphere of Agave lechuguilla, one of the most characteristic plant species in the Mexican arid regions. In general, these data suggest that environmental changes such as soil moisture reduction, changes in temperature, and vegetation removal could dramatically affect the terrestrial N cycle in CCB.

Vegetation communities with high soil carbon (C) inputs, e.g. grassland ecosystems, promote N protection via microbial communities in the soil whereas communities with low soil C inputs, e.g. desert scrub ecosystems, promote nitrification and are therefore susceptible to N loss. This study examines this relationship more closely by assessing the effects of two vegetation-soil systems on soil N transformation, in a grassland-desert scrub in Cuatro Cienegas Basin, Mexico. Metrics used in our study include: the belowground biomass of C, N and phosphorus (P) in both vegetation types; the availability of C, N and P in the soil; and the potential transformation of these nutrients by the microbial community which was characterized by 16S rRNA clone libraries. We found: (1) a higher NH4+ and microbial N concentration in the grassland soil than in the desert scrub soil, and (2) a different bacterial soil communities between both vegetation-soil systems. These findings suggest an interrelationship between nutrients in the belowground biomass, soil nutrient dynamics, and the soil bacterial community whereby grasslands promote a closed system that conserves N, whereas desert scrub vegetation exhibits an open system that sheds N.

Wetlands constitute the main natural source of methane on Earth due to their high content of natural organic matter (NOM), but key drivers, such as electron acceptors, supporting methanotrophic activities in these habitats are poorly understood. We performed anoxic incubations using freshly collected sediment, along with water samples harvested from a tropical wetland, amended with 13 C-methane (0.67 atm) to test the capacity of its microbial community to perform anaerobic oxidation of methane (AOM) linked to the reduction of the humic fraction of its NOM. Collected evidence demonstrates that electron-accepting functional groups (e.g., quinones) present in NOM fueled AOM by serving as a terminal electron acceptor. Indeed, while sulfate reduction was the predominant process, accounting for up to 42.5% of the AOM activities, the microbial reduction of NOM concomitantly occurred. Furthermore, enrichment of wetland sediment with external NOM provided a complementary electron-accepting capacity, of which reduction accounted for ∼100 nmol 13 CH 4 oxidized · cm −3 · day −1 . Spectroscopic evidence showed that quinone moieties were heterogeneously distributed in the wetland sediment, and their reduction occurred during the course of AOM. Moreover, an enrichment derived from wetland sediments performing AOM linked to NOM reduction stoichiometrically oxidized methane coupled to the reduction of the humic analogue anthraquinone-2,6-disulfonate. Microbial populations potentially involved in AOM coupled to microbial reduction of NOM were dominated by divergent biota from putative AOM-associated archaea. We estimate that this microbial process potentially contributes to the suppression of up to 114 teragrams (Tg) of CH 4 · year −1 in coastal wetlands and more than 1,300 Tg · year −1 , considering the global wetland area. IMPORTANCE The identification of key processes governing methane emissions from natural systems is of major importance considering the global warming effects triggered by this greenhouse gas. Anaerobic oxidation of methane (AOM) coupled to the microbial reduction of distinct electron acceptors plays a pivotal role in mitigating methane emissions from ecosystems. Given their high organic content, wetlands constitute the largest natural source of atmospheric methane. Nevertheless, processes controlling methane emissions in these environments are poorly understood. Here, we provide tracer analysis with 13 CH 4 and spectroscopic evidence revealing that AOM linked to the microbial reduction of redox functional groups in natural organic matter (NOM) prevails in a tropical wetland. We suggest that microbial reduction of NOM may largely contribute to the suppression of methane emissions from tropical wetlands. This is a novel avenue within the carbon cycle in which slowly decaying NOM (e.g., humic fraction) in organotrophic environments fuels AOM by serving as a terminal electron acceptor.

Methanogenesis and sulfate reduction are important microbial processes in hypersaline environments. However, key aspects determining substrate competition between these microbial processes have not been well documented. We evaluated competitive and non-competitive substrates for stimulation of both processes through microcosm experiments of hypersaline microbial mat samples from Guerrero Negro, Baja California Sur, Mexico, and we assessed the effect of these substrates on the microbial community composition. Methylotrophic methanogenesis evidenced by sequences belonging to methanogens of the family Methanosarcinaceae was found as the dominant methanogenic pathway in the studied hypersaline microbial mat. Nevertheless, our results showed that incubations supplemented with acetate and lactate, performed in absence of sulfate, also produced methane after 40 days of incubation, apparently driven by hydrogenotrophic methanogens affiliated to the family Methanomicrobiaceae. Sulfate reduction was mainly stimulated by addition of acetate and lactate; however, after 40 days of incubation, an increase of the H2S concentrations in microcosms amended with trimethylamine and methanol was also observed, suggesting that these substrates are putatively used for sulfate reduction. Moreover, 16S rRNA gene sequencing analysis showed remarkable differences in the microbial community composition among experimental treatments. In the analyzed sample amended with acetate, sulfate-reducing bacteria (SRB) belonging to the family Desulfobacteraceae were dominant, while members of Desulfohalobiaceae, Desulfomicrobiaceae, and Desulfovibrionaceae were found in the incubation with lactate. Additionally, we detected an unexpected high abundance of unclassified Hydrogenedentes (near 25%) in almost all the experimental treatments. This study contributes to better understand methanogenic and sulfate-reducing activities, which play an important role in the functioning of hypersaline environments.

The aim of this study was to evaluate the effect of mucilage and its removal, as well as phytohormones [gibberellic acid (GA3) and indole-3-acetic acid (IAA)] in light and in darkness on germination of five cactus species (Coryphanta maiz-tablasensis, Echinocactus platyacanthus, Ferocactus latispinus, Ferocactus pilosus and Stenocereus queretaroensis) from the Chihuahuan Desert. Three of them, C. maiz-tablasensis, E. platyacanthus and F. pilosus, are at risk. The mucilage layer occurred in all species. The sterilization treatment removed the mucilage even from the micropyle. Mucilage resulted in higher germination percentage in E. platyacanthus (88.5 % vs. 21.1 % without mucilage), F. latispinus (88.5 % vs. 48.2 %) and S. queretaroensis (96.0 % vs. 1.0 %), as well as a lower germination time for E. platyacanthus (10.0 days vs. 19.5 days without mucilage), F. pilosus (14.1 days vs. 16.4 days) and F. latispinus (7.8 days vs. 14.0 days). GA3 did affect germination percentage in E. platyacanthus (higher at 500 and 1000 mg l−1 than at 50 and 100 mg l−1), F. latispinus (higher at 1000 mg l−1 of GA3 than at the control and at the other concentrations) and F. pilosus (higher at 1000 mg l−1 of GA3 than at control and 50 mg l−1). The interaction of mucilage layer and GA3 was only significant for F. latispinus in that seeds with mucilage had higher germination at 0, 50, 100 and 250 mg l−1 of GA3 than seeds without mucilage, but at 500 and 1000 mg l−1 germination was high with and without mucilage. Most cactus seeds had no germination in darkness and auxins did not promote germination. Mucilage covers the micropyle and seeds without mucilage were internally more colored than seeds with mucilage in most species. We suggest that mucilage layer in the micropyle can function like a barrier regulating the passage of water to the inner seed.

Considering the great agronomic and environmental importance of denitrification, the aim of the present study was to study the temporal and spatial factors controlling the abundance and activity of denitrifying bacterial communities in a range of eight agricultural soils over 2 years. Abundance was quantified by qPCR of the nirS, nirK and nosZ genes, and the potential denitrification enzyme activity (DEA) was estimated. Our data showed a significant temporal variation considerably high for the abundance of nirK-harboring communities, followed by nosZ and nirS communities. Regarding soil parameters, the abundances of nosZ, nirS and nirK were mostly influenced by organic material, pH, and slightly by NO3 −, respectively. Soil texture was the most important factor regulating DEA, which could not be explained by the abundance of denitrifiers. Analyses of general patterns across lands to understand the soil functioning is not an easy task because the multiple factors influencing processes such as denitrification can skew the data. Careful analysis of atypical sites are necessary to classify the soils according to trait similarity and in this way reach a better predictability of the denitrifiers dynamics.

The OMEGA/Mars Express hyperspectral imager identified gypsum at several sites on Mars in 2005. These minerals constitute a direct record of past aqueous activity and are important with regard to the search of extraterrestrial life. Gale Crater was chosen as Mars Science Laboratory Curiosity's landing site because it is rich in gypsum, as are some desert soils of the Cuatro Ciénegas Basin (CCB) (Chihuahuan Desert, Mexico). The gypsum of the CCB, which is overlain by minimal carbonate deposits, was the product of magmatic activity that occurred under the Tethys Sea. To examine this Mars analogue, we retrieved gypsum-rich soil samples from two contrasting sites with different humidity in the CCB. To characterize the site, we obtained nutrient data and analyzed the genes related to the N cycle (nifH, nirS, and nirK) and the bacterial community composition by using 16S rRNA clone libraries. As expected, the soil content for almost all measured forms of carbon, nitrogen, and phosphorus were higher at the more humid site than at the drier site. What was unexpected is the presence of a rich and divergent community at both sites, with higher taxonomic diversity at the humid site and almost no taxonomic overlap. Our results suggest that the gypsum-rich soils of the CCB host a unique microbial ecosystem that includes novel microbial assemblies. Key Words: Cuatro Ciénegas Basin—Gale Crater—Gypsum soil microbial diversity—Molecular ecology—Nitrogen cycle. Astrobiology 12, 699–709.

Ecological succession is one of the most important concepts in ecology. However for microbial community succession, there is a lack of a solid theoretical framework regarding succession in microorganisms. This is in part due to microbial community complexity and plasticity but also because little is known about temporal patterns of microbial community shifts in different kinds of ecosystems, including arid soils. The Cuatro Cienegas Basin (CCB) in Coahuila, Mexico, is an arid zone with high diversity and endemisms that has recently been threatened by aquifer overexploitation. The gypsum-based soil system of the CCB is one of the most oligotrophic places in the world. We undertook a comparative 16S rRNA 454 pyrosequencing study to evaluate microbial community succession and recovery over a year after disturbance at two sites. Results were related to concurrent measurements of humidity, organic matter and total C and N content. While each site differed in both biogeochemistry and biodiversity, both present similar pattern of change at the beginning of the succession that diverged in later stages. After one year, experimentally disturbed soil was not similar to established and undisturbed adjacent soil communities indicating recovery and succession in disturbed soils is a long process.