Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico

A Transiently Hypersaline Microbial Mat Harbors a Diverse and Stable Archaeal Community in the Cuatro Cienegas Basin, Mexico

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 have been studied to understand the conditions of the Precambrian Earth. These microbial mats form elastic domes filled with biogenic gas, and the mats have a relatively large and stable subpopulation of archaea. For this reason, this site has been termed archaean domes (AD). The AD microbial community was analyzed by metagenomics over three seasons. The mat exhibited a highly diverse prokaryotic community dominated by bacteria. Bacterial sequences are represented in 37 phyla, mainly Proteobacteria, Firmicutes, and Actinobacteria, that together comprised >50% of the sequences from the mat. Archaea represented up to 5% of the retrieved sequences, with up to 230 different archaeal species that belong to 5 phyla (Euryarchaeota, Crenarchaeota, Thaumarchaeota, Korarchaeota, and Nanoarchaeota). The archaeal taxa showed low variation despite fluctuations in water and nutrient availability. In addition, predicted functions highlight stress responses to extreme conditions present in the AD, including salinity, pH, and water/drought fluctuation. The observed complexity of the AD mat thriving in high pH and fluctuating water and salt conditions within the CCB provides an extant model of great value for evolutionary studies, as well as a suitable analog to the early Earth and Mars.

Roots of the xerophyte Panicum turgidum host a cohort of ionizing-radiation-resistant biotechnologically-valuable bacteria

Bacterial communities associated with roots of Panicum turgidum, exposed to arid conditions, were investigated with a combination of cultural and metataxonomic approaches. Traditional culture-based techniques were used and 32 isolates from the irradiated roots were identified as belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria phyla. Four actinobacterial strains were shown to be ionizing-radiation (IR)-resistant: Microbacterium sp. PT8 (4.8 kGy (kGy)), Micrococcus sp. PT11 (4.4 kGy), Kocuria rhizophila PT10 (2.9 kGy) and Promicromonospora panici PT9^T (2.6 kGy), based on the D₁₀ dose necessary for a 90% reduction in colony forming units (CFU). Concerning the investigation of microbial communities in situ, metataxonomic analyses of the diversity of IR-resistant microorganisms associated with irradiated roots revealed a marked dominance of Actinobacteria (46.6%) and Proteobacteria (31.5%) compared to Bacteroidetes (4.6%) and Firmicutes (3.2%). Gamma irradiation not only changed the structure of bacterial communities, but also affected their functional properties. Comparative analyses of metabolic profiles indicated the induction of several pathways related to adaptation to oxidative stress in irradiated roots, such as DNA repair, secondary metabolites synthesis, reactive oxygen species (ROS)-mitigating enzymes, etc. P. turgidum is emblematic of desert-adapted plants. Until now, there is no other work that has focused on the microbial profile of irradiated roots of this xerophyte.

The adaptations of the microbial communities of the savanna soil over a period of wildfire, after the first rains, and during the rainy season

Annually, the Cerrado ecosystem alternates between dry periods and long rainy seasons. During the dry season, severe forest fires occur, consuming a considerable part of the native vegetation, which impacts directly on the microbiome of the soil. Evaluate the adaptations of the soil microbiome to drought, rain and wildfire. Sequencing of the 16S rRNA gene was carried out for three significant conditions: drought and forest fires ("Fire"), after the first recorded rains ("First_Rain"), and during the rainy season ("Rainy"). It has been shown that under the "Fire" condition, there was a predominance of Phylum Actinobacteria, followed by Proteobacteria and Firmicutes. With the advent of the rainy season, "First_Rain," there was a change in the predominant taxonomic groups, with a higher prevalence of members of Proteobacteria and Firmicutes. During the rainy season, Proteobacteria and Firmicutes continued as the most prevalent groups. However, it was noted that in this period, there was an increase in bacterial diversity when compared with other periods analyzed. These results show how environmental factors influence adaptations in microbial communities. This allows for a better understanding of how to link the structure of the microbial community to the performance of ecosystems, and assist in preventing the consequences of increased frequency of wildfires, and long periods of drought.

Diversity of Microorganisms in Biocrusts Surrounding Highly Saline Potash Tailing Piles in Germany

Potash tailing piles located in Germany represent extremely hypersaline locations that negatively affect neighbouring environments and limit the development of higher vegetation. However, biocrusts, as cryptogamic covers, inhabit some of these areas and provide essential ecological functions, but, nevertheless, they remain poorly described. Here, we applied high-throughput sequencing (HTS) and targeted four groups of microorganisms: bacteria, cyanobacteria, fungi and other eukaryotes. The sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Cyanobacteria and Actinobacteria. Additionally, we applied yanobacteria-specific primers for a detailed assessment of the cyanobacterial community, which was dominated by members of the filamentous orders Synechococcales and Oscillatoriales. Furthermore, the majority of reads in the studied biocrusts obtained by sequencing of the 18S rRNA gene belonged to eukaryotic microalgae. In addition, sequencing of the internal rDNA transcribed spacer region (ITS) showed the dominance of Ascomycota within the fungal community. Overall, these molecular data provided the first detailed overview of microorganisms associated with biocrusts inhabiting highly saline potash tailing piles and showed the dissimilarities in microbial diversity among the samples.

Desert Environments Facilitate Unique Evolution of Biosynthetic Potential in Streptomyces

Searching for new bioactive metabolites from the bacterial genus Streptomyces is a challenging task. Combined genomic tools and metabolomic screening of Streptomyces spp. native to extreme environments could be a promising strategy to discover novel compounds. While Streptomyces of desertic origin have been proposed as a source of new metabolites, their genome mining, phylogenetic analysis, and metabolite profiles to date are scarcely documented. Here, we hypothesized that Streptomyces species of desert environments have evolved with unique biosynthetic potential. To test this, along with an extensive characterization of biosynthetic potential of a desert isolate Streptomyces sp. SAJ15, we profiled phylogenetic relationships among the closest and previously reported Streptomyces of desert origin. Results revealed that Streptomyces strains of desert origin are closer to each other and relatively distinct from Streptomyces of other environments. The draft genome of strain SAJ15 was 8.2 Mb in size, which had 6972 predicted genes including 3097 genes encoding hypothetical proteins. Successive genome mining and phylogenetic analysis revealed the presence of putative novel biosynthetic gene clusters (BGCs) with low incidence in another Streptomyces. In addition, high-resolution metabolite profiling indicated the production of arylpolyene, terpenoid, and macrolide compounds in an optimized medium by strain SAJ15. The relative abundance of different BGCs in arid Streptomyces differed from the non-arid counterparts. Collectively, the results suggested a distinct evolution of desert Streptomyces with a unique biosynthetic potential.

Bacterial Diversity and Interaction Networks of Agave lechuguilla Rhizosphere Differ Significantly From Bulk Soil in the Oligotrophic Basin of Cuatro Cienegas

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.

Soil Property and Plant Diversity Determine Bacterial Turnover and Network Interactions in a Typical Arid Inland River Basin, Northwest China

Water sources from the lower reaches of the Heihe River northwest China, located in an arid area impacted by environmental stresses, have promoted changes to the local soil and plant conditions; however, our understanding of variations and drivers of soil bacterial communities in an arid inland river basin remains unclear. Therefore, we collected 39 soil samples from a riparian oasis zone (ROZ) to the circumjacent desert zone (CDZ) at the lower reaches of Heihe River to evaluate bacterial communities based on the 16S rRNA gene data. We found that the bacterial community composition differed between ROZ and CDZ habitats, with significantly higher relative abundance of the phyla Gemmatimonadetes and Acidobacteria in ROZ, whereas the abundance of the phyla Actinobacteria and Deinococcus–Thermus was greater in CDZ. The difference in the bacterial community was almost entirely generated by the species turnover rather than the nestedness among all samples. In addition, we found that bacterial α-diversity index showed no significant difference between ROZ and CDZ habitats. The distance-decay analysis showed that spatial distance, plant community, soil property, and plant functional trait were correlated with bacterial community variations. However, the variation partition analysis (VPA) revealed that both soil properties and plant community strongly explained the difference [such as soil water content (WC), soil silt content, and plant community structure] compared with plant functional traits in bacterial β-diversity and species turnover. Based on a co-occurrence network analysis, we found that the bacterial network of ROZ, which had more negative correlations, higher average connectivity, shorter average path length, and smaller modularity, was more complex than the network of CDZ. This suggested that the bacterial community was more stable and less vulnerable to change in the ROZ habitat than in the CDZ habitat. Overall, our findings suggest that the heterogeneity of soil properties and plant community collectively affect the structure of the soil bacterial community in an arid inland river basin. However, the influence of plant functional traits on the variation of the bacterial community depends on soil properties and plant community.

Microbial composition, potential functional roles and genetic novelty in gypsum-rich and hypersaline soils of Monegros and Gallocanta (Spain)

Soil microbial communities (both Bacteria and Archaea) were studied after 16S rRNA genes massive sequencing in two hypersaline and gypsum-rich contrasted sites located in NE Spain. Soil microbial communities were also locally analysed according to environmental variables, including geological, physico-chemical, biogeochemically, and climatic data. Typical soil characteristics, climate data, and plant composition clearly split the two sites and major differences among the microbial communities for the areas were initially expected. Overall, high values of microbial species richness (up to 2300 taxa) and ecological diversity was detected in both sites. High genetic novelty levels were found mostly to environmental sequences, highlighting the high potential for microbiological studies. In contrast to the initial expectations, a substantial overlapping between Monegros and Gallocanta microbes was observed, indicating a high similarity despite of the geographical, botanical and environmental distances between sites, in agreement with both high dispersal and local selection inherent to the microbial world. The potential biogeochemical cycling showed small differences between sites, with presence of photosynthetic green and purple sulfur bacteria, cyanobacteria and aerobic and anaerobic chemolitotrophs. Potential for aerobic methane oxidation and anaerobic methanogenesis was observed in both sites, with predominance of potential nitrification mostly by ammonia-oxidizing archaea, nitrite oxidation and denitrification, and minor contribution for nitrate reduction and nitrate ammonification. The predicted functions based on the taxonomic composition showed high overlapping between the two studied regions, despite their difference in gypsum richness.

Spatial variability in soil pH and land use as the main influential factor in the red beds of the Nanxiong Basin, China

Soil pH is the main factor affecting soil nutrient availability and chemical substances in soil. It is of great significance to study the spatial variability of soil pH for the management of soil nutrients and the prediction of soil pollution. In order to explore the causes of spatial variability in soil pH in red-bed areas, the Nanxiong Basin in south China was selected as an example, and soil pH was measured in the topsoil by nested sampling (0-20 cm depth). The spatial variability characteristics of soil pH were analyzed by geostatistics and classical statistical methods, and the main factors influencing spatial variability in soil pH are discussed. The coefficient of variation in the red-bed areas of Nanxiong Basin was 17.18%, indicating moderate variability. Geostatistical analysis showed that the spherical model is the optimal theoretical model for explaining variability in soil pH, which is influenced by both structural and random factors. Analysis of the spatial distribution and pattern showed that soil pH is relatively high in the northeast and southwest, and is lower in the northwest. These results indicate that land use patterns and topographic factors are the main and secondary influencing factors, respectively.

Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach

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 microbial dynamics in response to stress. We traced the responses to anthropogenic perturbation caused by water depletion in microbial mats from Cuatro Cienegas Basin (CCB), Mexico, by using a time-series spatially resolved analysis in a novel combination of three computational approaches. First, we implemented MEBS (Multi-genomic Entropy-Based Score) to evaluate the dynamics of major biogeochemical cycles across spatio-temporal scales with a single informative value. Second, we used robust Time Series-Ecological Networks (TS-ENs) to evaluate the total percentage of interactions at different taxonomic levels. Lastly, we utilized network motifs to characterize specific interaction patterns. Our results indicate that microbial mats from CCB contain an enormous taxonomic diversity with at least 100 phyla, mainly represented by members of the rare biosphere (RB). Statistical ecological analyses point out a clear involvement of anaerobic guilds related to sulfur and methane cycles during wet versus dry conditions, where we find an increase in fungi, photosynthetic, and halotolerant taxa. TS-ENs indicate that in wet conditions, there was an equilibrium between cooperation and competition (positive and negative relationships, respectively), while under dry conditions there is an over-representation of negative relationships. Furthermore, most of the keystone taxa of the TS-ENs at family level are members of the RB and the microbial mat core highlighting their crucial role within the community. Our results indicate that microbial mats are more robust to perturbation due to redundant functions that are likely shared among community members in the highly connected TS-ENs with density values close to one (≈0.9). Finally, we provide evidence that suggests that a large taxonomic diversity where all community members interact with each other (low modularity), the presence of permanent of low-abundant taxa, and an increase in competition can be potential buffers against environmental disturbance in microbial mats.

Isolation of halophilic bacteria associated with saline and alkaline-sodic soils by culture dependent approach

Cultivable halophilic microorganisms were isolated and identified from saline and alkaline-sodic soils: Cuatro Cienegas, Sayula and San Marcos lakes. Physicochemical characteristics of soils were determined to understand the relationship between those and the microorganisms isolated. The Cuatro Cienegas soils had a neutral pH, EC of 2.3–8 dS cm⁻¹, classified as moderately saline. Whereas, the soils from Sayula and San Marcos lakes, had an alkaline pH, EC 15 to 65 dS m⁻¹, typical of saline-sodic. We identified 23 cultivable halophilic bacteria using 16s rDNA, being Halobacillus sp., Marinococcus sp., and Alkalibacillus sp. the predominant genus by culture dependent approach. We found a correlation between the soils anion and cation content with the occurrence of different genus of halophilic bacteria in each studied site. Alkalibacillus sp. was predominant in Sayula and San Marcos lakes and was related to the high Na⁺ content; while Bacillus sp. and Halobacillus sp. were predominant in Cuatro Cienegas, their occurrence was related to a high content of Ca²⁺, Mg²⁺, and SO₄^2-.

Environmental Controls on Soil Microbial Communities in a Seasonally Dry Tropical Forest

Several studies have shown that rainfall seasonality, soil heterogeneity, and increased nitrogen (N) deposition may have important effects on tropical forest function. However, the effects of these environmental controls on soil microbial communities in seasonally dry tropical forests are poorly understood. In a seasonally dry tropical forest in the Yucatan Peninsula (Mexico), we investigated the influence of soil heterogeneity (which results in two different soil types, black and red soils), rainfall seasonality (in two successive seasons, wet and dry), and 3 years of repeated N enrichment on soil chemical and microbiological properties, including bacterial gene content and community structure. The soil properties varied with the soil type and the sampling season but did not respond to N enrichment. Greater organic matter content in the black soils was associated with higher microbial biomass, enzyme activities, and abundances of genes related to nitrification (amoA) and denitrification (nirK and nirS) than were observed in the red soils. Rainfall seasonality was also associated with changes in soil microbial biomass and activity levels and N gene abundances. Actinobacteria, Proteobacteria, Firmicutes, and Acidobacteria were the most abundant phyla. Differences in bacterial community composition were associated with soil type and season and were primarily detected at higher taxonomic resolution, where specific taxa drive the separation of communities between soils. We observed that soil heterogeneity and rainfall seasonality were the main correlates of soil bacterial community structure and function in this tropical forest, likely acting through their effects on soil attributes, especially those related to soil organic matter and moisture content.IMPORTANCE Understanding the response of soil microbial communities to environmental factors is important for predicting the contribution of forest ecosystems to global environmental change. Seasonally dry tropical forests are characterized by receiving less than 1,800 mm of rain per year in alternating wet and dry seasons and by high heterogeneity in plant diversity and soil chemistry. For these reasons, N deposition may affect their soils differently than those in humid tropical forests. This study documents the influence of rainfall seasonality, soil heterogeneity, and N deposition on soil chemical and microbiological properties in a seasonally dry tropical forest. Our findings suggest that soil heterogeneity and rainfall seasonality are likely the main factors controlling soil bacterial community structure and function in this tropical forest. Nitrogen enrichment was likely too low to induce significant short-term effects on soil properties, because this tropical forest is not N limited.