Dataset's files
primary
| Action | DRS | |||
|---|---|---|---|---|
| SRR15322421_1.fastq.gz | Fastqsanger.gz | |||
| SRR15322421_2.fastq.gz | Fastqsanger.gz | |||
| SRR15322422_1.fastq.gz | Fastqsanger.gz | |||
| SRR15322422_2.fastq.gz | Fastqsanger.gz | |||
| SRR15322423_1.fastq.gz | Fastqsanger.gz |
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Project description:Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel "dry condition" control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.
1000-01-01 | S-EPMC4508562 | BioStudies
Project description:BACKGROUND: To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. METHODOLOGY/PRINCIPAL FINDINGS: We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH. CONCLUSIONS/SIGNIFICANCE: After long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural soil showed a higher diversity and a better ecosystem function for plant health but a loss of extremophilic bacteria. Interestingly, we detected that indigenous desert microorganisms promoted plant health in desert agro-ecosystems.
2011-01-01 | S-EPMC3166316 | BioStudies
Project description:For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.
1000-01-01 | S-EPMC3535587 | BioStudies
Project description:Soil salinization is a growing environmental problem caused by both natural and human activities. Excessive salinity in soil suppresses growth, decreases species diversity, and alters the community composition of plants; however, the effect of salinity on soil microbial communities is poorly understood. Here, we characterize the soil microbial community along a natural salinity gradient in Gurbantunggut Desert, Northwestern China. Microbial diversity linearly decreased with increases in salinity, and community dissimilarity significantly increased with salinity differences. Soil salinity showed a strong effect on microbial community dissimilarity, even after controlling for the effects of spatial distance and other environmental variables. Microbial phylotypes (n = 270) belonging to Halobacteria, Nitriliruptoria, [Rhodothermi], Gammaproteobacteria, and Alphaproteobacteria showed a high-salinity niche preference. Out of nine potential phenotypes predicted by BugBase, oxygen-related phenotypes showed a significant relationship with salinity content. To explore the community assembly processes, we used null models of within-community (nearest-taxon index [NTI]) and between-community (βNTI) phylogenetic composition. NTI showed a significantly negative relationship with salinity, suggesting that the microbial community was less phylogenetically clustered in more-saline soils. βNTI, the between-community analogue of NTI, showed that deterministic processes have overtaken stochastic processes across all sites, suggesting the importance of environmental filtering in microbial community assembly. Taken together, these results suggest the importance of salinity in soil microbial community composition and assembly processes in a desert ecosystem. IMPORTANCE Belowground microorganisms are indispensable components for nutrient cycling in desert ecosystems, and understanding how they respond to increased salinity is essential for managing and ameliorating salinization. Our sequence-based data revealed that microbial diversity decreased with increasing salinity, and certain salt-tolerant phylotypes and phenotypes showed a positive relationship with salinity. Using a null modeling approach to estimate microbial community assembly processes along a salinity gradient, we found that salinity imposed a strong selection pressure on the microbial community, which resulted in a dominance of deterministic processes. Studying microbial diversity and community assembly processes along salinity gradients is essential in understanding the fundamental ecological processes in desert ecosystems affected by salinization.
2019-01-01 | S-EPMC6372838 | BioStudies
Project description:This study assessed the influence of rhizocompartment types (i.e., root, rhizosphere soil, root-zone soil, and intershrub bulk soil) on the diversity of soil microbial communities under desert leguminous plant shrubs. Moreover, the influence and variations of soil physicochemical factors in interactions among leguminous plants, soil, and microbes were investigated. Both 16S rRNA high-throughput genome sequencing and conventional soil physicochemical index determination were used to characterize both the bacterial diversity and soil physicochemical properties in the rhizocompartments of two Hedysarum species (Hedysarum mongolicum and Hedysarum scoparium) in the Mu Us Desert of China. All nutrient indices (except total phosphorus and available phosphorus) in rhizosphere soil were uniformly higher than those in both root-zone soil and intershrub bulk soil (p < .05). The bacterial community diversity in the root, undershrub soil (i.e., rhizosphere and root zone), and intershrub bulk soil also showed significant differences (p < .05). The bacterial community in the root is mainly composed of Proteobacteria, Actinobacteria, Bacteroidetes, Tenericutes, and Chloroflexi, among which bacteria of the Proteobacteria genus are dominant. Root endophyte and rhizosphere soil microbiomes were mainly influenced by soil nutrients, while bacterial communities in root-zone soil and intershrub bulk soil were mainly influenced by soil pH and NH4 +-N. The rhizocompartment types of desert leguminous plants impose a significant influence on the diversity of soil microbial communities. According to these findings, nitrogen-fixing rhizobia can co-exist with nonsymbiotic endophytes in the roots of desert leguminous plants. Moreover, plants have a hierarchical filtering and enriching effect on beneficial microbes in soil via rhizocompartments. Soil physicochemical factors have a significant influence on both the structure and composition of microbial communities in various rhizocompartments, which is derived from the interactions among leguminous plants, soil, and microbes.
2020-01-01 | S-EPMC7593153 | BioStudies
Project description:Life in desert soil is marked by episodic pulses of water and nutrients followed by long periods of drought. While the desert flora and fauna flourish after rainfall the response of soil microorganisms remains unclear and understudied. We provide the first systematic study of the role of soil aqueous habitat dynamics in shaping microbial community composition and diversity. Detailed monitoring of natural microbial communities after a rainfall event revealed a remarkable decrease in diversity and a significant transition in community composition that were gradually restored to pre-rainfall values during soil desiccation. Modelling results suggest a critical role for the fragmented aqueous habitat in maintaining microbial diversity under dry soil conditions and diversity loss with wetting events that increase connectivity among habitats. This interdisciplinary study provides new insights into wetting and drying processes that promote and restore the unparalleled microbial diversity found in soil.
2017-01-01 | S-EPMC5382909 | BioStudies
Project description:Soil microbial communities play a crucial role in ecological restoration, but it is unknown how co-occurrence networks within these communities respond to grazing exclusion. This lack of information was addressed by investigating the effects of eight years of grazing exclusion on microbial networks in an area of <i>Stipa glareosa</i> P. Smirn desert steppe in northern China. Here, we show that fungal networks were more sensitive to grazing exclusion than bacterial networks. Eight years of grazing exclusion decreased the soil fungal community stability via changes in plant composition and reductions in soil total organic carbon, in this case triggering negative effects on the <i>S. glareosa</i> desert steppe. The results provide new insights into the response mechanisms of soil microbes to grazing exclusion and offer possible solutions for management issues in the restoration of degraded desert steppe.
2020-01-01 | S-EPMC7505065 | BioStudies
Project description:The High Arctic is dominated by polar desert habitats whose microbial communities are poorly understood. In this study, we used next generation sequencing to describe the ?- and ?-diversity of microbial communities in polar desert soils from the Kongsfjorden region of Svalbard. Ten phyla dominated the soils and accounted for 95% of all sequences, with the Proteobacteria, Actinobacteria, and Chloroflexi being the major lineages. In contrast to previous investigations of Arctic soils, relative Acidobacterial abundances were found to be very low as were the Archaea throughout the Kongsfjorden polar desert landscape. Lower Acidobacterial abundances were attributed to characteristic circumneutral soil pHs in this region, which has resulted from the weathering of underlying carbonate bedrock. In addition, we compared previously measured geochemical conditions as possible controls on soil microbial communities. Phosphorus, pH, nitrogen, and calcium levels all significantly correlated with ?-diversity, indicating landscape-scale lithological control of available nutrients, which in turn, significantly influenced soil community composition. In addition, soil phosphorus and pH significantly correlated with ?-diversity, particularly with the Shannon diversity and Chao 1 richness indices.
2016-01-01 | S-EPMC4814466 | BioStudies
Project description:The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that ?-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing ?-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.
2016-01-01 | S-EPMC5041089 | BioStudies
Project description:Desert microbes are expected to be substantially sensitive to global environmental changes, such as precipitation changes and elevated nitrogen deposition. However, the effects of precipitation changes and nitrogen enrichment on their diversity and community composition remain poorly understood. We conducted a field experiment over 2 years with multi-level precipitation and nitrogen addition in a desert shrubland of northern China, to examine the responses of soil bacteria and fungi in terms of diversity and community composition and to explore the roles of plant and soil factors in structuring microbial communities. Water addition significantly increased soil bacterial diversity and altered the community composition by increasing the relative abundances of stress-tolerant (dormant) taxa (e.g., Acidobacteria and Planctomycetes); however, nitrogen addition had no substantial effects. Increased precipitation and nitrogen did not impact soil fungal diversity, but significantly shifted the fungal community composition. Specifically, water addition reduced the relative abundances of drought-tolerant taxa (e.g., the orders Pezizales, Verrucariales, and Agaricales), whereas nitrogen enrichment decreased those of oligotrophic taxa (e.g., the orders Agaricales and Sordariales). Shifts in microbial community composition under water and nitrogen addition occurred primarily through changing resource availability rather than plant community. Our results suggest that water and nitrogen addition affected desert microbes in different ways, with watering shifting stress-tolerant traits and fertilization altering copiotrophic/oligotrophic traits of the microbial communities. These findings highlight the importance of resource availability in driving the desert microbial responses to short-term environmental changes.
2018-01-01 | S-EPMC5811472 | BioStudies