Insights on comparative bacterial diversity between different arid zones of Cholistan Desert, Pakistan.
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ABSTRACT:
SUBMITTER: Amin A
PROVIDER: S-EPMC7196105 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:One of the most diverse ecological niches for microbial bioprospecting is soil, including that of drylands. Drylands are one of the most abundant biomes on Earth, but extreme cases, such as deserts, are considered very rare in Europe. The so-called Tabernas Desert is one of the few examples of a desert area in continental Europe, and although some microbial studies have been performed on this region, a comprehensive strategy to maximize the isolation of environmental bacteria has not been conducted to date. We report here a culturomics approach to study the bacterial diversity of this dryland by using a simple strategy consisting of combining different media, using serial dilutions of the nutrients, and using extended incubation times. With this strategy, we were able to set a large (254 strains) collection of bacteria, the majority of which (93%) were identified through 16S ribosomal RNA (rRNA) gene amplification and sequencing. A significant fraction of the collection consisted of Actinobacteria and Proteobacteria, as well as Firmicutes strains. Among the 254 isolates, 37 different genera were represented, and a high number of possible new taxa were identified (31%), of which, three new Kineococcus species. Moreover, 5 out of the 13 genera represented by one isolate were also possible new species. Specifically, the sequences of 80 isolates held a percentage of identity below the 98.7% threshold considered for potentially new species. These strains belonged to 20 genera. Our results reveal a clear link between medium dilution and isolation of new species, highlight the unexploited bacterial biodiversity of the Tabernas Desert, and evidence the potential of simple strategies to yield surprisingly large numbers of diverse, previously unreported, bacterial strains and species.
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Project description:Tick infestation is the major problem for animal health that causes substantial economic losses, particularly in tropical and subtropical countries. To better understand the spatial distribution of tick species and risk factors associated with tick prevalence in livestock in Pakistan, ticks were counted and collected from 471 animals, including 179 cattle, 194 buffaloes, 80 goats and 18 sheep, on 108 livestock farms in nine districts, covering both semi-arid and arid agro-ecological zones.In total, 3,807 ticks representing four species were collected: Hyalomma anatolicum (n?=?3,021), Rhipicephalus microplus (n?=?715), Hyalomma dromedarii (n?=?41) and Rhipicephalus turanicus (n?=?30). The latter species is reported for the first time from the study area. Rhipicephalus microplus was the predominant species in the semi-arid zone, whereas H. anatolicum was the most abundant species in the arid zone. The overall proportion of tick-infested ruminants was 78.3% (369/471). It was highest in cattle (89.9%), followed by buffaloes (81.4%), goats (60.0%) and sheep (11.1%). The median tick burden significantly differed among animal species and was highest in cattle (median 58), followed by buffaloes (median 38), goats (median 19) and sheep (median 4.5). Female animals had significantly higher tick burdens than males and, in large ruminants, older animals carried more ticks than younger animals. The intensity of infestation was significantly lower in indigenous animals compared to exotic and crossbred cows. Analysis of questionnaire data revealed that the absence of rural poultry, not using any acaricides, traditional rural housing systems and grazing were potential risk factors associated with a higher tick prevalence in livestock farms.Absence of rural poultry, not performing acaricide treatments, traditional rural housing systems and grazing were important risk factors associated with higher tick prevalence in livestock farms. Age, gender, breed and animal species significantly affected the intensity of tick infestation. This report also describes the presence of R. turanicus in the Punjab Province of Pakistan for the first time. The outcomes of this study will be useful in the planning of integrated control strategies for ticks and tick-borne diseases in Pakistan.
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Project description:Despite desert ecosystem being crucial to our understanding of natural geography, species evolution and global climate change, there is limited information on the dynamics of their composition and the diversity of endophytic fungi communities driven by plant identity and organ differentiation. Here, an extensive investigation of endophytic fungal microbiome in root, stem, and leaf organs associated with five xerophyte shrubs in an extremely arid desert, Northwest China, were examined. The fungal community dominated by Dothideomycetes and Pleosporales. Shrub species strongly drive the niche-based processes of endophytic fungi across the root, stem and leaf compartments. The diversity and composition of endophytic fungi in stem showed higher variability among plant species than leaf and root. The fungal communities in root libraries were more diverse and exhibited a remarkable differentiation of community composition. We further demonstrated the significant host preferences and tissue specificity of desert endophytic fungi, and unique specific taxa were also observed. The co-occurrence network revealed the coexistence of fungal endophytes in arid desert, and the root fungal network harbored the highest interspecies connectivity. Members of Pleosporales were the most common keystone species in the root fungal network. This is the first report of mycobiota in both plant species and organ differentiation in an extremely arid desert ecosystem.
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Project description:BackgroundTo 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 findingsWe 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/significanceAfter 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.
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Project description:Many studies suggest that species diversity and abiotic factors promote ecosystem multifunctionality. However, whether ecosystem multifunctionality is impacted by phylogenetic diversity remains controversial. The present study tested this in an arid desert ecosystem in Ebinur Lake Basin using soil C:N ratio, soil pH, and soil salinity as abiotic factors, and species diversity and phylogenetic diversity as indicators of plant diversity. The effects of plant diversity and abiotic factors on single ecosystem functions (nutrient cycling, carbon stocks, water regulation, and wood production) and ecosystem multifunctionality were studied. We used structural equation modeling to assess the relationships among different functional groups and factors. The results showed that: (1) abiotic factors, particularly pH and C:N ratio in soil, had the strongest positive impact on multifunctionality (P < 0.001). The phylogenetic diversity and species diversity showed inconsistent changes, and their contribution to multifunctionality were not outstanding. (2) Abiotic factors were closely related to different ecosystem functions. Soil C:N had a significant positive effect on carbon stocks (P < 0.001), with an effect index of 0.89. Soil pH significantly enhanced nutrient cycling and water regulation. The role of plant diversity varied with the combination of different ecosystem functions. Phylogenetic diversity and species diversity influenced wood production, but showed opposite functions. (3) The importance of four single-ecosystem functions in an arid region was ranked as follows: carbon stocks > water regulation > nutrient cycling > wood production, emphasizing the importance of carbon elements in these ecosystems. These results improve our understanding of the drivers of multifunctionality in arid ecosystems, facilitating the elucidation of the influence of abiotic factors and phylogenetic diversity.
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Project description:BackgroundActinobacteria are famous for the production of unique secondary metabolites that help in controlling the continuously emerging drug resistance all over the globe. This study aimed at the investigation of an extreme environment the Cholistan desert, located in southern Punjab, Pakistan, for actinobacterial diversity and their activity against methicillin resistant Staphylococcus aureus (MRSA). The Cholistan desert is a sub-tropical and arid ecosystem with harsh environment, limited rainfall and low humidity. The 20 soil and sand samples were collected from different locations in the desert and the actinobacterial strains were selectively isolated. The isolated strains were identified using a polyphasic taxonomic approach including morphological, biochemical, physiological characterization, scanning electron microscopy (SEM) and by 16S rRNA gene sequencing.ResultsA total of 110 desert actinobacterial strains were recovered, which were found to be belonging to 3 different families of the order Actinomycetales, including the family Streptomycetaceae, family Pseudonocardiaceae and the family Micrococcaceae. The most frequently isolated genus was Streptomyces along with the genera Pseudonocardia and Arthrobacter. The isolated strains exhibited promising antimicrobial activity against methicillin resistant Staphylococcus aureus (MRSA) with zone of inhibition in the range of 9-32 mm in antimicrobial screening assays. The chemical profiling by thin layer chromatography, HPLC-UV/Vis and LC-MS analysis depicted the presence of different structural classes of antibiotics.ConclusionThe study revealed that Cholistan desert harbors immense actinobacterial diversity and most of the strains produce structurally diverse bioactive secondary metabolites, which are a promising source of novel antimicrobial drug candidates.
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Project description:Species pool hypothesis is broadly known and frequently tested in various regions and vegetation types. However it has not been tested in the arid Xinjiang region of China due to lack of data. Here with systematic data from references and field survey, we comprehensively examined species pool hypothesis in this region. Took species richness in 0.1° × 0.1° grid cells as regional species richness (RSR) which were obtained from the distribution maps of vascular plant species, and took species diversity of 190 and 103 plots in forest and grassland biomes across Xinjiang as local species richness (LSR), together with the digitalized soil pH and climate data, we tested the species pool hypothesis in this region. We found that: (1) the average RSR was higher in mountains than that in basins and it was negatively correlated with soil pH in mountains while positively correlated with soil pH in basins in Xinjiang; (2) RSR showed a positive correlation with mean annual precipitation (MAP) while showed a hump-shaped pattern with mean annual temperature (MAT); and the changing patterns of LSR were different for forest and grassland along the geographical and climate gradients; (3) LSR of forest was more affected by RSR than by climate, while on the contrary, LSR of grassland was more affected by climate than by RSR. Our results validated the species pool hypothesis in revealing that RSR had a significant role in shaping LSR patterns in addition to climate. We concluded that the relative effects of climate vs. RSR on LSR differed markedly between the forest and grassland communities across Xinjiang. Our results also showed that RSR revealed a contrasting relationship with soil pH in mountains and in basins, which might reflect differences in evolutionary processes of various habitats. In summary, our research systematically analyzed the correlation of species richness in regional and local scales in Xinjiang which provides more insights into the understanding of species pool hypothesis.
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