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Siciliano, S. D.

Publications and source records attributed to Siciliano, S. D..

3 recordsLinked to original sources

Aridity drives global convergence of desert microbiomes and biogeochemical activities

Deserts cover a third of the worlds surface, supporting unique biomes and ecosystem services. Yet, we lack a comprehensive assessment of what defines and drives the microbial communities that dominate life in these regions. Here, we conducted a standardized field survey in contrasting cold, hot, and polar deserts across the seven continents, and observed geographically distant deserts share similar structure, function, and activities. Desert communities are dominated by genomically streamlined Actinobacteriota and Chloroflexota, and compared with non-desert soils, are significantly enriched with stress tolerance genes, mobile genetic elements, and antiviral strategies, revealing previously unknown ecological and evolutionary dynamics. Metabolically, these communities exhibit reduced capacity for carbohydrate and protein degradation, and instead are enriched for chemosynthetic carbon fixation, continuous energy harvesting using atmospheric trace gases and sunlight, and energy reserve biosynthesis. All sampled soils mediated respiration, trace gas oxidation, and carbon fixation, with detectable activity even in hyper-arid Atacama and Antarctic soils at the margins of life. Driver analyses identified aridity as the primary overriding driver of the microbial communities and biogeochemical activities. Collectively, these findings suggest that aridity selects for metabolically self-sufficient taxa capable of continuously meeting energy and carbon needs independently of vegetation-derived inputs, while enduring physicochemical stressors and potentially elevated viral pressure. These new insights are integral to forecast the future of soils amid increasing desertification. Significance statementDesert soils occupy a vast and expanding portion of Earth, yet what defines and governs their dominant microbial life remains incompletely defined. By assessing the composition, capabilities, and activities of microbial communities across deserts on all seven continents, we identify unifying signatures of life under extreme water limitation. We show microbial communities are highly self-sufficient, capable of acquiring energy and carbon even where plant inputs are minimal. This planetary-scale understanding of the desert microbiome has important ramifications for forecasting potential shifts of microbial communities and the services they provide as desertification intensifies.

microbiology↗

Root Microbial Functions and Robust Network Drive High-yielding Canola Genotype

HighlightA high-yielding canola genotypes productivity is linked to specifically recruited root bacteria, enriched carbon and phosphorus metabolism genes, and a robust microbial network. Plants and their root microbiomes have co-evolved complex relationships that influence growth and development. While plant genotype is known to shape root microbiomes, a detailed understanding of this interplay remains limited. We used shotgun metagenomic sequencing to examine the composition, function, and microbial association networks of root bacterial communities in two Brassica napus (canola) genotypes with contrasting yields: NAM-23 and NAM-30. Root samples were collected at three developmental stages (vegetative, flowering, and maturation) across three field sites. Growth stage significantly influenced alpha diversity and community structure, but not KEGG pathway functions. Genotype had minimal effect on overall diversity and function, but specifically influenced the recruitment of certain bacterial taxa and the topology of microbial association networks. NAM-23, the high-yielding genotype, was enriched in plant growth-promoting bacteria (Rahnella) and genes related to carbohydrate and phosphorus metabolism. Additionally, NAM-23 exhibited a more robust and connected microbial network, with higher degree, betweenness, clustering coefficient, and more genotype-specific hub taxa, suggesting enhanced resilience to environmental stress. Our findings provide a high-resolution view of genotype-specific interactions with the root microbiome, highlighting key microbial features associated with high yield. These insights support microbiome-informed strategies for crop improvement in sustainable agriculture.

microbiology↗

Exploring The Genome of The Oribatid Mite, Oppia Nitens: Environmental Stress Response and Toxicity Adaptation

Oribatid mites are one of the most abundant groups of microarthropods in soil. Oppia nitens, belonging to the family Oppiidae, one of the largest and most diverse families of oribatid mites, has been developed as a standardized model test organism for assessing soil contamination. However, the limited availability of genomic information for this species hinders our understanding of its physiological adaptation and sensitivity to chemical and environmental stressors in soil. Hence, we present the annotated O. nitens draft genome assembled using both Oxford Nanopore Technologies and Illumina sequencing platforms as a basis to identify potential genes that can be linked to adaptation to chemical and environmental stressors. The sequences were assembled into 65 scaffolds spanning 125.4Mb with a 24.5% GC content and an N50 length of 4.41Mb. Genome quality and completeness were checked using arthropod Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis, which identified 93.5 % complete single-copy orthologs, 3.4% complete but duplicated orthologs, 0.5% fragmented, and 2.6% missing orthologs (n=2934). The NCBI Eukaryotic Genome Annotation Pipeline annotated 15,291 genes, 16,969 mRNAs, and 14,938 proteins. Here, we describe the O. nitens complete draft genome and discuss its utility as a genetic basis for further investigations and understanding of the molecular mechanisms and physiological functions in adaptations to environmental change, especially tolerance to metal stress.

genomics↗