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PubMed2025

Native edaphoclimatic regions shape soil communities of crop wild progenitors.

Unveiling the soil biological communities ecologically associated with crop wild progenitors (CWPs) in their habitats of origin is essential for advancing productive and sustainable agriculture. A field survey was conducted to investigate the edaphoclimatic conditions and soil bacterial, fungal, protist, and invertebrate communities of 125 populations of direct progenitors of major crops for world agriculture. The wild populations clustered into four ecoregions shaped by two edaphoclimatic dimensions: one summarizing variations in soil sand contents and nutrients concentrations, and the other featuring changes in aridity, soil pH, and carbon storage potential. We identified a common soil core community across CWPs that varied significantly along deserts to tropical seasonal forests and savannas. The assembly of the soil core community was driven by varying environmental preferences amongst soil biodiversity kingdoms, reflecting potential shifts in their functional profiles. The tropical ecoregion exhibited higher proportion of acidophilic bacteria, fungal, and protist parasites, whilst desert ecosystems harboured greater abundances of saprophytic fungi and heterotrophic protists. Moreover, CWPs displayed unique microhabitats that incorporate variability into the soil community assembly. Our work reveals the biogeography of soil communities associated with CWPs, the first step towards the development of microbial rewilding initiatives.

centres of origin↗

PubMed2026

Climate and soil shape Daqu wheat quality and seed microbiome via rhizosphere taxa and microbial assembly.

The grain quality and seed microbiome of Daqu wheat are fundamental determinants of Daqu fermentation performance; however, the mechanisms by which cultivation environments influence these traits via rhizosphere microbial communities remain unclear. Bacterial and fungal communities across the bulk soil-rhizosphere-seed continuum of three wheat cultivars grown in four ecoregions were characterized using absolute quantitative amplicon sequencing. The rhizosphere microbiome was treated as a central intermediary, while the response variables were seed microbial diversity and grain-quality traits, including starch content, protein content, and grain hardness. Twelve physicochemical properties of soil and 11 climatic factors were integrated into a multidimensional association framework. Environmental conditions exerted stronger influences on both seed quality traits and microbial diversity than cultivar identity. Distinct regional signatures were also evident in rhizosphere microbiomes, with environmental gradients explaining community variation more effectively than geographic distance. Bacterial communities exhibited greater sensitivity to environmental fluctuations than fungi. Mantel analyses identified available nitrogen, precipitation, and atmospheric pressure as significant drivers of core rhizosphere taxa (P < 0.05). iCAMP revealed that stochastic processes predominantly governed rhizosphere bacterial assembly, whereas stochastic and deterministic mechanisms jointly shaped fungal assembly. Partial least squares path modeling further uncovered a rhizosphere-mediated environment-seed cascade, wherein sunlight intensity and duration, atmospheric pressure, and soil nitrogen directly or indirectly affected seed wet gluten content, grain hardness, and seed microbial diversity through their influences on rhizosphere microbiota. Rhizosphere bacterial diversity was negatively associated with seed bacterial diversity (path coefficient = -0.118, P < 0.05), indicating that rhizosphere communities may shape seed endophytic bacterial assemblages via environmental filtering and competitive interactions. Collectively, these findings elucidate how environments shape the quality and seed microbiomes of Daqu wheat, providing scientific guidance for optimal site selection and the standardized production of high-quality brewing wheat for industrial Baijiu.

Triticum↗

PubMed2026

Hidden genomic structure and widespread structural polymorphism across environmental gradients in the spiny sea star Marthasterias glacialis.

Genomic regions of reduced recombination can preserve linkage among co-adapted alleles, facilitating local adaptation despite high connectivity. Such regions-often generated by chromosomal inversions-may be especially important in highly dispersive marine taxa yet remain poorly documented in echinoderms. Here, we combined a chromosome-level reference genome with genome-wide ddRAD-seq from 296 Marthasterias glacialis individuals across 19 Atlantic-Mediterranean locations to quantify population structure and scan for recombination-suppressed haploblocks. Genome-wide neutral markers showed significant population differentiation together with evidence of high connectivity, revealed by the presence of inter-ecoregion migrants. Additionally, we identified 16 polymorphic haploblocks with patterns consistent with putative chromosomal inversions spanning 18.6% of the genome. Haploblock haplotypes were strongly environmentally and geographically structured and contained genes with key functions in stress response, osmoregulation and thermal tolerance. Haplotype distributions also paralleled previously described mitochondrial lineages despite nuclear gene flow, consistent with a model of ancient divergence followed by secondary contact. Overall, our results suggest a role for widespread structural polymorphism in adaptive differentiation in Echinodermata, providing a framework for linking echinoderm genome rearrangements to ecological divergence. Marthasterias glacialis thus emerges as a promising system to explore how structural variation contributes to adaptation and genome evolution in highly dispersive organisms.

Animals↗

PubMed2024

Adaptive or non-adaptive? Cranial evolution in a radiation of miniaturized day geckos.

Lygodactylus geckos represent a well-documented radiation of miniaturized lizards with diverse life-history traits that are widely distributed in Africa, Madagascar, and South America. The group has diversified into numerous species with high levels of morphological similarity. The evolutionary processes underlying such diversification remain enigmatic, because species live in different ecological biomes, ecoregions and microhabitats, while suggesting strikingly high levels of homoplasy. To underscore this evolutionary pattern, here we explore the shape variation of skull elements (i.e., cranium, jaw and inner ear) using 3D geometric morphometrics and phylogenetic comparative methods on computed tomography scans (CT-scan) of a sample encompassing almost all recognized taxa within Lygodactylus. The results of this work show that skull and inner ear shape variation is low (i.e., there is high overlapping on the morphospace) across geographic regions, macrohabitats and lifestyles, implying extensive homoplasy. Furthermore, we also found a strong influence of allometry shaping cranial variation both at intra and interspecific levels, suggesting a major constraint underlying skull architecture, probably as a consequence of its miniaturization. The remaining variation that is not allometric is independent of phylogeny and ecological adaptation and can probably be interpreted as the result of intrinsic developmental plasticity. This, in turn, supports the interpretation that speciation in this group is largely concordant with a non-adaptive hypothesis, which results mainly from vicariant processes.

Animals↗