Biology subjects

Mimmo, T.

Publications and source records attributed to Mimmo, T..

8 recordsLinked to original sources

bioRxiv2026

Sedimentary ancient DNA reveals rhizosphere-like plant-microbe association signals in a 2-million-year-old Arctic ecosystem

Plant-microbe interactions in the rhizosphere are central to nutrient cycling and ecosystem functioning. Sedimentary ancient DNA (sedaDNA) is a promising yet underexplored tool for reconstructing past microbial communities and investigating ecological interactions among plants, animals, and microorganisms. Here, we reanalyse the previously published Kap Kobenhavn Formation (Northern Greenland) sedaDNA dataset to move beyond taxonomic ecosystem reconstruction and test whether ancient sediments preserve structured, rhizosphere-compatible plant-microbe association signals. Our results show that this ancient boreal ecosystem hosted several rhizosphere-associated taxa, comparable to those in modern boreal soils. Several bacterial genera co-occurred repeatedly with specific plant families, forming a rhizosphere-like taxonomic core with predicted plant-growth-promoting traits related to nutrient acquisition, colonisation, and stress tolerance. Although sedaDNA co-occurrence cannot demonstrate direct symbiosis, the consistency of taxonomic, network, and functional signals suggests that ancient sediments preserve interconnected ecological structure. Our findings extend sedaDNA-based ecosystem reconstruction beyond taxonomy and provide a possibility for investigating plant-microbe association signals in deep time.

plant biology↗

bioRxiv2025

Double knockout of rice OsVIT1 and OsVIT2 genes reveals a trade-off between iron biofortification and iron excess tolerance

Rice (Oryza sativa L.) is a staple food for half of the worlds population, but lacks essential nutrients such as iron (Fe). Fe deficiency is one of the most common nutritional problems in humans, and biofortification of rice grains is a cost-effective approach to deliver more Fe to peoples diet. Two Vacuolar Iron Transporters, OsVIT1 and OsVIT2, were shown to negatively regulate Fe translocation to rice developing panicles, as single mutants osvit1 and osvit2 have increased Fe concentration in seeds. Importantly, rice plants are frequently cultivated in waterlogged soils that are highly reductive and prone to Fe3+ reduction to the more soluble Fe2+, which can accumulate and cause Fe toxicity. Little is known about which genes control Fe excess detoxification. OsVIT1 and OsVIT2 transport Fe into the vacuole, and OsVIT2 is induced under Fe excess, but whether they play a role in Fe detoxification was not demonstrated. We generated double mutants osvit1osvit2 using CRISPR-Cas9 to test whether loss of function of both genes could increase Fe concentration in seeds, and to test whether their loss of function has impact in rice Fe excess tolerance. We showed that osvit1osvit2 double mutants accumulated more Fe in brown rice. Fe accumulation was clear in embryo scutellum and plumule, suggesting VIT transporters have a role in determining Fe spatial distribution. We also showed that root uptake contributed significantly for increased Fe accumulation in osvit1osvit2 seeds, suggesting OsVIT1 and OsVIT2 are involved in sequestering Fe in vegetative tissues and decreasing translocation. Strikingly, we found that osvit1osvit2 plants were more sensitive to Fe excess, revealing a trade-off between Fe biofortification and Fe excess tolerance. Our data indicates OsVIT1 and OsVIT2 are key for Fe excess detoxification, which should be considered in their use as targets for biofortification.

plant biology↗

bioRxiv2024

Unravelling the ancient fungal DNA from the Iceman's gut

Here, we explore the possible ancient fungal species in the gut of Otzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria). While ancient DNA (aDNA) has been extensively used to study human, animal, and plant evolution, this research focuses on ancient microbial diversity, specifically fungi. Fungal DNA is often underestimated in metagenomic samples, however here we hypothesise the possibility of retrieving ancient fungal sequences from Otzis gut. A robust bioinformatic pipeline has been developed to detect and authenticate fungal aDNA from stomach, small intestine, and large intestine samples. We revealed the presence of Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, that were particularly abundant in the stomach and small intestine. We suggest that Otzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they thrived in his gut after his death due to their adaptability to harsh and cold environments. This research provides insight into the coexistence of ancient humans with specific fungal species and proposes and validates a conservative bioinformatic approach for detecting fungal aDNA in historical metagenomic samples. Significance statementDespite their essential interactions with all kingdoms of life, limited molecular studies have focused on ancient fungi. Here, we developed a thorough bioinformatic pipeline that allowed us to detect the presence of ancient DNA likely belonging to Pseudogymnoascus destructans and P. verrucosus in the gut of Otzi, a human naturally mummified over 3,000 years ago in the Tyrolean Alps. Both species can survive harsh environmental conditions, and P. destructans is known for its pathogenicity, suggesting that Otzi may have accidentally ingested them and providing valuable insights into how ancient humans coexisted with specific fungal species. We propose a highly reliable methodology for detecting ancient fungal DNA in metagenomic studies of historical samples that can have broader applications to understand ancient ecosystems and their interactions.

microbiology↗

bioRxiv2021

IDENTIFYING PLANT GENES SHAPING MICROBIOTA COMPOSITION IN THE BARLEY RHIZOSPHERE

A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plants capacity of shaping rhizosphere microbes.

plant biology↗

bioRxiv2021

Identification of an isoflavonoid transporter required for the nodule establishment of the Rhizobium-Fabaceae symbiotic interaction

Nitrogen (N) as well as Phosphorus (P) are key nutrients determining crop productivity. Legumes have developed strategies to overcome nutrient limitation by e.g., forming a symbiotic relationship with N-fixing rhizobia and the release of P-mobilizing exudates and are thus able to grow without supply of N or P fertilizers. The legume-rhizobial symbiosis starts with root release of isoflavonoids, that act as signaling molecules perceived by compatible bacteria. Subsequently, bacteria release nod factors, which induce signaling cascades allowing the formation of functional N-fixing nodules. We report here the identification and functional characterization of a plasma membrane-localized MATE-type transporter (LaMATE2) involved in the release of genistein from white lupin roots. The LaMATE2 expression in the root is upregulated under N deficiency as well as low phosphate availability, two nutritional deficiencies that induce the release of this isoflavonoid. LaMATE2 silencing reduced genistein efflux and even more the formation of symbiotic nodules, supporting the crucial role of LaMATE2 in isoflavonoid release and nodulation. Furthermore, silencing of LaMATE2 limited the P-solubilization activity of lupin root exudates. Transport assays in yeast vesicles demonstrated that LaMATE2 acts as a proton-driven isoflavonoid transporter.

plant biology↗

bioRxiv2021

The hidden effects of agrochemicals on plant metabolism and root-associated microorganisms

Agrochemicals are commonly used in agriculture to protect crops and ensure yields. Several of them are mobile within the plant and, being perceived as xenobiotics regardless of their protective/curative roles, they induce a reprogramming of secondary metabolism linked to the detoxification processes even in the absence of phenotype symptoms. Moreover, it is well documented that plants, thanks to the root exudation of different metabolites, are able to shape the microbial population at the rhizosphere and to significantly affect the processes occurring therein. Here we show that plant metabolic response to foliarly-applied pesticides is much broader than what previously thought and includes diverse and compound-specific hidden processes. Among others, stress-related metabolism and phytohormones profile underwent a considerable reorganization. Moreover, a distinctive microbial rearrangement of the rhizosphere was recorded following foliar application of pesticides. Such effects have unavoidably energetic and metabolic costs for the plant paving the way to both positive and negative aspects. The understanding of these effects is crucial for an increasingly sustainable use of pesticides in agriculture. HighlightThe foliar application of pesticides induces a broad metabolic reprogramming in plant and shapes the microbial population of the rhizosphere.

plant biology↗

bioRxiv2020

Millimeter-resolution mapping of citrate exuded from soil grown roots using a novel, low-invasive sampling technique

The reliable sampling of root exudates in soil grown plants is experimentally challenging. This study aimed at developing a citrate sampling and mapping technique with millimetre-resolution using DGT (diffusive gradients in thin films) ZrOH binding gels. Citrate adsorption kinetics, DGT capacity and stability of ZrOH gels were evaluated. ZrOH gels were applied to generate 2D maps of citrate exuded by white lupin roots grown in rhizotrosn in a phosphorus deficient soil. Citrate was adsorbed quantitatively and rapidly by the ZrOH gels, these gels can be stored after sampling for several weeks prior to analysis. The DGT capacity of the ZrOH gel for citrate depends on the ionic strength and the pH of the soil solution but was suitable for citrate sampling. 2D citrate maps of rhizotron grown plants have been generated for the first time at a millimetre resolution to measure an illustrated plant response to P fertilization. DGT-based citrate sampling is suitable for studying the root exudation in soil environments, at unprecedented spatial resolution. By changing binding material, the technique is also applicable to other exudate classes and might be used for the evaluation of whole root exudation crucial in specific cultivar breeding. HighlightWe present a novel, reliable, easy to use, non-destructive citrate sampling- and two-dimensional high-resolution imaging technique for soil grown plant roots.

plant biology↗

bioRxiv2020

The indole-alkaloid gramine shapes the bacterial communities thriving at the barley root-soil interface

Microbial communities proliferating at the root-soil interface, collectively referred to as the rhizosphere microbiota, represent an untapped beneficial resource for plant growth, development and health. Integral to a rational manipulation of the microbiota for sustainable agriculture is the identification of the molecular determinants of these communities. In plants, biosynthesis of allelochemicals is centre stage in defining inter-organismal relationships in the environment. Intriguingly, this process has been moulded by domestication and breeding selection. The indole-alkaloid gramine, whose occurrence in barley (Hordeum vulgare L.) is widespread among wild genotypes but has been counter selected in several modern varieties, is a paradigmatic example of this phenomenon. This prompted us to investigate how exogenous applications of gramine impacted on the rhizosphere microbiota of two, gramine-free, elite barley varieties grown in a reference agricultural soil. High throughput 16S rRNA gene amplicon sequencing revealed that applications of gramine interfere with the proliferation of a subset of soil microbes with a relatively broad phylogenetic assignment. Strikingly, growth of these bacteria appeared to be rescued by barley plants in a genotype- and dosage-independent manner. In parallel, we discovered that host recruitment cues can interfere with the impact of gramine application in a host genotype-dependent manner. Interestingly, this latter effect displayed a bias for members of the phyla Proteobacteria. These initial observations indicate that gramine can act as a determinant of the prokaryotic communities inhabiting the root-soil interface.

plant biology↗