Biology subjects

Giolai, M.

Publications and source records attributed to Giolai, M..

9 recordsLinked to original sources

bioRxiv2026

City life: airborne DNA metagenomic biodiversity monitoring reveals dynamic changes across time and space

Airborne environmental DNA can capture biodiversity across the tree of life, but low sample biomass makes rapid, untargeted detection technically challenging. We combined 45-min air collection, nanopore sequencing and real-time taxonomic analysis in a shotgun metagenomic workflow capable of producing results within 3 hours. Across 77 samples from 13 London sites, including a year of weekly sampling at the Natural History Museum Wildlife Garden, we detected 1,916 species spanning bacteria, fungi, plants and animals. Communities varied spatially and seasonally, shifting from plant dominance in spring to ascomycete dominance in summer and basidiomycete dominance in late autumn and winter. Plant read abundance increased with upwind vegetation, linking airborne signals to surrounding habitat. Detection of catalogued garden plants depended on reference availability, dispersal biology, plant size and proximity to the collector. Together, these findings establish airborne shotgun metagenomics as a platform for rapid, repeated and scalable biodiversity assessment across space and time.

ecology↗

bioRxiv2025

Arabidopsis arenosa influences its microbiome as a serpentine soil adaptation strategy

There is growing evidence that microbes can facilitate plant growth in metal-rich soils. However, our current understanding of how plants recruit their microbiomes under abiotic stress remains incomplete. Serpentine soils are elementally skewed, with high concentrations of magnesium and nickel, often accompanied by other heavy metals, which can limit calcium availability and present unique challenges to plant growth. These soils are also nutrient-poor, prone to erosion, and have low water-holding capacity. To date, the mechanisms by which plants adapt to serpentine soils remain poorly understood and the role of plant-associated microbiomes in this process has not been described. Here, we focus on Arabidopsis arenosa populations adapted to serpentine conditions and investigate their bacterial and fungal microbiomes to better understand the role of plant-associated microbes in serpentine adaptation. We show that serpentine soils harbour distinct plant-associated microbiomes across different plant niches and that the plant genetic background plays a key role in shaping microbial community composition. Finally, we identify serpentine-specific bacterial and fungal variants that may contribute to plant adaptation under these challenging soil conditions.

ecology↗

bioRxiv2024

A Comparison of Nanopore Data Types, Basecalling, and Assembly Algorithms: Whole Plant Genome Assembly and Methylation Analysis from a Single MinION Flow cell

BackgroundOxford Nanopore Technologies MinION sequencer is a compact, USB-powered device that has been available since 2014. Since the release of the earliest model, the throughput and error rate of the platform have improved dramatically and it has become possible to consider sequencing and assembly of eukaryotic organisms using a single nanopore flow cell. Here, we present MinION sequence data, assembly and methylation analysis for the Columbia (Col-0) accession of the model plant Arabidopsis thaliana. Further, we demonstrate the effect that recent developments (specifically the Q20+ chemistry and basecaller improvements) have had on read accuracy and assembly quality. FindingsDNA extracted from leaves of A. thaliana Col-0 was sequenced on two MinION flow cells, together amounting to 115x coverage of the 135 Mb genome. Reads were assembled and polished using several bioinformatics pipelines for nanopore sequence data. We performed CpG methylation analysis directly from the nanopore data, and this correlated well with a previously published bisulfite dataset. ConclusionsOur results suggest that a single MinION flow cell can generate sufficient data to assemble a genome of 135Mb, indicate functional elements, and unlock genomics for researchers of novel species from $600 in under 5 days. Here we release the full nanopore read sets for both flow cells, together with the nanopore-only assemblies. The data presented here is expected to be of particular interest to those in the Arabidopsis community, designing genome projects (with functional annotations), expanding our understanding of epigenetics across the tree of life, and for designing university or high school practicals teaching genomics and epigenomics. HighlightWe evaluate the effect of recent nanopore chemistry and software improvements on the ability to assemble a complete genome and conduct methylation analysis using data from a single MinION flow cell.

genomics↗

bioRxiv2022

Air-seq: Measuring air metagenomic diversity in an agricultural ecosystem

BackgroundAll species shed DNA into their environment during life or in death providing an opportunity to monitor biodiversity via its environmental DNA. Biodiversity monitoring using environmental DNA based technologies has become an important tool in understanding ecosystems. In recent years promising progress for non-invasive and, more importantly, non-destructive monitoring has been made by combining the retrieval of information transmitted by released environmental DNA with high-throughput sequencing technologies. Important ecosystems under continuous threat by disease but essential for food supplies are agricultural systems, often farmed as large monocultures and so highly vulnerable to disease outbreaks. Pest and pathogen monitoring in agricultural ecosystems is therefore key for efficient and early disease prevention and management. Air is rich in biodiversity, but has the lowest DNA concentration of all environmental media and yet it is required for windborne spread by many of the worlds most damaging crop pathogens. Our work and recent research suggests that ecosystems can be monitored efficiently using airborne nucleic acid information. ResultsHere we show that the airborne DNA of microbes can be recovered, sequenced and taxonomically classified, including down to the species level. Monitoring a field growing key crops we show that Air-seq can identify the presence of agriculturally significant pathogens and quantify their changing abundance over a period of 1.5 months often correlating with weather variables. ConclusionWe add to the evidence that aerial environmental DNA can be used as a source for biomonitoring in agricultural and more general terrestrial ecosystems. The ability to detect fluxes and occurrence patterns of species and strains with high throughput sample processing and analysis technologies highlights the value of airborne environmental DNA in monitoring biodiversity changes and tracking of taxa of human interest or concern.

genomics↗

bioRxiv2021

How low can you go? Driving down the DNA input requirements for nanopore sequencing

The requirement for large amounts of purified DNA limits many sequencing experiments, especially when seeking to avoid pre-amplification or when using third generation technology to sequence molecules directly. We wanted to test the limits of current nanopore sequencing input requirements and devised a set of experiments to evaluate extraction and library preparation approaches for low inputs. We found an optimised bead beating approach combined with a magnetic bead protocol, rather than traditional spin columns for DNA extraction, improved both molecule length, integrity score and DNA yield. Through reducing the DNA input to as little as 6.25 % of recommended (25 ng versus 400 ng) and reaction volumes in half, library construction can be completed, and sequencing begun within 20 minutes of sample collection. Applying these approaches, we demonstrated that our pipeline can be used as a cheap and effective method to de novo assemble a genome and identify genes from low quantities and quality of DNA. With our rapid extraction protocol using transportable equipment and low input library construction we were able to generate a de novo assembly from a single insect (Drosophila melanogaster) spanning 125 Mbp / 85 % of the reference genome, over 96.9% complete BUSCO genes, with a contig N50 over 1.2 Mbp, including chromosome arm sized contigs, for a modest consumable cost under {pound}600.

genomics↗

bioRxiv2020

A low-cost pipeline for soil microbiome profiling

BackgroundCommon bottlenecks in environmental microbiome studies are the consumable and personnel costs necessary for genomic DNA extraction and sequencing library construction. This is harder for challenging environmental samples such as soil, which is rich in PCR inhibitors. To address this, we have established a low-cost genomic DNA extraction method for inhibitor rich samples alongside an Illumina-compatible 16S and ITS rRNA gene amplicon library preparation workflow that uses common laboratory equipment. We evaluated the performance of our genomic DNA extraction method against two leading commercial soil genomic DNA kits (MoBio PowerSoil(R) and MP Biomedicals FastDNA SPIN) and a recently published non-commercial extraction method by Zou et al. (2017). Our benchmarking experiment used four different soil types (coniferous, broad leafed, and mixed forest plus a standardised cereal crop compost mix) assessing the quality and quantity of the extracted genomic DNA by analysing sequence variants of 16S V4 and ITS rRNA amplicons. ResultsWe found that our genomic DNA extraction method compares well to both commercially available genomic DNA extraction kits in DNA quality and quantity. The MoBio PowerSoil(R) kit, which relies on silica column-based DNA extraction with extensive washing delivered the cleanest genomic DNA e.g. best A260:A280 and A260:A230 absorbance ratios. The MP Biomedicals FastDNA SPIN kit, which uses a large amount of binding material, yielded the most genomic DNA. Our method fits between the two commercial kits, producing both good yields and clean genomic DNA with fragment sizes of approximately 10 kb. Comparative analysis of detected amplicon sequence variants shows that our method correlates well with the two commercial kits. ConclusionHere we present a low-cost genomic DNA extraction method for inhibitor rich sample types such as soil that can be coupled to an Illumina-compatible simple two step amplicon library construction workflow for 16S V4 and ITS marker genes. Our method delivers high quality genomic DNA at a fraction of the cost of commercial kits and enables cost-effective, large scale amplicon sequencing projects. Notably our extracted gDNA molecules are long enough to be suitable for downstream techniques such as full gene sequencing or even metagenomics shotgun approaches using long reads (PacBio or Nanopore), 10x Genomics linked reads, Dovetail genomics etc.

genomics↗

bioRxiv2019

Spatially resolved transcriptomics reveals plant host responses to pathogens

BackgroundThorough understanding of complex model systems requires the characterisation of processes in different cell types of an organism. This can be achieved with high-throughput spatial transcriptomics at a large scale. However, for plant model systems this is still challenging as suitable transcriptomics methods are sparsely available. Here we present Grid-seq, an easy to adopt, micro-scale spatial-transcriptomics workflow that allows to study expression profiles across small areas of plant tissue at a fraction of the cost of existing sequencing-based methods.\n\nResultsWe compare the Grid-seq method with widely used library preparation methods (Illumina TruSeq). In spatial experiments we show that the Grid-seq method is sensitive enough to identify expression differences across a plant organ. We further assess the spatial transcriptome response of Arabidopsis thaliana leaves exposed to the bacterial molecule flagellin-22.\n\nConclusionWe show that our method can be used to identify known, rapidly flagellin-22 elicited genes, plant immune response pathways to bacterial attack and spatial expression patterns of genes associated with these pathways.

genomics↗

bioRxiv2018

Arabidopsis thaliana populations support long-term maintenance and parallel expansions of related Pseudomonas pathogens

Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild plant pathogens, we carried out a multi-year multi-site survey of Pseudomonas in the natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a pathogenic clade present in all sites. Sequencing of 1,524 Pseudomonas genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically distinct pathogenic sublineages. These sublineages have expanded in parallel within the same populations and are differentiated both at the level of gene content and disease phenotype. Such coexistence of diverse sublineages indicates that in contrast to crop systems, no single strain has been able to overtake these A. thaliana populations in the recent past. Our results suggest that the selective pressures acting on a plant pathogen in wild hosts may be more complex than those in agricultural systems.

microbiology↗

bioRxiv2017

A critical comparison of technologies for a plant genome sequencing project

A high quality genome sequence of your model organism is an essential starting point for many studies. Old clone based methods are slow and expensive, whereas faster, cheaper short read only assemblies can be incomplete and highly fragmented, which minimises their usefulness. The last few years have seen the introduction of many new technologies for genome assembly. These new technologies and new algorithms are typically benchmarked on microbial genomes or, if they scale appropriately, human. However, plant genomes can be much more repetitive and larger than human, and plant biology makes obtaining high quality DNA free from contaminants difficult. Reflecting their challenging nature we observe that plant genome assembly statistics are typically poorer than for vertebrates. Here we compare Illumina short read, PacBio long read, 10x Genomics linked reads, Dovetail Hi-C and BioNano Genomics optical maps, singly and combined, in producing high quality long range genome assemblies of the potato species S. verrucosum. We benchmark the assemblies for completeness and accuracy, as well as DNA, compute requirements and sequencing costs. We expect our results will be helpful to other genome projects, and that these datasets will be used in benchmarking by assembly algorithm developers.

genomics↗