Biology subjects

Green, P.

Publications and source records attributed to Green, P..

13 recordsLinked to original sources

bioRxiv2026

Modifying integrated nursery management through the lens of mycorrhizal ecology improves radiata pine seedling performance and reshapes root mycobiome structure at operational industry scale

Early management decisions in operational forestry are critical for plantation success because it strongly influences seedling quality at planting. Beyond shaping seedling morphology, nursery inputs can also restructure root-associated fungal communities which has consequences for nutrient acquisition, stress tolerance and disease suppression after planting. In this study, we altered nutrient and fungicide inputs based on mycorrhizal ecological theory and quantified the effects of these treatments on key dimensions of the growth performance of radiata pine seedlings. In parallel, we profiled the root-associated mycobiome, assigning fungal taxa to functional guilds and summarizing their richness, diversity, relative abundance and community structure. Using a composite performance index that integrates the key morphological and health measures into a single response variable, together with conventional statistical models with machine learning approaches, we identified management practises that promote both plant performance and a favourable root fungal community and determined the consistent microbiome changes linked to overall quality of the seedlings. These results suggest that microbial feedback loops occur even in highly managed nursery conditions. More broadly, by combining a composite performance index with predictive modelling, we provide a practical way to test complex management combinations and identify microbiome features associated with high-quality planting stock.

ecology↗

bioRxiv2025

Amino acid biostimulant increases pine photosynthetic efficiency and growth through optimised mycobiome and nitrogen assimilation

BackgroundAmino-acid biostimulants have emerged as powerful alternatives to conventional inorganic nitrogen fertilisers, yet their potential in forestry species like radiata pine (Pinus radiata) remains largely unexplored. In this study, we reveal physiological mechanisms of enhanced growth of radiata pine seedlings that are achieved by substituting standard inorganic fertigation, either partially or entirely, with amino-acid-based biostimulants. ResultsAmino-acid fertigation notably increased shoot biomass, plant height, and collar diameter. Critically, this approach reshaped the root fungal community, selectively enriching fungi with diverse ecological roles, including several taxa known for auxin production. These microbial shifts correlated directly with elevated auxin concentrations observed in needle tissues, providing a plausible mechanism for the enhanced growth. Machine learning models further identified key fungal genera that strongly associated with plant biomass, reinforcing microbiome shifts as a contributing mechanism to enhanced growth. Additionally, amino-acid fertigation improved nitrogen assimilation, correlating positively with increased chlorophyll content and photosynthetic efficiency. ConclusionsOur findings highlight that the transition from inorganic source to amino-acid biostimulants not only enhances plant growth and nitrogen use but also promotes a beneficial root microbiome, thereby offering a sustainable pathway to nursery production of radiata pine.

plant biology↗

bioRxiv2025

Using landscape biodiversity metrics to assess rewilding: a space-for-time comparison between the Knepp Estate and an agricultural baseline at Boothby Wildland

O_LIThe biodiversity crisis is often framed in terms of the reduction of species found at a site: a (alpha) diversity. However, changes in species composition across a landscape - b (beta) diversity - caused by biotic homogenisation are part of the same crisis. Much biotic homogenisation in British terrestrial landscapes in the post-war period (1945 onwards) has been driven by agricultural conversion and intensification. Restoration efforts must therefore contend with restoring agricultural land to some desired state, and rewilding has emerged as a potential solution to this problem. C_LIO_LIHere we quantify rewilding success by comparing a- and b-diversity of plant assemblages across two study systems in different stages of rewilding. Boothby Wildland is an arable farm recently given over to rewilding, while the Knepp Estate is an ex-arable and dairy farm currently >20 years into rewilding. We assessed a-diversity within, and b- diversity across, these two landscapes using 3 years of plant survey data (2022-2024). C_LIO_LIWe confirmed expected differences between a baseline and rewilded landscape and explored the changes in a brand new rewilded landscape in its early years of progress. As expected, the plant community at the Knepp Estate is relatively stable while that of Boothby Wildland is changing rapidly, and we discuss the landscape impacts of different herbivory regimes on recovery. C_LIO_LISynthesis and applications. We also show that spatial metrics for SESMPD and SESMNTD can distinguish between a rewilded and degraded landscape. This suggests that changes in the structure of biodiversity across landscapes can be quantified using analyses that account for spatial structure in metrics. We call for further research to see if a spatial approach of this kind can be used as a general metric of success in rewilding. C_LI

ecology↗

bioRxiv2024

Putative neofunctionalization of a Poales-specific EXO70 clade

EXO70s are uniquely expanded in land plants compared to all other eukaryotic lineages. The functional implications of this expansion and diversification on the conserved role of EXO70 as a subunit of the octameric exocyst complex have remained unresolved. We previously demonstrated barley (Hordeum vulgare) EXO70FX12, a member of the monocot-specific EXO70FX clade, is required for resistance to wheat stripe rust in conjunction with the leucine-rich repeat receptor kinase (LRR-RK) HvPUR1. Through phylogenetic analysis, we identified unique features of the EXO70FX clade, leading us to hypothesize that this clade experienced neofunctionalization. Using structural predictions and protein-protein interaction assays, we demonstrate that HvEXO70FX12 lost the ability to serve as a subunit within the exocyst complex. We predict that the EXO70FX clade has largely lost exocyst association and represents a novel acquisition that emerged during Poales diversification for immunity.

plant biology↗

bioRxiv2024

Discovery of functional NLRs using expression level, high-throughput transformation, and large-scale phenotyping

Protecting crops from pests and diseases is vital for the sustainable agricultural systems needed for food security. Introducing functional resistance genes to enhance the plant immune system is an effective method of disease control, but identifying new immune receptors is time-consuming and resource intensive. We observed that functional immune receptors of the NLR class show a signature of high expression in uninfected plants across both monocot and dicot species. Here we show that this signature, combined with high throughput crop transformation, can be used to rapidly identify candidate NLRs from diverse plant species and validate pathogen resistance directly in crop plants. As a proof of concept, we generated a wheat transgenic library carrying 995 NLRs from 18 grass species. Screening the collection with the stem rust pathogen Puccinia graminis, which is a major threat to wheat production, we confirm 19 new resistance genes. This pipeline facilitates resistance gene discovery, unlocking a large gene pool of diverse and non-domesticated plant species and providing in-planta gene validation of disease resistance directly in crops.

plant biology↗

bioRxiv2024

Role of the CTCF Binding Site in Human T-Cell Leukemia Virus-1 Pathogenesis

During HTLV-1 infection, the virus integrates into the host cell genome as a provirus with a single CCCTC binding protein (CTCF) binding site (vCTCF-BS), which acts as an insulator between transcriptionally active and inactive regions. Previous studies have shown that the vCTCF-BS is important for maintenance of chromatin structure, regulation of viral expression, and DNA and histone methylation. Here, we show that the vCTCF-BS also regulates viral infection and pathogenesis in vivo in a humanized (Hu) mouse model of adult T-cell leukemia/lymphoma. Three cell lines were used to initiate infection of the Hu-mice, i) HTLV-1-WT which carries an intact HTLV-1 provirus genome, ii) HTLV-1-CTCF, which contains a provirus with a mutated vCTCF-BS which abolishes CTCF binding, and a stop codon immediate upstream of the mutated vCTCF-BS which deletes the last 23 amino acids of p12, and iii) HTLV-1-p12stop that contains the intact vCTCF-BS, but retains the same stop codon in p12 as in the HTLV-1-CTCF cell line. Hu-mice were infected with mitomycin treated or irradiated HTLV-1 producing cell lines. There was a delay in pathogenicity when Hu-mice were infected with the CTCF virus compared to mice infected with either p12 stop or WT virus. Proviral load (PVL), spleen weights, and CD4 T cell counts were significantly lower in HTLV-1-CTCF infected mice compared to HTLV-1-p12stop infected mice. Furthermore, we found a direct correlation between the PVL in peripheral blood and death of HTLV-1-CTCF infected mice. In cell lines, we found that the vCTCF-BS regulates Tax expression in a time-dependent manner. The scRNAseq analysis of splenocytes from infected mice suggests that the vCTCF-BS plays an important role in activation and expansion of T lymphocytes in vivo. Overall, these findings indicate that the vCTCF-BS regulates Tax expression, proviral load, and HTLV pathogenicity in vivo. Author SummaryHuman T-cell leukemia virus type 1 (HTLV-1) is a cause of leukemia and lymphoma, and several inflammatory medical disorders. The virus integrates in the host cell DNA, and it includes a single binding site for a cellular protein designated CTCF. This protein is important in regulation of many viruses, as well as properties of normal and malignant cells. In order to define the role of CTCF in HTLV-1 pathogenesis in vivo, we analyzed a mutant virus lacking the binding site in humanized mice. We found that this mutation slowed virus spread and attenuated the development of disease. Gene expression studies demonstrated a dynamic role of CTCF in regulating viral gene expression and T lymphocyte activation.

microbiology↗

bioRxiv2024

Assisted colonisation prospects for the black-veined white butterfly in England

The black-veined white butterfly, Aporia crataegi, reached the north-western edge of its European geographic distribution in the British Isles in the 19th century, but became extinct in the early 20th century, following several cold decades. Substantial areas of potential breeding habitat in southern Britain are currently available to this species, which requires scattered hawthorn (Crataegus monogyna) and suckering blackthorn scrub (Prunus spinosa), including infrequently cut hedgerows. These habitats are needed at a relatively large scale as the butterfly occurs as networks of colonies (metapopulations), ranging over large tracts of connected landscape. A number of events have increased habitat availability over the past 70 years (myxomatosis reduced rabbit populations, which permitted host plant scrub regeneration; hedgerow management policies reduced cutting frequencies; rewilding and landscape connectivity initiatives are resulting in additional scrub). However, while A. crataegi males occasionally disperse several kilometres, it is unlikely that A. crataegi females will cross the English Channel in sufficient numbers to establish populations in southern England, without assistance. Here, we (i) provide a review of the literature on species interactions, the habitat requirements, distribution and dispersal of A. crataegi and (ii) provide evidence that southern, eastern and central England are likely to be climatically suitable for reintroductions of A. crataegi. Substantial areas of England are already expected to be amongst the climatically most suitable parts of Europe for this insect. We identify a landscape of at least 100 km2 containing multiple patches of suitable habitats, and highlight co-benefits for other species that inhabit scrubland and successional mosaics. We use a climate-matching approach to assess climatically-similar locations to obtain source material most likely to establish in Britain. Areas of northern France and mid elevations in the Iberian Peninsula, including in the Pyrenees, provide potential suitable source locations due to close climatic matching and a large number of species records. We recommend reestablishment from more than one source, providing genetic diversity in the reintroduced population, enabling subsequent local adaptation to British conditions. We highlight the opportunity for monitored releases to be undertaken within the landscape highlighted here, so as to evaluate population growth, host plant use, and rates of colonisation away from release sites that differ in their management, habitat, host plant characteristics, and proximity to other sites. This approach would aim to develop knowledge as a living lab to inform future best practice releases. In conclusion, the black-veined white, A. crataegi, has potential to become a model species for assisted colonisation projects where natural and human-created barriers have prevented range expansion into regions where the 21st century climate is suitable for a species.

ecology↗

bioRxiv2022

Barley MLA3 recognizes the host-specificity determinant PWL2 from rice blast (M. oryzae)

Plant nucleotide-binding leucine-rich repeat immune receptors (NLRs) directly or indirectly recognize pathogen-secreted effector molecules to initiate plant defense. Recognition of multiple pathogens by a single NLR is rare and usually occurs via monitoring for changes to host proteins; few characterized NLRs have been shown to recognize multiple effectors. The barley NLR Mla has undergone functional diversification and Mla alleles recognize host-adapted isolates of barley powdery mildew (Blumeria graminis f. sp. hordei; Bgh). Here, we show that Mla3 also confers resistance to rice blast (Magnaporthe oryzae) in a dosage dependent manner. Using a forward genetic screen, we discovered that the recognized effector from M. oryzae is PWL2, a host range determinant factor that prevents M. oryzae from infecting weeping lovegrass (Eragrostis curvula). Mla3 has therefore convergently evolved the capacity to recognize effectors from diverse pathogens.

plant biology↗

bioRxiv2021

A lineage-specific Exo70 is required for receptor kinase-mediated immunity in barley

In the evolution of land plants, the plant immune system has experienced expansion in immune receptor and signaling pathways. Lineage-specific expansions have been observed in diverse gene families that are potentially involved in immunity, but lack causal association. Here, we show that Rps8-mediated resistance in barley to the fungal pathogen Puccinia striiformis f. sp. tritici (wheat stripe rust) is conferred by a genetic module: LRR-RK and Exo70FX12, which are together necessary and sufficient. The Rps8 LRR-RK is the ortholog of rice extracellular immune receptor Xa21 and Exo70FX12 is a member of the Poales-specific Exo70FX clade. The Exo70FX clade emerged after the divergence of the Bromeliaceae and Poaceae, and comprises from 2 to 75 members in sequenced grasses. These results demonstrate the requirement of a lineage-specific Exo70FX12 in Rps8 LRR-RK immunity and suggest that the Exo70FX clade may have evolved a specialized role in receptor kinase signaling.

plant biology↗

bioRxiv2021

Induced neural differentiation of human mesenchymal stem cells affects lipid metabolism pathways

Neuronal membranes contain exceptionally high concentrations of long-chain polyunsaturated fatty acids (PUFA), docosahexaenoic acid (DHA) and arachidonic acid (ARA), which are essential for neuronal development and function. Adult bone-marrow-derived mesenchymal stem cells (MSC) can be induced to possess some neuronal characteristics. Here we examined the effects of neuronal induction on the PUFA metabolism specific pathways. Differentiated cells contained ~30% less ARA than MSC. The expression of specific ARA metabolizing enzymes was upregulated, notably that of prostaglandin E2 synthase which increased more than 15-fold, concomitantly with a 3-fold increase in the concentration of PGE2 in the medium. Moreover, induced differentiation was associated with enhanced incorporation of exogenous DHA, upregulation of acyl-CoA synthases, fatty acid binding proteins, choline kinase (CK) and phosphatidylserine synthases as well as increased total cellular phospholipids (PL). These findings suggest that active ARA metabolites may be important in the differentiation process and that neuronal induction prepares the resulting cells for increased DHA incorporation through the action of specific enzymes.

neuroscience↗

bioRxiv2018

Speed breeding in growth chambers and glasshouses for crop breeding and model plant research

1.To meet the challenge of feeding a growing population, breeders and scientists are continuously looking for ways to increase genetic gain in crop breeding. One way this can be achieved is through \"speed breeding\" (SB), which shortens the breeding cycle and accelerates research studies through rapid generation advancement. The SB method can be carried out in a number of ways, one of which involves extending the duration of a plants daily exposure to light (photoperiod) combined with early seed harvest in order to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. Here we present glasshouse and growth chamber-based SB protocols with supporting data from experimentation with several crop species. These protocols describe the growing conditions, including soil media composition, lighting, temperature and spacing, which promote rapid growth of spring and winter bread wheat, durum wheat, barley, oat, various members of the Brassica family, chickpea, pea, grasspea, quinoa and the model grass Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale-up plant numbers for single seed descent (SSD) purposes. Conversely, instructions on how to perform SB on a small-scale by creating a benchtop SB growth cabinet that enables optimization of parameters at a low cost are provided. We also outline the procedure for harvesting and germinating premature wheat, barley and pea seed to reduce generation time. Finally, we provide troubleshooting suggestions to avoid potential pitfalls.

plant biology↗

bioRxiv2017

Deep Sequencing: Intra-Terrestrial Metagenomics Illustrates The Potential Of Off-Grid Nanopore DNA Sequencing

Genetic and genomic analysis of nucleic acids from environmental samples has helped transform our perception of the Earths subsurface as a major reservoir of microbial novelty. Many of the microbial taxa living in the subsurface are under-represented in culture-dependent investigations. In this regard, metagenomic analyses of subsurface environments exemplify both the utility of metagenomics and its power to explore microbial life in some of the most extreme and inaccessible environments on Earth. Hitherto, the transfer of microbial samples to home laboratories for DNA sequencing and bioinformatics is the standard operating procedure for exploring microbial diversity. This approach incurs logistical challenges and delays the characterization of microbial biodiversity. For selected applications, increased portability and agility in metagenomic analysis is therefore desirable. Here, we describe the implementation of sample extraction, metagenomic library preparation, nanopore DNA sequencing and taxonomic classification using a portable, battery-powered, suite of off-the-shelf tools (the \"MetageNomad\") to sequence ochreous sediment microbiota while within the South Wales Coalfield. While our analyses were frustrated by short read lengths and a limited yield of DNA, within the assignable reads, Proteobacterial (-, {beta}-, {gamma}-Proteobacteria) taxa dominated, followed by members of Actinobacteria, Firmicutes and Bacteroidetes, all of which have previously been identified in coals. Further to this, the fungal genus Candida was detected, as well as a methanogenic archaeal taxon. To the best of our knowledge, this application of the MetageNomad represents an initial effort to conduct metagenomics within the subsurface, and stimulates further developments to take metagenomics off the beaten track.

microbiology↗

bioRxiv2016

Defining the genetic architecture of stripe rust resistance in the barley accession HOR1428

Puccinia striiformis f. sp. hordei, the causal agent of barley stripe rust, is a destructive fungal pathogen that significantly affects barley cultivation. A major constraint in breeding resistant cultivars is the lack of mapping information of resistance (R) genes and their introgression into adapted germplasm. A considerable number of R genes have been described in barley to P. striiformis f. sp. hordei, but only a few loci have been mapped. Previously, Chen and Line (1999) reported two recessive seedling resistance loci in the Ethiopian landrace HOR 1428. In this study, we map two loci that confer resistance to P. striiformis f. sp. hordei in HOR 1428, which are located on chromosomes 3H and 5H. Both loci act as additive effect QTLs, each explaining approximately 20% of the phenotypic variation. We backcrossed HOR 1428 to the cv. Manchuria and selected based on markers flanking the RpsHOR128-5H locus. Saturation of the RpsHOR1428-5H locus with markers in the region found KASP marker K_1_0292 in complete coupling with resistance to P. striiformis f. sp. hordei and was designated Rps9. Isolation of Rps9 and flanking markers will facilitate the deployment of this genetic resource into existing programs for P. striiformis f. sp. hordei resistance.

plant biology↗