Plastic pollution in terrestrial environments is a growing concern, with an increasing focus on the impact of plastic additives on soil ecosystems. We evaluated the impact of additives from conventional plastics (ACP) and biodegradable plastics (ABP) on the soil nematode, Pratylenchus neglectus. The additives represented five functional classes (antioxidants, colourants, flame retardants, nucleating agents, and plasticisers). P. neglectus exhibited concentration-dependent mortality when exposed to the additives, with Tartrazine, an ABP colourant, inducing higher mortality compared to the conventional counterpart. No significant changes in the locomotory patterns of P. neglectus were observed, whereas oxidative stress significantly increased in response to all assistive treatments. Exposure to most of the additives resulted in a significant decline in nematode reproduction; ACPs generally caused more severe effects than ABPs. Our findings highlight a complexity in how plastic additives impact soil organisms and challenge the assumption that ABPs may be universally safer for ecosystems. The study emphasises the importance of conducting ecotoxicological assessments of specific ABPs on important species to inform the design of environmentally sustainable plastics. The results also suggest that P. neglectus could serve as a valuable sentinel organism for evaluating the ecological impacts of plastic pollution in soil.

Members of the Haloferacaceae, a family of extremely halophilic archaea, exhibit unique physiological and genetic traits that make them promising candidates for biotechnological applications. These organisms thrive in hypersaline environments and tolerate a wide range of stresses, including high temperatures, UV radiation, and toxic metals. Their ability to grow on agro-industrial waste, coupled with their inherent resistance to contamination and the simplicity of downstream processing via osmotic shock, makes them ideal for sustainable bioproduction. Species such as Haloferax mediterranei have been explored for the biosynthesis of polyhydroxyalkanoates, carotenoids, halocins, and enzymes functional under extreme conditions. Species of Haloferacaceae can also bioremediate saline environments contaminated with hydrocarbons, heavy metals, and nitrogenous waste. Advances in genetic tools, including CRISPR interference, inducible promoters, and knock-in/knock-out systems, particularly in H. volcanii, have significantly expanded the engineering potential of these archaea. However, there remains a need for further innovation in genetic tools for this family. This review highlights the expanding potential of the Haloferacaceae for circular bioeconomy applications and identifies key technological gaps limiting their broader industrial adoption.

Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a “model clade.” These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a “model clade” and make suggestions for building global networks to support future studies in the model order Brassicales.

Herbal leys (multispecies swards) can potentially deliver greater agronomic and environmental benefits than conventional grass-clover swards in grazed agroecosystems. However, despite their popularity in agri-environment schemes, little is known about the effect of herbal leys on soil physical (e.g., porosity), chemical (e.g., carbon), and biological (e.g., soil fauna) characteristics. In the UK, a 2-ha replicated-field experiment utilising a herbal or grass-clover ley (n = 3 per sward) aimed to investigate the effect of sward type on soil quality. Each sward was rotationally grazed by weaned lambs (3.2 LU ha(-1)) over two grazing seasons, with soil physiochemical and biological characteristics assessed after 2-years using techniques such as X-ray micro-Computed Tomography (mu CT) and microbial shallow shotgun sequencing. Soil chemical characteristics (e.g., pH) were unaffected by sward type. Similarly, topsoil (0-10 cm) organic carbon stocks measured after 2-years did not differ between the herbal (26.1 +/- 1.1 t C ha(-1)) and grass-clover ley (25.7 +/- 1.1 t C ha(-1)). X-ray mu CT analysis revealed greater pore connectivity (Euler number) in grass-clover ley intact soil cores (0-10 cm depth, 7.5 cm width) than herbal ley cores dominated by Plantago lanceolata (p = 0.008). However, there was no sward-type difference in aggregate stability or general pore characteristics, determined using X-ray mu CT, in air-dried 4 mm aggregates obtained from 0-5 or 5-10 cm depth, nor did sward type affect earthworm abundance, microbial community composition or the functional gene profile. This study is the first to explore the effects of a commercial herbal ley on physical, chemical, and biological soil quality indicators in a rotationally grazed sheep pasture. While no improvements in soil quality indicators were observed after 2-years, these findings have significant implications for agri-environment schemes promoting herbal leys to achieve soil quality and sustainability, with further research needed to optimise the seed mixture and management regime to deliver greater long-term below-ground ecosystem service benefits.

Unprecedented plastic production has resulted in over six billion tons of harmful waste. Certain insect taxa emerge as potential agents of plastic biodegradation. Through a comprehensive manual and bibliometric literature analysis, this review analyses and consolidates the growing literature related to insect-mediated plastic breakdown. Over 23 insect species, representing Coleoptera, Lepidoptera, and 4 other orders, have been identified for their capacity to consume plastic polymers. Natural and synthetic polymers exhibit high-level similarities in molecular structure and properties. Thus, in conjunction with comparative genomics studies, we link plastic-degrading enzymatic capabilities observed in certain insects to the exaptation of endogenous enzymes originally evolved for digesting lignin, cellulose, beeswax, keratin and chitin from their native dietary substrates. Further clarification is necessary to distinguish mineralisation from physicochemical fragmentation and to differentiate microbiome-mediated degradation from direct enzymatic reactions by insects. A bibliometric analysis of the exponentially growing body of literature showed that leading research is emerging from China and the USA. Analogies between natural and synthetic polymer’s degradation pathways will inform engineering robust enzymes for practical plastic bioremediation applications. By aggregating, analysing, and interpreting published insights, this review consolidates our mechanistic understanding of insects as a potential natural solution to the escalating plastic waste crisis.

Marinococcus sp. PL1-022 was isolated from Pearse Lakes, Western Australia. The sequenced genome consists of a chromosome (3,140,198 bp; 48.2% GC) and two plasmids (58,083 bp and 19,399 bp; 41.4 and 50.7% GC-content, respectively). Isolation of Marinococcus sp. PL1-022 adds to the increasing repertoire of culturable extremophiles.

Idiomarina sp. PL1-037 was isolated from Pearse Lakes, Rottnest Island, Western Australia. The sequenced completed genome for PL1-037 is composed of a single chromosome (2,804,934  bp) with a GC content of 47.1%. Isolation of Idiomarina sp. PL1-037 provides insights about culturable extremophiles from the Pearse lakes microbiome.

Lomandra is the largest genus in Asparagaceae subfamily Lomandroideae and possesses economic, ecological, and ethnobotanical significance in Australia. Lomandra comprises four sections, L. section Capitatae, L. section Macrostachya, L. section Typhopsis and L. section Lomandra, the latter comprising series Lomandra and series Sparsiflorae, all recognized based solely on morphology. In this study, phylogenetic relationships were estimated for 79 Lomandroideae individuals, including 45 Lomandra species and subspecies (c. 63% of species and subspecies diversity). We generated genome-scale plastome sequence data and used maximum likelihood and Bayesian inference criteria for phylogenetic estimation. Lomandra was non-monophyletic, with Xerolirion divaricata nested within it. Two major clades were recovered: Capitatae-Macrostachya (CM) and Lomandra-Typhopsis (LT). The CM clade included a monophyletic Lomandra section Capitatae with a base chromosome number x = 7, and L. section Macrostachya (x = 8); the LT clade included L. sections Typhopsis and Lomandra, both x = 8. Section Lomandra series Lomandra and series Sparsiflorae were both recovered as non-monophyletic. Morphological characters were assessed to identify combinations of characters that characterize clades. A base chromosome number of x = 8 was plesiomorphic for Lomandra. The largest number of Lomandra species occupy the Mediterranean ecoregion and occupancy of sclerophyll vegetation was reconstructed as ancestral for the genus.

Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on every continent except Antarctica. Following the recent re -circumscription of 15 Caesalpinioideae genera as presented in Advances in Legume Systematics 14, Part 1, and using as a basis a phylogenomic analysis of 997 nuclear gene sequences for 420 species and all but five of the genera currently recognised in the subfamily, we present a new higher -level classification for the subfamily. The new classification of Caesalpinioideae comprises eleven tribes, all of which are either new, reinstated or re -circumscribed at this rank: Caesalpinieae Rchb. (27 genera / ca. 223 species), Campsiandreae LPWG (2 / 5-22), Cassieae Bronn (7 / 695), Ceratonieae Rchb. (4 / 6), Dimorphandreae Benth. (4 / 35), Erythrophleeae LPWG (2 /13), Gleditsieae Nakai (3 / 20), Mimoseae Bronn (100 / ca. 3510), Pterogyneae LPWG (1 / 1), Schizolobieae Nakai (8 / 42-43), Sclerolobieae Benth. & Hook. f. (5 / ca. 113). Although many of these lineages have been recognised and named in the past, either as tribes or informal generic groups, their circumscriptions have varied widely and changed over the past decades, such that all the tribes described here differ in generic membership from those previously recognised. Importantly, the approximately 3500 species and 100 genera of the former subfamily Mimosoideae are now placed in the reinstated, but newly circumscribed, tribe Mimoseae. Because of the large size and ecological importance of the tribe, we also provide a clade-based classification system for Mimoseae that includes 17 named lower -level clades. Fourteen of the 100 Mimoseae genera remain unplaced in these lower -level clades: eight are resolved in two grades and six are phylogenetically isolated monogeneric lineages. In addition to the new classification, we provide a key to genera, morphological descriptions and notes for all 163 genera, all tribes, and all named clades. The diversity of growth forms, foliage, flowers and fruits are illustrated for all genera, and for each genus we also provide a distribution map, based on quality-controlled herbarium specimen localities. A glossary for specialised terms used in legume morphology is provided. This new phylogenetically based classification of Caesalpinioideae provides a solid system for communication and a framework for downstream analyses of biogeography, trait evolution and diversification, as well as for taxonomic revision of still understudied genera.

This review examines the role of Pseudomonas spp. bacteria as biocontrol agents against crop diseases, focusing on their mechanisms of action, efficacy, and potential applications in sustainable agriculture. Pseudomonas spp., ubiquitous in soil ecosystems and root microbiomes, have attracted attention for their ability to suppress phytopathogens and enhance plant health through various mechanisms. These include direct competition for nutrients, production of antimicrobial compounds and volatile organic compounds, competition using type VI secretion systems, and indirect induction of systemic resistance. Our review shows that Pseudomonas strains effectively control a wide range of diseases across diverse plant species, with some strains demonstrating efficacy comparable to chemical fungicides. However, the review also highlights challenges in achieving consistent performance when using Pseudomonas inoculants under field conditions due to various biotic and abiotic factors. Strategies to optimize biocontrol potential, such as formulation techniques, application methods, and integration with other management practices, are discussed. The advantages of Pseudomonas-based biocontrol for sustainable agriculture include reduced reliance on chemical pesticides, enhanced crop productivity, and improved environmental sustainability. Future research directions should focus on understanding the complex interactions within the plant microbiome, optimizing delivery systems, and addressing regulatory hurdles for commercial deployment. This review underscores the significant potential of Pseudomonas spp. in sustainable crop protection while acknowledging the need for further research to fully harness their capabilities in agricultural systems.

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods(1,2). A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome(3,4). Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins(5-7). However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes(8). This 15-fold increase in genus-level sampling relative to comparable nuclear studies(9) provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

The Haloferacaceae are a family of extremely halophilic archaea with many species producing enzymes and products beneficial for industrial biotechnology. They are, however, relatively under-characterised with regards to genetics and gene products. This study aims to use existing sequence data to highlight genetic diversity, create pangenomes for three genera, and provide secondary metabolite and pathway analysis. This will establish current knowledge and identify key gaps in research. We show that the Haloferacaceae have significant genetic diversity between genera, with numerous gene gain and loss events in key genera. It also found that the model genus, Haloferax, has relatively low identified secondary metabolites compared to other genera within the family. Additionally, this study has identified potential biotechnology targets for heterologous expression in model organisms.

Eucalypts are a large and ecologically important group of plants on the Australian continent, and understanding their evolution is important in understanding evolution of the unique Australian flora. Previous phylogenies using plastome DNA, nuclear-ribosomal DNA, or random genome-wide SNPs, have been confounded by limited genetic sampling or by idiosyncratic biological features of the eucalypts, including widespread plastome introgression. Here we present phylogenetic analyses of Eucalyptus subgenus Eudesmia (22 species from western, northern, central and eastern Australia), in the first study to apply a target-capture sequencing approach using custom, eucalypt-specific baits (of 568 genes) to a lineage of Eucalyptus. Multiple accessions of all species were included, and target-capture data were supplemented by separate analyses of plastome genes (average of 63 genes per sample). Analyses revealed a complex evolutionary history likely shaped by incomplete lineage sorting and hybridization. Gene tree discordance generally increased with phylogenetic depth. Species, or groups of species, toward the tips of the tree are mostly supported, and three major clades are identified, but the branching order of these clades cannot be confirmed with confidence. Multiple approaches to filtering the nuclear dataset, by removing genes or samples, could not reduce gene tree conflict or resolve these relationships. Despite inherent complexities in eucalypt evolution, the custom bait kit devised for this research will be a powerful tool for investigating the evolutionary history of eucalypts more broadly.

Factors affecting fertilizer decisions made by grain growers are changing in the context of changing climatic conditions and growing volatility in global fertilizer and grain markets. To ensure sustainable development of grain industries in light of this uncertainty, research, development, extension, and adoption activities associated with growers’ fertilizer decisions need to be focused on factors to which they are most sensitive. The aim of this paper is to understand the factors that have the greatest influence on grain producer’s fertilizer strategies, how these factors have changed over recent years, and what is the relative importance of agronomic, socioeconomic, and logistical factors affecting these strategies. A telephone survey of 425 grain-growing businesses in Western Australia was conducted, and survey results were analyzed statistically. We show for the first time that grain growers’ fertilizer decisions are most sensitive to agronomic factors (especially the amount and distribution of rainfall). Logistic factors (such as difficulties fertilizing increasing areas in short periods of time) are growing in influence as farm size, cropping areas, and the number of fertilizer applications within seasons increase. Fertilizer decisions have become less sensitive to socioeconomic factors over the last 10 to 15 years. To ensure sustainable development of grain production, research through to adoption activities should focus on agronomic issues (such as seasonal forecasting) and logistic issues (such as improving planning, organizational, and technical capacity for developing and implementing fertilizer strategies).

Primary Myelofibrosis (PMF) is an aggressive myeloproliferative neoplasm (MPN) characterized by constitutional symptoms, cytopenias, splenomegaly, extramedullary hematopoiesis, bone marrow (BM) fibrosis, and a propensity to transform to acute myeloid leukemia (AML). Despite advances in understanding the underlying genetic abnormalities in MPN and the development of JAK2 inhibitors to treat MF, there is an urgent need to devise new treatment strategies, particularly for triple negative myelofibrosis (TN-MF) cases that lack mutations in the JAK2 kinase pathway and who have inferior outcomes. To identify potential oncogenic drivers in TN-MF, we performed cytogenetic analyses and targeted exome sequencing of 98 genes commonly mutated in myeloid malignancies in 584 MF patients identified from the Total Cancer Care database at Moffitt Cancer Center. Notably, there were no significant differences in the somatic mutation profiles (other than JAK2 activating mutations) between TN vs. JAK2/CALR/MPL mutant MF patients. However, trisomy of chromosome 8 occurs more frequently in TN-MF vs. other subtypes (26.7% vs. 6.2%, p=0.0001). To identify oncogenic drivers in trisomy 8+ TN-MF, we performed scRNA-seq analysis from 18,651 cells ( n=15,850 from 3 normal donors and n=2,801 from a trisomy 8+ TN-MF patient) and identified a total of 1,260 genes that are differentially regulated in hematopoietic stem cells (HSCs) of trisomy 8+ TN-MF compared to normal donors. Among these, 131 genes were located on chromosome 8 and MYC was one of the top 5 genes that are significantly upregulated in trisomy 8+ HSCs. Additional immunohistochemistry staining demonstrated that MYC protein levels in BM cells were significantly higher in trisomy 8+ TN-MF patients vs. trisomy 8- patients. To assess whether MYC might be a driver of MPN, we established an Mx1-Cre +/-;Rosa26 LSL-MYC/LSL-MYC transgenic mouse model that inducibly overexpresses MYC in HSCs following treatment of polyinosinic-polycytidylic acid (pIpC). Forced MYC expression induced profound anemia, monocytosis, megakaryocytic atypia, splenomegaly, increased BM collagen deposition/fibrosis, extramedullary hematopoiesis in spleen and liver, and significantly reduced OS vs. Mx1-Cre +/- wild type controls (median OS 258 days vs. not reached (NR), p<0.0001). MYC also promoted expansion of HSCs, myeloid progenitors, and Gr-1 +/CD11b + mature myeloid cells in BM and spleen; thus, MYC was sufficient to provoke MF-like disease independent of JAK2 pathway mutations. Subsequent scRNA-seq analysis of 25,232 cells ( n=13,552 from control and n=11,680 from a MYC transgenic mouse) revealed that S100a9 mRNA levels were increased by MYC in most major hematopoietic cell types. Supporting oncogenic roles of S100A9 in MYC-driven MF, deletion of S100a9 in Mx1-Cre +/-;Rosa26 LSL-MYC/LSL-MYC;S100a9 -/- mice abolished MYC-induced MF phenotypes and significantly improved OS (median OS NR vs. 225 days, p=0.0345). To test whether inhibition of MYC can suppress MF disease progression in vivo, lethally irradiated CD45.1 +/CD45.2 + WT mice were transplanted with BM cells harvested from CD45.2 + Mx1-Cre +/-;Rosa26 LSL-MYC/LSL-MYC mice that were treated with pIpC 20 weeks prior to transplant. MYCi975, a small molecule that inhibits MYC, reduced MYC and S100a9 protein levels in BM and spleen cells. Further, MYCi975 effectively suppressed MYC-driven MF phenotypes and disease progression, and significantly improved OS (median OS NR vs. 252 days, p=0.0109). In summary, our studies are the first to describe an oncogenic role of MYC in MF pathogenesis, where MYC provokes an alarmin-driven inflammatory circuit, and where the MYC-S100A9 axis represents a therapeutic vulnerability for TN-MF patients. Accordingly, our results provide a strong rationale for testing agents targeting MYC or S100A9 in early phase clinical trials in MPNs having increased MYC levels or activity.

Amelioration and management of large volumes of tailings resulting from alumina refining is a major challenge owing to the high alkalinity and salinity of residues. Blended byproduct caps are a potential new and more cost-effective approach to tailings management, where tailings are blended with other local byproducts in order to reduce pH, salinity and toxic elements. Here, alkaline bauxite residue was blended with four byproducts (waste acid, sewage water, fly ash and eucalypt mulch) to create a range of potential capping materials. We leached and weathered materials in the glasshouse with deionized water over nine weeks to investigate if byproducts on their own or in combination improved cap conditions. Combining all four byproducts (10 wt % waste acid, 5 wt % sewage water, 20 wt % fly ash and 10 wt % eucalypt mulch) achieved lower pH (9.60) compared to any byproduct applied individually, or un-remediated bauxite residue (pH 10.7). Leaching decreased EC by dis-solving and exporting salts and minerals from the bauxite residue. Fly ash addition increased organic carbon (likely from non-combusted organic material) and nitrogen, while eucalypt mulch increased inorganic phos-phorus. Addition of byproducts also decreased the concentration of potentially toxic elements (e.g., Al, Na, Mo and V) and enhanced pH neutralisation. Initial pH with single byproduct treatments was 10.4-10.5, which decreased to between 9.9-10.0. Further lowering of pH and salinity as well as increased nutrient concentrations may be possible through higher addition rates of byproducts, incorporation of other materials such as gypsum, and increasing leaching/weathering time of tailings in situ.

Context Ammonia (NH3) volatilisation can be a significant nitrogen (N) loss pathway in the grains industry following the surface broadcast application of urea. However, the extent of urea volatilisation from acidic soils and the soil properties that regulate this N loss pathway have not been investigated widely. Aims We conducted a laboratory incubation experiment to measure NH3 volatilisation loss potential following the broadcast application of urea prills (1–2 mm diameter; 50 kg N ha−1) onto moistened acidic and neutral cropping soils, sampled from four long-term cropping research sites. Methods The selected soils varied in pH, clay content, organic carbon, pH buffering capacity (pHBC) and cation exchange capacity. Volatilised NH3 was captured in a phosphoric acid trap after 7, 14 and 21 days and then measured using colorimetric analysis. We compared the measured NH3 losses with predicted NH3 losses derived from an existing empirical NH3 volatilisation prediction model. Key results Of the applied urea-N, 0.9–25% was volatilised. Cumulative NH3 losses were strongly related (R2 = 0.77) with soil pHBC derived from a pedotransfer function. The existing NH3 loss model generally had poor predictive capacity (RMSE = 34%). Conclusions Using clay content as a surrogate variable for pHBC in the predictive model for sandy kaolinitic soils where it is largely a function of organic carbon content can cause poor estimates of NH3 volatilisation loss potential. Implications Grain production on sandy, acidic soils with low pHBC could lead to substantial NH3 volatilisation losses if urea is broadcast.

Despite whole genome sequencing (WGS), why do many single gene disorder cases remain unsolved, impeding diagnosis and preventative care for people whose disease-causing variants escape detection? Early WGS data analytic steps prioritize protein-coding sequences. To simultaneously prioritize variants in non-coding regions rich in transcribed and critical regulatory sequences, we developed GROFFFY, an analytic tool which integrates coordinates for regions with experimental evidence of functionality. Applied to WGS data from solved and unsolved hereditary hemorrhagic telangiectasia (HHT) recruits to the 100,000 Genomes Project, GROFFFY-based filtration reduced the mean number of variants per DNA from 4,867,167 to 21,486, without deleting disease-causal variants. In three unsolved cases (two related), GROFFFY identified ultra-rare deletions within the 3 prime untranslated region (UTR) of the proto-oncogene SMAD4, where germline loss-of-function alleles cause combined HHT and colonic polyposis. Sited >5.4kb distal to coding DNA, the deletions did not modify or generate microRNA binding sites, but instead disrupted the sequence context of the final cleavage and polyadenylation site necessary for protein production: By iFoldRNA, an AAUAAA-adjacent 16 nucleotide deletion brought the cleavage site into inaccessible neighboring secondary structures, while a 4-nucleotide deletion unfolded the downstream RNA polymerase II roadblock. Monocyte SMAD4 RNA expression differed between patients and controls in resting and cycloheximide-stressed states. Patterns predicted the mutational site for an unrelated case, where a complex insertion was subsequently identified. In conclusion, a new type of functional rare variant is described, exposing novel regulatory systems based on polyadenylation. Extension of coding sequence-focused gene panels is required to capture these variants.