Daniel Murphy

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.

Microplastics (MPs) and nanoplastics (NPs) are pervasive contaminants in agricultural soils, raising concerns over their environmental fate, food chain infiltration, and potential human health impacts. This review critically examines their primary sources—plastic mulching, biosolids, organic fertilisers, and atmospheric deposition—while distinguishing findings from laboratory, semi-field, and field studies. We assess their effects on soil health, microbial diversity, and crop productivity, emphasising methodological challenges in detecting and quantifying MPs. Plant and soil toxicity studies often use exaggerated MP concentrations (up to 50% by volume), whereas field data indicate much lower yet cumulatively significant levels (typically below 0.1% w/w). This discrepancy reveals the potential for long-term accumulative ecological risks and misrepresentations in many toxicity studies. Accurate toxicity assessments and analytical methodologies are crucial, as exaggerated MP concentrations in studies may misrepresent real-world risks. The review also evaluates plant uptake pathways, exploring bioaccumulation evidence and research discrepancies. In addition, we highlight the role of MPs as carriers of hazardous additives and pollutants, distinguishing their intrinsic effects from those of associated chemicals. A significant gap remains in standardised risk assessments and regulatory frameworks, limiting effective governance despite increasing environmental exposure. We propose future research priorities, including improved detection methods, long-term field studies, environmentally relevant toxicity studies and policy interventions, to mitigate the risks MPs and NPs pose in soil-based food systems. This review highlights the urgent need for coordinated scientific and regulatory efforts to address the growing challenges of agricultural plastic contamination.
Graphical Abstract

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.

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.

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.

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.

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 (µCT) 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 µCT 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 µCT, 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.
[Display omitted]