Biological soil crusts (BSCs) are formed by phototrophic organisms at the soil surface and play a key role in structuring microbial communities and biogeochemical processes in dryland ecosystems. Similar surface associated communities occur in temperate agricultural soils, but their development, assembly dynamics and functional significance remain poorly understood. We investigated the temporal development of the soil surface microbiome following tillage and during subsequent growth of a winter wheat crop, integrating multi-kingdom amplicon sequencing with metagenomic analysis to track phototrophic, bacterial, fungal and protist communities, together with co-amplified macroscopic phototrophs. Distinct surface communities of phototrophs, bacteria and protists established rapidly, within 4 weeks of tillage, and underwent marked succession from early dominance by yellow-green algae (Xanthophyceae) to cyanobacteria, charophytes and ultimately mosses. Across all taxonomic groups, community assembly at the soil surface increasingly shifted towards dispersal limitation over time, whereas bulk soil communities were predominantly shaped by ecological drift. By the end of the growing season, the soil surface had developed a functional profile distinct from bulk soil, characterised by a greater representation of photosynthetic processes, largely due to eukaryotic algal carbon fixation, alongside increased genetic potential for heterotrophic carbon, nitrogen, phosphorus and sulphur cycling. These functional shifts were associated with enrichment of Actinobacteria, Bacteroidetes and Proteobacteria. Our results demonstrate that the soil surface of temperate agricultural systems represents a dynamic and functionally differentiated microbial habitat, which shares key biological features with dryland BSCs while exhibiting distinct functional and successional trajectories, revealing an overlooked component of managed temperate ecosystems.

Surface flow constructed wetlands (CWs) are a nature-based wastewater treatment technology designed to serve as a buffer between wastewater treatment plants (WWTPs) and the receiving environment. While the treatment efficacy of CWs has been investigated, surface flow systems are susceptible to hydraulic inefficiencies, and a comprehensive understanding of the factors influencing pollutant transport remains limited, hindering their optimisation and predictability. The hydraulic performance of a CW, determined by the efficiency of flow hydrodynamics, dictates the residence time and spatial interactions between pollutant-laden water and purification mechanisms, such as those provided by vegetation and substrate. However, unstandardised designs and a limited understanding of water-sediment-plant interactions often result in sub-optimal hydraulic conditions, such as short-circuiting and dead zones, which impair treatment efficiency. This study investigates the influence of inter-seasonal climate variability, vegetation growth cycles, and operational conditions on the interplay between hydraulic performance, and subsequent pollution removal efficacy, in a full-scale integrated surface flow CW located in Norfolk, UK. Five tracer test campaigns were conducted during 2022-2023 using Rhodamine WT dye and fluorometric sensors to evaluate seasonal variations in hydraulic behaviour across four interconnected vegetated Cells. Hydraulic performance was characterised using indices such as mean residence time, tank-in-series model, hydraulic efficiency, effective volume ratio, short-circuiting, mixing, and dispersion coefficients. To understand the roles of CW design, operation, vegetation, and climate on hydraulic performance, high-resolution LiDAR vegetation scans, nutrient concentrations, and climate monitoring data were collected concurrently with the tracer tests. The combined mean residence time ranged from 30.03 h in autumn to 47.67 h in summer. Individual Cell hydraulic indexes revealed significant non-uniform flow patterns, with 80 % of tracer tests indicating poor (λ < 0.5) hydraulic efficiency and 55 % exhibiting dead zones occupying >50 % of the Cell volume. These inefficiencies were predominantly driven by smaller Cell geometries, sub-optimal inlet-outlet configurations, high influent hydraulic loading rates (0.47 to 0.66 m3/day/m2), and high emergent vegetation cover. Despite these hydraulic deviations, Cell nutrient removal performance was more strongly influenced by vegetation growth stage and seasonal water physicochemical conditions. These findings provide novel field-scale data into how design, seasonal, and operational factors influence CW performance, highlighting the critical need for enhanced design and management strategies to optimise hydraulic and treatment performance in CWs, particularly in climate variability.

Free-water surface constructed wetlands (CWs) are sustainable, low emission, nature-based solutions for water and wastewater treatment. However, the discharge of nutrient-rich effluents from CWs treating wastewater can adversely impact freshwater ecosystems and exacerbate eutrophication. Despite their ecological benefits, limited research exists on the treatment efficiency and pollutant dynamics of CWs under varying seasonal and environmental pressures. This study investigates the treatment efficiency of an integrated CW (ICW) serving as a nature-based solution for treating partially treated wastewater before release into the environment. Located in Ingoldisthorpe, Norfolk, near the East coast of the UK, the ICW receives 1014 +/- 538 m3/day of effluent from a wastewater treatment plant (WWTP). The system comprises four interconnected vegetated ponds (i.e. Cell) with a mean effective volume of 2697 m3, operating at an average depth of 0.19 m. Seasonal variations in vegetation density and coverage range from sparse in winter and spring to dense in summer and autumn. Bi-monthly field investigations were conducted over one year (August 2022-June 2023) to examine the impacts of inter-seasonal climate variability on the ICW's treatment performance. Removal rates of solute and solid pollutants, including nitrate (NH3-), nitrate-nitrogen (NH3- N), ammonium (NH4+), total nitrogen (TN) orthophosphate (PO43- ), sulphate (SO42- ), non-purgeable total organic carbon (NPOC), total inorganic carbon (TIC), and total solids (TS), were quantified. Significant seasonal variations were observed in Concentration Removal Rates (CRR) and Mass Removal Rates (MRR) for all nutrients. Nitrate CRRs ranged from -39.1 % to +51.64 %, corresponding to reductions of up to 14.57 mg/L and increases of 26.71 mg/L in effluent concentrations, while MMRs varied between -77.13 % to +84.25 %, reflecting changes of -38.93 kg/day to +26.69 kg/day. For phosphate, CRRs ranged from -22.79 % to +2.57 %, and MMRs ranged from -71 % to +93.22 %, equivalent to -0.57 kg/day to +0.26 kg/day. These findings highlight the dynamic and sensitive mechanisms influencing nutrient removal in CWs, driven by seasonal hydraulic conditions, vegetation phenology, and climatic factors. The study provides critical insights for optimizing CW design and management under fluctuating environmental conditions to enhance their resilience, ensure regulatory compliance, and maintain long-term treatment efficiency. This understanding is essential for guiding future regulatory policies and ensuring that CWs meet water quality standards in response to climate pressures.

The transport of microplastics in the hyporheic zone remains poorly understood with few studies attempting to quantify microplastic hyporheic exchange processes. A laboratory scale erosimeter was utilized in combination with fluorometric techniques to experimentally quantify the dispersion of 3D pore-scale microplastics across the hyporheic zone. Rhodamine WT dye, Polypropylene (PP), polyethylene (PE), and polymethyl methacrylate (PMMA) were well-mixed within the riverbed and individually tested using solute transport theory for three sediment diameters and five bed shear velocities (u∗) common in the natural environment. Effective dispersion coefficients for solutes significantly differed from that of PE and PMMA in most cases, where their critical sinking velocity within sediment pore water was observed and a method for predicting polymer dispersion was proposed. When u∗ ≥ 0.0304 m/s, PMMA followed similar pathways to solutes and the effective dispersion scaling model was successfully implemented to predict its fate. PP near the riverbed interface ascended to the surface but was immobilized deeper in the riverbed, likely due to aggregation and flocculation processes. When polymer buoyancy became the dominant process, high concentrations of lighter than water microplastics ascended into the water column and high concentrations of denser than water microplastics descended through pore water, which is concerning for real-world groundwater systems. These findings provide valuable insights to guide future policy and mitigation strategies of microplastic contamination in fluvial systems by advancing our understanding of microplastic transport. Further data collection will enhance our ability to accurately quantify these transport processes and strengthen mitigation efforts, especially within high permeability sediments.

A novel carbon monoxide (CO)-oxidizing bacterial strain designated as SB112T was enriched and isolated from Ilex aquifolium leaves from Tocil Wood Nature Reserve in Coventry, UK. The strain was Gram reaction-negative, aerobic, rod-shaped, motile with a polar flagellum and non-spore-forming. Growth of strain SB112T was observed at 10-45 °C, pH 6.0-12.0 and NaCl concentrations of 1-3%. The genomic DNA G+C content was 58.3 mol%, and the major fatty acids (>10%) of strain SB112T were C18 : 1 ω7c, C18 : 1 ω7c 11-methyl and C19 : 0 cyclo ω7c. Major polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol and a phospholipid. Strain SB112ᵀ contains ubiquinone-10 as the major respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SB112T formed a separate lineage within the family Phyllobacteriaceae, showing sequence identities of 97.7%, 97.6% and 97.5%, with its closest relatives Aminobacter niigataensis, Aminobacter aminovorans and Mesorhizobium plurifarium, respectively. Phylogenomic analyses using whole-genome sequences consistently placed this strain within the family Phyllobacteriaceae. However, its phylogenetic position did not correspond to any known genus within this family. The genome of strain SB112T was found to possess the form II coxL gene, which encodes the large subunit of the CO dehydrogenase and potentially enables CO oxidation. The average nucleotide identity and digital DNA-DNA hybridization with members of closely related genera yielded values below the thresholds for prokaryotic species delineation (95-96 and 70%, respectively). Based on the phenotypic, chemotaxonomic, phylogenetic, genomic and physiological properties, strain SB112T is considered to represent a novel species of a new genus Foliimonas within the family Phyllobacteriaceae for which the name Foliimonas ilicis gen. nov., sp. nov. is proposed. The type of strain is SB112T (=LMG 33802T, =NCAIM B.02691T).

Recent evidence shows that arbuscular mycorrhizal (AM) symbiosis, as defined by the presence of arbuscules, is established by two distinct fungal groups, with the distinctive ‘fine root endophyte’ morphotype formed by fungi from the subphylum Mucoromycotina rather than the sub-phylum Glomeromycotina. While FRE forming fungi are globally distributed, there is currently no understanding of the genomic basis for their symbiosis or how this symbiosis compares to that of other mycorrhizal symbionts. We used culture-independent metagenome sequencing to assemble and characterise the metagenome-assembled genome (MAG) of a putative arbuscule forming fine root endophyte, which we show belonged to the family Planticonsortiaceae within the order Densosporales. The MAG shares key traits with Glomeromycotina fungi, which indicate obligate biotrophy, including the absence of fatty acid and thiamine biosynthesis pathways, limited enzymatic abilities to degrade plant cell walls, and a high abundance of calcium transporters. In contrast to Glomeromycotina fungi, it exhibits a higher capacity for degradation of microbial cell walls, a complete cellulose degradation pathway, low abundances of copper, nitrate and ammonium transporters, and a complete pathway for vitamin B6 biosynthesis. These differences, particularly those typically associated with saprotrophic functions, highlight the potential for contrasting interactions between Mucoromycotina and Glomeromycotina fungi with their host plant and the environment. In turn, this could support niche differentiation in resource acquisition and complementary ecological functions.

Additional file 3. Lists of bacterial and fungal OTUs identified as rhythmic through analysis of a 72-hour time-course under 12L12D.

Background The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions. Results Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape ( Brassica napus L.). By recovering 1,059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of “Kill-the-Winner” dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of “viral priming”, which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation. Conclusions Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability.

The rhizosphere microbiome is a major determinant of plant health, which can interact with the host directly and indirectly to promote or suppress productivity. Oil palm is one of the world's most important crops, constituting over a third of global vegetable oil production. Currently there is little understanding of the oil palm microbiome and its contribution to plant health and productivity, with existing knowledge based almost entirely on culture dependent studies. We investigated the diversity and composition of the oil palm fungal microbiome in the bulk soil, rhizosphere soil, and roots of 2-, 18-, and 35-year old plantations in Selangor, Malaysia. The fungal community showed substantial variation between the plantations, accounting for 19.7% of community composition, with compartment (root, rhizosphere soil, and bulk soil), and soil properties (pH, C, N, and P) contributing 6.5 and 7.2% of community variation, respectively. Rhizosphere soil and roots supported distinct communities compared to the bulk soil, with significant enrichment of Agaricomycetes, Glomeromycetes, and Lecanoromycetes in roots. Several putative plant pathogens were abundant in roots in all the plantations, including taxa related to Prospodicola mexicana and Pleurostoma sp. The mycorrhizal status and dependency of oil palm has yet to be established, and using 18S rRNA primers we found considerable between-site variation in Glomeromycotinian community composition, accounting for 31.2% of variation. There was evidence for the selection of Glomeromycotinian communities in oil palm roots in the older plantations but compartment had a weak effect on community composition, accounting for 3.9% of variation, while soil variables accounted for 9% of community variation. While diverse Mucoromycotinian fungi were detected, they showed very low abundance and diversity within roots compared to bulk soil, and were not closely related to taxa which have been linked to fine root endophyte mycorrhizal morphology. Many of the fungal sequences showed low similarity to established genera, indicating the presence of substantial novel diversity with significance for plant health within the oil palm microbiome.

There is great interest in using biochar (BC) as a soil amendment to provide a long-term repository of carbon to mitigate climate change. BC can have major impacts on soil biogeochemical cycling processes, largely by the sorption and protection of organic matter from microbial turnover. Application of BC to agricultural soil could also affect the efficacy, fate and environmental impact of pesticides. In the current study we investigated the effect of BC on bioavailability of the fungicide azoxystrobin in soil. We found that application of BC had no effect on sorption or degradation of azoxystrobin, even at a rate of 2% w/w. While azoxystrobin reduced dehydrogenase activity, BC addition greatly increased dehydrogenase, although the inhibitory effect of azoxystrobin was still evident in BC amended soil. Using Terminal Restriction Fragment Length Polymorphism of fungal SSU rRNA gene ITS regions it was found that azoxystrobin altered the structure of the soil fungal community, although this effect was dampened by BC addition. BC application had minor effects on fungal community structure. We conclude that measurement of the effect of BC on pesticide bioavailability by analysis of biodegradation rate and non-target effects on fungal community structure gave contrasting conclusions.

There is considerable current interest in using biochar (BC) as a soil amendment to sequester carbon to mitigate climate change. However, the implications of adding BC to agricultural soil for the environmental fate of pesticides remain unclear. In particular, the effect of biochars on desorption behavior of compounds is poorly understood. This study examined the influence of BC on pesticide chemical and biological accessibility using the herbicide isoproturon (IPU). Soils amended with 1% and 2% BC showed enhanced sorption, slower desorption, and reduced biodegradation of IPU. Addition of 0.1% BC had no effect on sorption, desorption or biodegradation of IPU. However, the mineralization of (14)C-IPU was reduced by all BC concentrations, reducing by 13.6%, 40.1% and 49.8% at BC concentrations of 0.1%, 1% and 2% respectively. Further, the ratio of the toxic metabolite 4-isopropyl-aniline to intact IPU was substantially reduced by higher BC concentrations. Hydroxypropyl-β-cyclodextrin (HPCD) extractions were used to estimate the IPU bioaccessibility in the BC-amended soil. Significant correlations were found between HPCD-extracted (14)C-IPU and the IPU desorbed (%) (r(2)=0.8518, p<0.01), and also the (14)C-IPU mineralized (%) (r(2)=0.733; p<0.01) for all BC-amended soils. This study clearly demonstrates how desorption in the presence of BC is intimately related to pesticide biodegradation by the indigenous soil microbiota. BC application to agricultural soils can affect the persistence of pesticides as well as the fate of their degradation products. This has important implications for the effectiveness of pesticides as well as the sequestration of contaminants in soils.