Interpersonal variability of the human gut virome confounds disease signal detection in IBD.

Viruses are increasingly recognised as important components of the human microbiome, fulfilling numerous ecological roles including bacterial predation, immune stimulation, genetic diversification, horizontal gene transfer, microbial interactions, and augmentation of metabolic functions. However, our current view of the human gut virome is tainted by previous sequencing requirements that necessitated the amplification of starting nucleic acids. In this study, we performed an original longitudinal analysis of 40 healthy control, 19 Crohn's disease, and 20 ulcerative colitis viromes over three time points without an amplification bias, which revealed and highlighted the interpersonal individuality of the human gut virome. In contrast to a 16 S rRNA gene analysis of matched samples, we show that α- and ß-diversity metrics of unamplified viromes are not as efficient at discerning controls from patients with inflammatory bowel disease. Additionally, we explored the intrinsic properties of unamplified gut viromes and show there is considerable interpersonal variability in viral taxa, infrequent longitudinal persistence of intrapersonal viruses, and vast fluctuations in the abundance of temporal viruses. Together, these properties of unamplified faecal viromes confound the ability to discern disease associations but significantly advance toward an unbiased and accurate representation of the human gut virome.

Factors controlling shallow subsurface dissolved reactive phosphorus concentration and loss kinetics from poorly drained saturated grassland soils.

Shallow subsurface pathways dominate dissolved reactive phosphorus (DRP) losses in grassland soils that are: poorly drained, shallow, or have a perched water table in wetter months causing saturation-excess runoff. Saturated conditions can lead to anoxia, which can accelerate phosphorus (P) loss. Two scales of investigation were utilized in this study. First, at the field scale, soil cores were extracted to 2.5 m, subdivided and samples extracted using water extractable P (WEP) and sodium-bicarbonate-dithionite extractable P (NaBD-P). Second, at the laboratory scale, detailed incubation studies using field-moist grassland topsoils from sites in Ireland and New Zealand examined the kinetics of WEP under anoxic (WEPanox ) and oxic (WEPox ) conditions with imposed temperature and soil P fertilizer input treatments. Results from soil-core samples showed that redox-sensitive NaBD-P concentrations were depleted where artificial drainage lines were installed (100 cm deep), but WEP concentrations available to shallow flow were enriched in topsoil. The laboratory scale incubation experiment investigated the influence of temperature (3 vs. 18 °C), anoxia (designed to simulate saturation following a rainfall event), and superphosphate fertilizer (10 to 60 kg P ha-1  yr-1 ) on WEP concentrations over 24 h in three grassland topsoils (clay, silt, and sandy loam textures). Concentrations increased with fertilizer rate, temperature, and-in two soils-anoxic conditions. This was commensurate with nitrate (NO3 - ) depletion and the reductive dissolution of iron and manganese. The release of P during anoxia was complete within 24 h. The results highlighted late winter to spring as the riskiest period for topsoil P losses in shallow subsurface flow due to wet soil conditions, increasing temperatures, and low soil NO3 - concentrations. This knowledge highlights the necessity to consider and refine tests used to assess topsoil P loss risk, where in the landscape P losses are likely, and what strategies can be used to mitigate losses.

A comparative study of thermally and chemically treated dairy waste: Impacts on soil phosphorus turnover and availability using 33P isotope dilution.

Dairy processing sludge (DPS) and DPS-derived secondary products such as struvite, biochar, hydrochar and ash (collectively known as SRUBIAS) are emerging as alternatives to fertilizers produced from mined rock phosphate. However, little is known about how these products affect soil P availability and daily P turnover rates.. A lack of such information prevents precision nutrient management planning using these products out on farms. This study used a novel isotope dilution technique (IPD) with 33P as a tracer to compare P turnover in soils amended with chemically (alum-treated DPS and struvite) and thermally (biochar, hydrochar, ash) treated DPS. Results showed that thermally treated products exhibited poor agronomic performance as P fertilizers, potentially inhibiting P availability when applied to soils. For example, a P deficient soil amended with hydrochar treatment at the highest application rates did not record a build-up of available P to agronomic target values. In ash and biochar treated P deficient soils, available P increased but only with very high application rates of 150 and 80 mg P kg -1. The application of these products as fertilizers could have negative implications for both environmental and agronomic goals. Conversely, chemically treated fertilisers demonstrated better agronomic performance. The same agronomic target value was reached with application rates of only 20 mg P kg -1 soil for DPS and 50 mg P kg -1 soil for struvite. However, the techniques deployed revealed that these products exhibited slower rates of available and exchangeable P build-up when compared with chemical fertilisers. This suggests that these bio-based alternatives require higher application rates or earlier application times compared to conventional chemical fertilizers. Regulations providing advice on P use in agricultural soils need to account for slower P turnover in soils receiving recycled fertilizers. The IPD technique is transferrable to all wastes to examine their performance as fertilizers.

A comparative study of MIR and NIR spectral models using ball-milled and sieved soil for the prediction of a range soil physical and chemical parameters.

This study evaluated the influence on predicted physical and chemical parameters of soil particle sizes commonly used in the infrared spectra acquisition, < 0.100 mm (ball-milled) and < 2 mm for MIR and NIR ranges, respectively. The influences were evaluated through the accuracy (RMSEP and RPIQ) results and the chemical information extracted by multivariate classification and regression models. For this a national population of soils containing 888 samples from 225 modal soil profiles, each with the reference values of sand, silt, clay, pH(CaCl2), pH(Water), total carbon, organic carbon (OC), cation exchange capacity, nitrogen, aluminium and bulk density, was used. Spectra were collected in MIR and NIR ranges using samples with both particle sizes. For each soil attribute, 29 random calibration and validation sets were generated and SVM, PLS and Cubist regression models were built. This same strategy was used to classify the soil samples according to their respective horizons (1 or 2-7) using SVM, PLS-DA and random forest algorithms. Results obtained by the randomised calibration and validation set did not present positive or negative bias on the RMSEP and RPIQ values based on soil particle sizes. In general, random variations of the RMSEP and RPIQ values were observed for all soil attributes. In addition, ball-milled and < 2 mm spectral models did not present large differences in both accuracy parameters simultaneously. The median Matthews correlation coefficient values calculated by the classification models showed minor variations of 2.61% and 0.65% for samples from both particle sizes in MIR and NIR ranges, respectively. The 'Variable Importance in Projection' or VIP scores, calculated by PLS and PLS-DA models, did not show any large variation in the chemical information extracted from MIR and NIR spectra for models built using samples from both particle sizes. The results from this study show that scanning ball-milled or < 2 mm sieved soil samples will result in spectra models in MIR and NIR ranges with the same accuracy and same chemical information. This suggests there is a big potential to eliminate the ball-milling sample step in soil laboratories that use MIR and NIR vibrational spectroscopy techniques to predict soil attributes, thereby reducing the time and costs associated with soil analysis.

Investigation of differential levels of phosphorus fixation in dolomite and calcium carbonate amended red soil.

BACKGROUND: The pH adjustment of acidic red soils with lime materials is beneficial for the reduction of phosphorus (P) fixation. However, the reasons for varying levels of P activation after adding different lime materials have not been fully investigated. Therefore, this study examined changes in soil labile P and P forms after phosphate application to calcium carbonate (CaCO3 ) and dolomite amended red soil during a 120-day incubation period. Also change of P sorption properties in the amended soil samples from day 120 were examined through a sorption-desorption experiment. RESULTS: The increase of soil H2 O-P and NaHCO3 -P in the CaCO3 and dolomite amended soil treatments was mainly ascribed to the decline of the NaOH-P. However, when compared with the control treatment after 120 days, soil Olsen-P significantly increased by 34% and 66% in the CaCO3 and dolomite treatments. The Hedley P fractionation results demonstrated that the CaCO3 application caused a notable increase of HCl-P (stable Ca-P), which was 88.4% higher than that in the dolomite treatment. However, the formation of stable P was strongly suppressed in the dolomite treatment due to the presence of magnesium (Mg), which was identified by the negative relationship between M3-Mg and HCl-P. In line with these findings, P sorption-desorption work showed weaker P binding energy in the dolomite treatment relative to the CaCO3 treatment. CONCLUSION: In terms of increasing P availability in red soil, this study suggests that dolomite should be used to substitute CaCO3 in order to reduce the soil P fixation. © 2021 Society of Chemical Industry.

Trends and influential factors of high ecological status mobility in Irish Rivers.

The decline in high ecological water status in rivers is a significant concern in European countries. It is thus important to investigate the factors that cause sites to lose high status in order to undertake measures to protect and restore high status water quality. Analysis of 20 years of water quality data reveals strong mobility between high status and non-high status (especially good status) rivers. Associations between this mobility and socio-economic and physical environmental variables were estimated by multinomial logistic regression at national scale and regional scale. Based on reported changes in water quality status cross across 1990, 2000 and 2010, four classes of the mobility of high status were defined in this study: those sites that maintain high status (maintain), enter high status (enter), fluctuate between high and non-high status (fluctuate) and exit from high status (exit). The national results indicate that agricultural activity as indicated by variables representing intensity of livestock farming (organic nitrogen) and tillage farming (cereal share) and elevation had significant negative impacts on high status rivers. Meanwhile, significant differences in population density and septic tank density between 'exit', 'maintain', 'fluctuate' and 'enter' classes indicate that these factors played important roles in the stability of high status rivers. The regional outcomes reveal differential significant pressures across regions. For example, rainfall and elevation had positive impacts on high status rivers in the north-west region, while organic nitrogen had a negative effect in the south-west. This paper demonstrates the challenge in achieving the Water Framework Directive goal of maintaining high status rivers, given the sensitive and highly differentiated nature of areas that have lost high status or fluctuated in and out of high status. This paper also suggests the necessity for localised policies and mitigation measures.

Leached phosphorus apportionment and future management strategies across the main soil areas and cropping system types in northern China.

Excess phosphorus (P) leached from high fertiliser input cropping systems in northern China is having detrimental effects on water quality. Before improved management can be directed at specific soils and cropping system types estimates of P leached loss apportionment and mitigation potentials across the main soil (fluvo-aquic soil, FAS; cinnamon soil, CS; black soil, BS) areas and cropping systems (protected vegetable fields, PVFs; open vegetable fields, OVFs; cereal fields, CFs) are needed. The present study designed and implemented conventional fertilisation and low input system trials at 75 sites inclusive of these main soils and cropping system types in northern China. At all sites, a uniform lysimeter design (to 0.9 m depth) enabled the collection and analysis of leachate samples from 7578 individual events between 2008 and 2018. In addition, site-specific static and dynamic activity data were recorded. Results showed that annual total phosphorus (TP) leached losses across the main soil areas and cropping systems were 4.99 × 106 kg in northern China. A major finding was PVFs contributed to 48.5% of the TP leached losses but only accounted for 5.7% of the total cropping areas. The CFs and OVFs accounted for 40.3% and 11.2% of the TP leached losses, respectively. Across northern China, the TP leached losses in PVFs and OVFs were greatest in FAS areas followed by CS and BS areas. The higher TP leached losses in FAS areas were closely correlated with greater P fertiliser inputs and irrigation practices. From a management perspective in PVFs and OVFs systems, a decrease of P inputs by 10-30% would not negatively affect yields while protecting water quality. The present study highlights the importance of decreasing P inputs in PVFs and OVFs and supporting soil P nutrient advocacy for farmers in China.

Reductive dissolution of phosphorus associated with iron-oxides during saturation in agricultural soil profiles.

In soils with a fragipan or poor permeability, water may remain in a soil profile long enough to make it anoxic and reductive. The reductive dissolution of iron (Fe)- and manganese (Mn)-oxides can release associated phosphorus (P). Therefore, the dissolved P would be vulnerable to subsurface flow and could contaminate nearby streams. It was hypothesized that single rainfall events could cause subsurface P concentrations to increase via reductive dissolution in wet winter-spring conditions. Also, dissolution-being microbially mediated-would be buffered by the presence of nitrate (NO3 - ), which is preferred as an electron acceptor over Fe and Mn in microbial reactions. Unsaturated zone monitoring occurred from May to September in 2017 and 2019, using Teflon suction cups below the surface of a grassland soil in New Zealand. Events in July and August in 2017 and 2019 resulted in reducing conditions [Fe(III)/sulfate-reducing] and up to 77 and 96% greater P and Fe release, respectively. In an additional experiment in 2019, 100 mm of flood irrigation was applied, and 10 mg NO3 - -N + carbon was injected into half the cups at the site. The other cups received no N. Cups treated with N yielded up to 45% total dissolved P and 21% less Fe than the no-N cups. A laboratory incubation of soils from the site confirmed that NO3 - inhibited P release. This effect may act to decrease the amount of P lost in subsurface flow in systems regularly fertilized with N but should not be relied on as a method to mitigate P losses.

Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens.

BACKGROUND: The gut phageome comprises a complex phage community of thousands of individual strains, with a few highly abundant bacteriophages. CrAss-like phages, which infect bacteria of the order Bacteroidales, are the most abundant bacteriophage family in the human gut and make an important contribution to an individual's core virome. Based on metagenomic data, crAss-like phages form a family, with four sub-families and ten candidate genera. To date, only three representatives isolated in pure culture have been reported: ΦcrAss001 and two closely related phages DAC15 and DAC17; all are members of the less abundant candidate genus VI. The persistence at high levels of both crAss-like phage and their Bacteroidales hosts in the human gut has not been explained mechanistically, and this phage-host relationship can only be properly studied with isolated phage-host pairs from as many genera as possible. RESULTS: Faeces from a healthy donor with high levels of crAss-like phage was used to initiate a faecal fermentation in a chemostat, with selected antibiotics chosen to inhibit rapidly growing bacteria and selectively enrich for Gram-negative Bacteroidales. This had the objective of promoting the simultaneous expansion of crAss-like phages on their native hosts. The levels of seven different crAss-like phages expanded during the fermentation, indicating that their hosts were also present in the fermenter. The enriched supernatant was then tested against individual Bacteroidales strains isolated from the same faecal sample. This resulted in the isolation of a previously uncharacterised crAss-like phage of candidate genus IV of the proposed Alphacrassvirinae sub-family, ΦcrAss002, that infects the gut commensal Bacteroides xylanisolvens. ΦcrAss002 does not form plaques or spots on lawns of sensitive cells, nor does it lyse liquid cultures, even at high titres. In keeping with the co-abundance of phage and host in the human gut, ΦcrAss002 and Bacteroides xylanisolvens can also co-exist at high levels when co-cultured in laboratory media. CONCLUSIONS: We report the isolation and characterisation of ΦcrAss002, the first representative of the proposed Alphacrassvirinae sub-family of crAss-like phages. ΦcrAss002 cannot form plaques or spots on bacterial lawns but can co-exist with its host, Bacteroides xylanisolvens, at very high levels in liquid culture without impacting on bacterial numbers. Video abstract.

Proximal seminal vesicle displacement and margins for prostate cancer radiotherapy.

INTRODUCTION: Guidelines recommend that the proximal seminal vesicles (PrSV) should be included in the clinical target volume for locally advanced prostate cancer patients undergoing radiotherapy. Verification and margins for the prostate may not necessarily account for PrSV displacement. The purpose was to determine the inter-fraction displacement of the PrSV relative to the prostate during radiotherapy. METHODS: Fiducials were inserted into the prostate, and right and left PrSV (RSV and LSV) in 30 prostate cancer patients. Correctional shifts for the prostate, right and left PrSV and pelvic bones were determined from each patient's 39 daily orthogonal portal images relative to reference digitally reconstructed radiographs. RESULTS: There was a significant displacement of the RSV relative to the prostate in all directions: on average 0.38 mm (95% confidence interval (CI) 0.26 to 0.50) to the left, 0.80-0.81 mm (CI 0.68 to 0.93) superiorly and 1.51 mm (CI 1.36 to 1.65) posteriorly. The LSV was significantly displaced superiorly to the prostate 1.09-1.13 mm (CI 0.97 to 1.25) and posteriorly 1.81 mm (CI 1.67 to 1.96), but not laterally (mean 0.06, CI -0.06 to 0.18). The calculated PTV margins (left-right, superior-inferior, posterior-anterior) were 4.9, 5.3-5.6 and 4.8 mm for the prostate, 5.2, 7.1-8.0 and 9.7 mm for the RSV, and 7.2, 7.5-7.6 and 8.6 mm for the LSV. CONCLUSION: There is a significant displacement of the PrSV relative to the prostate during radiotherapy. Greater margins are recommended for the PrSV compared to the prostate.

Alum split applications strengthened phosphorus fixation and phosphate sorption in high legacy phosphorus calcareous soil.

High phosphorus (P) saturation arising from historic P inputs to protected vegetable fields (PVFs) drives high P mobilisation to waterbodies. Amendment of soils with alum has shown potential in terms of fixing labile P and protecting water quality. The present 15 month pot experiment investigated P stabilisation across single alum application (Alum-1 treatment, 20 g alum/kg soil incorporated into soil before the maize was sown), alum split applications (Alum-4 treatment, 5 g alum/kg soil incorporated into soil before each crop was sown i.e. 4 × 5 g/kg) and soil only treatment (Control). Results showed that the Alum-1 treatment caused the strongest stabilisation of soil labile P after maize plant removal, whereas the P stabilisation effect was gradually weakened due to the transformation of soil non-labile P to labile P and the reduced active Al3+ in soil solution. For the Alum-4 treatment, soil labile P decreased gradually with each crop planting and was lower than the Alum-1 treatment at the end of the final crop removal, without any impairment on plant growth. The better P stabilisation at the end of Alum-4 treatment was closely correlated with a progressive supply of Al3+ and a gradual decrease of pH, which resulted in higher contents of poorly-crystalline Al, Fe and exchangeable Ca. These aspects were conducive to increasing the soil P stabilisation and phosphate sorption. In terms of management, growers in continuous cropping systems could utilise split alum applications as a strategy to alleviate P losses in high-P enriched calcareous soil.

Assessing the impact of fine sediment on high status river sites.

The European Union (EU) Water Framework Directive (WFD) designates as "high status" rivers, lakes, transitional and coastal waters that are close to natural status and relatively un-impacted by anthropogenic activities. These high status water-bodies (HSWs) are sensitive areas that require special attention. Ireland had a globally important distribution of HSWs (10.5% of rivers and 16.2% of lakes classified as high ecological status in Europe occurred in Ireland), but there have been declines of almost 50% between 1987 and 2018, with excessive sediment implicated as a pressure. In this study, an extensive assessment of macro-invertebrate sediment metrics were used to assess sediment as a pressure in sixty-five high or formerly high status river sites in Ireland that were determined to have either: "Lost" their high status (e.g. gone from high to good, moderate, poor or bad; 20 sites); consistently "Maintained" high status (24 sites); or "Gained" in status (e.g. from good to high; 21 sites). Macro-invertebrate taxa occurring in the sixty-five sites were pre-dominantly sediment sensitive taxa. However, for two specific sediment metrics, the Proportion of Sediment-sensitive Index (PSI) and the Empirically-weighted PSI (E-PSI), significant differences were observed between sites that Lost status and those that Maintained status, implying that at some sites, sediment is impacting on macro-invertebrates. However, no significant difference between Lost and Gained sites was observed, leaving an important caveat. While weak to moderate relationships were observed between the macro-invertebrate sediment metrics and the physical sediment variables, no difference between status categories for any of the physical sediment variables was observed. Further research priorities should consider the sampling resolution of these physical variables (e.g. patch vs reach scale), the properties of sediment (e.g. chemical composition) in addition to concentration, the potential interaction of multiple-stressors, and the life cycle characteristics of invertebrate taxa.

Soil chemical and fertilizer influences on soluble and medium-sized colloidal phosphorus in agricultural soils.

Colloid-facilitated transport can be important for preferential transfer of phosphorus (P) through the soil profile to groundwater and may in part explain elevated P concentrations in surface water during baseflow and particularly high flow conditions. To investigate the potential for colloidal P (Pcoll) mobilisation in soils, this study assessed the role of soil chemical properties and P fertilizer type on medium-sized soil Pcoll (200-450 nm) and its association with soil solution soluble bioavailable P (<450 nm). Hillslope soils from three agricultural catchments were sampled and untreated and treated (cattle slurry and synthetic fertilizer) subsamples were incubated. Soil supernatants were analysed for P and soil Water Dispersible Colloids (WDC) were extracted for analysis of P and P-binding materials. Soils physicochemical properties including degree of P saturation (DPS) and P sorption properties were determined. Results indicated that medium-sized Pcoll was mostly unreactive P associated to some extent to amorphous forms of Fe. Medium-sized Pcoll concentrations correlated negatively with soil maximum P sorption capacity and soluble P concentrations increased with increasing DPS. In soil with low sorption properties, cattle slurry increased soluble P concentrations by 0.008-0.013 mg l-1 and DPS but did not influence medium-sized Pcoll. Synthetic fertilizer increased medium-sized reactive Pcoll by 0.011 mg l-1 (0.088 mg kg-1 soil) and DPS in a soil with lower DPS whereas it decreased it by 0.005 mg l-1 (0.040 mg kg-1 soil) in a soil with higher DPS. Additional soil parameters (M3-Fe, M3-Al, M3-P, and DPS) should be included in soil testing, especially in Cambisol/Podzol soils, to identify critical areas where risks of Pcoll mobilisation are important. Further research should include the roles of finer colloidal and nanoparticulate (<200 nm) soil P fractions and soluble P to inform understanding of plant uptake and assess environmental risk.

Generation of Nonpolar Deletion Mutants in Listeria monocytogenes Using the "SOEing" Method.

The ability to manipulate chromosomally encoded genes is a fundamental biological tool for the analysis of gene function. Here, we provide in greater depth a protocol for the creation of nonpolar unlabelled gene deletions in Listeria monocytogenes that are facilitated by the splicing overlap extension PCR technique. For mutagenesis in L. monocytogenes, we describe the pKSV7 plasmid-based approach, which facilitates the introduction of a spliced amplicon in place of the corresponding segment of chromosomal DNA.

Understanding phosphate sorption characteristics of mineral amendments in relation to stabilising high legacy P calcareous soil.

In China, excessive phosphorus (P) application in protected vegetable fields has led to high legacy P stores. Soil amendment with alum or dolomite is one of many best management practices (BMPs) used to reduce P losses in calcareous soils. However, both the kinetics and mechanisms of P sorption and soil available P in amended soils are understudied. Herein, both aspects were looked at under controlled conditions. Firstly, a sorption study which coupled P concentrations with poorly-crystalline Al hydroxides and dolomite was conducted. Results from this batch experiment showed that P sorption on poorly-crystalline Al hydroxides was homogenous and occurred mainly via displacement of inner-sphere hydroxyl (Al-OH) instead of the formation of AlPO4. However, the amount of sorbed P reached maximum sorption of 73.1 mg g-1 and did not change with further increase in P concentration. It was observed that P adsorbed onto the dolomite surface at low P concentrations, whereas hydroxyl replacement and uneven cluster precipitation of Ca3(PO4)2 occurred at high P concentrations. A second 90 day incubation experiment investigated changes to soil available P and sorption-desorption across variable rates of amendments (0-50 g kg-1). Results showed that alum amendment at a rate of 50 g kg-1 decreased soil CaCl2-P and Olsen-P concentrations by 91.9% and 57.8%, respectively. However, Olsen-P increased when the dolomite rates were <20 g kg-1. Phosphorus sorption-desorption of the amended soil showed alum had higher P sorption efficiency than dolomite at low addition rates (<10 g kg-1). However, soil amended with high dolomite rates (>10 g kg-1) could sorb more P in comparison with alum when P concentrations were increased. The P status of the amended soil was closely connected to the P sorption mechanisms on mineral amendments, soil P concentrations and soil properties.

Ranking connectivity risk for phosphorus loss along agricultural drainage ditches.

Agricultural drainage systems comprising both in-field pipe drains and surface ditches are typically installed to remove excess water from agricultural land. These drainage networks can provide connectivity between phosphorus (P) sources and surface waters thereby increasing the risk of P loss to rivers and streams. The objective of this study was to derive a farm-scale drainage ranking that categorises drainage ditches in terms of P loss risk based on connectivity and physic-chemical characteristics. Ten pilot farms were selected to characterise drainage networks through ground survey and, sediment and water sampling. Five drainage ditch categories were derived based on landscape setting and connectivity. Each category recorded soluble and reactive P concentrations above environmental water quality standards. To assess the risk of surface ditches as a connectivity vector between agricultural P and surface waters ditches were ranked in order of P loss risk by integrating landscape position and sediment P chemistry. Elevated sediment P with high equilibrium P concentration (EPCo) were associated with ditches connected to farm yards, and in sediment sampled at ditch outlets, suggesting P deposition over time indicative of a legacy P source. The greatest risk of P loss was attributed to ditches connecting farm yards to streams, and ditches that connected the drainage network to surface waters, or Outlets. These results rank connectivity risk for P loss along agricultural drainage ditches for farm level risk assessment to target P loss mitigation measures to the appropriate locations.

Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease.

The human gut virome is thought to significantly impact the microbiome and human health. However, most virome analyses have been performed on a limited fraction of known viruses. Using whole-virome analysis on a published keystone inflammatory bowel disease (IBD) cohort and an in-house ulcerative colitis dataset, we shed light on the composition of the human gut virome in IBD beyond this identifiable minority. We observe IBD-specific changes to the virome and increased numbers of temperate phage sequences in individuals with Crohn's disease. Unlike prior database-dependent methods, no changes in viral richness were observed. Among IBD subjects, the changes in virome composition reflected alterations in bacterial composition. Furthermore, incorporating both bacteriome and virome composition offered greater classification power between health and disease. This approach to analyzing whole virome across cohorts highlights significant IBD signals, which may be crucial for developing future biomarkers and therapeutics.

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific.

The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterized, and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. We performed longitudinal metagenomic analysis of fecal viruses in healthy adults that reveal high temporal stability, individual specificity, and correlation with the bacterial microbiome. Using a database-independent approach that uses most of the sequencing data, we uncovered the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of viral genomes and de novo taxonomic annotation identified several groups of crAss-like and Microviridae bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as Bacteroides, Prevotella, and Faecalibacterium. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.

An integrated assessment of nitrogen source, transformation and fate within an intensive dairy system to inform management change.

From an environmental perspective optimised dairy systems, which follow current regulations, still have low nitrogen (N) use efficiency, high N surplus (kg N ha-1) and enable ad-hoc delivery of direct and indirect reactive N losses to water and the atmosphere. The objective of the present study was to divide an intensive dairy farm into N attenuation capacity areas based on this ad-hoc delivery. Historical and current spatial and temporal multi-level datasets (stable isotope and dissolved gas) were combined and interpreted. Results showed that the farm had four distinct attenuation areas: high N attenuation: characterised by ammonium-N (NH4+-N) below 0.23 mg NH4+-N l-1 and nitrate (NO3--N) below 5.65 mg NO3--N l-1 in surface, drainage and groundwater, located on imperfectly to moderately-well drained soils with high denitrification potential and low nitrous oxide (N2O) emissions (av. 0.0032 mg N2O-N l-1); moderate N attenuation: characterised by low NO3--N concentration in drainage water but high N2O production (0.0317 mg N2O-N l-1) and denitrification potential lower than group 1 (av. δ15N-NO3-: 16.4‰, av. δ18O-NO3-: 9.2‰), on well to moderately drained soils; low N attenuation-area 1: characterised by high NO3--N (av. 6.90 mg NO3--N l-1) in drainage water from well to moderately-well drained soils, with low denitrification potential (av. δ15N-NO3-: 9.5‰, av. δ18O-NO3-: 5.9‰) and high N2O emissions (0.0319 mg N2O l-1); and low N attenuation-area 2: characterised by high NH4+-N (av. 3.93 mg NH4+-N l-1 and high N2O emissions (av. 0.0521 mg N2O l-1) from well to imperfectly drained soil. N loads on site should be moved away from low attenuation areas and emissions to air and water should be assessed.

Spatial and temporal variability in costs and effectiveness in phosphorus loss mitigation at farm scale: A scenario analysis.

Current policy instruments under the EU Water Framework Directive (WFD) to mitigate phosphorus (P) loss require that P use on farms is managed through regulation of farm gate P balances. Regulation at farm scale does not account for spatial variability in nutrient use and soil fertility at field scale, affecting the costs and effectiveness of farm gate measures. This study simulated the implementation of a P loss mitigation measure coupled with improving soil fertility so that farm productivity would not be compromised. The measure was simulated at field scale and the costs and effectiveness assessed at farm scale. Effectiveness was expressed as the time taken for excessive soil P levels to decline to levels that matched off-takes and this varied temporally and spatially within and between farms ranging from 1 to 8 years. Sub-optimum soil fertility was corrected on all fields across both farms, with applications of other soil nutrients and lime to protect productivity. An increase in costs ranging from 1.5 to 116% was predicted in the first two years of the measure on both farms after-which savings of 15-31% were predicted for each subsequent year until the measure was effective in year 9. Despite initial cost increase, there was no statistically significant difference in costs over the time taken for the measure to be effective, when compared to baseline costs. Successful implementation of measures should consider the impact on farm costs and time taken for measures to environmentally effective. Adoption of measures could improve if demonstrating to farmers that costs will not vary significantly from current practice and in time may results in savings if measures are paired with correcting soil fertility and increasing yields. This 'win-win' approach could be used into the future to ensure successful implementation and uptake of measures within the farming community.