Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh.

IMPORTANCE: Through the use of DNA sequencing, our study shows that there is no significant difference in the antibiotic resistance genes found in stool samples taken from individuals with high exposure to poultry routinely fed antibiotics and those without such exposure. This finding is significant as it suggests limited transmission of antibiotic resistance genes between poultry and humans in these circumstances. However, our research also demonstrates that commercially reared poultry are more likely to possess resistance genes to antibiotics commonly administered on medium-sized farms. Additionally, our study highlights the under-explored potential of wastewater as a source of various antibiotic resistance genes, some of which are clinically relevant.

Abundance and phylogenetic distribution of eight key enzymes of the phosphorus biogeochemical cycle in grassland soils.

Grassland biomes provide valuable ecosystem services, including nutrient cycling. Organic phosphorus (Po) represents more than half of the total P in soils. Soil microorganisms release organic P through enzymatic processes, with alkaline phosphatases, acid phosphatases and phytases being the key P enzymes involved in the cycling of organic P. This study analysed 74 soil metagenomes from 17 different grassland biomes worldwide to evaluate the distribution and abundance of eight key P enzymes (PhoD, PhoX, PhoA, Nsap-A, Nsap-B, Nsap-C, BPP and CPhy) and their relationship with environmental factors. Our analyses showed that alkaline phosphatase phoD was the dataset's most abundant P-enzyme encoding genes, with a wide phylogenetic distribution. Followed by the acid phosphatases Nsap-A and Nsap-C showed similar abundance but a different distribution in their respective phylogenetic trees. Multivariate analyses revealed that pH, Tmax , SOC and soil moisture were associated with the abundance and diversity of all genes studied. PhoD and phoX genes strongly correlated with SOC and clay, and the phoX gene was more common in soils with low to medium SOC and neutral pH. In particular, P-enzyme genes tended to respond in a positively correlated manner among them, suggesting a complex relationship of abundance and diversity among them.

Arable soil nitrogen dynamics reflect organic inputs via the extended composite phenotype.

Achieving food security requires resilient agricultural systems with improved nutrient-use efficiency, optimized water and nutrient storage in soils, and reduced gaseous emissions. Success relies on understanding coupled nitrogen and carbon metabolism in soils, their associated influences on soil structure and the processes controlling nitrogen transformations at scales relevant to microbial activity. Here we show that the influence of organic matter on arable soil nitrogen transformations can be decoded by integrating metagenomic data with soil structural parameters. Our approach provides a mechanistic explanation of why organic matter is effective in reducing nitrous oxide losses while supporting system resilience. The relationship between organic carbon, soil-connected porosity and flow rates at scales relevant to microbes suggests that important increases in nutrient-use efficiency could be achieved at lower organic carbon stocks than currently envisaged.

An overlooked mechanism underlying the attenuated temperature response of soil heterotrophic respiration.

Biogeochemical reactions occurring in soil pore space underpin gaseous emissions measured at macroscopic scales but are difficult to quantify due to their complexity and heterogeneity. We develop a volumetric-average method to calculate aerobic respiration rates analytically from soil with microscopic soil structure represented explicitly. Soil water content in the model is the result of the volumetric-average of the microscopic processes, and it is nonlinearly coupled with temperature and other factors. Since many biogeochemical reactions are driven by oxygen (O2) which must overcome various resistances before reaching reactive microsites from the atmosphere, the volumetric-average results in negative feedback between temperature and soil respiration, with the magnitude of the feedback increasing with soil water content and substrate quality. Comparisons with various experiments show the model reproduces the variation of carbon dioxide emission from soils under different water content and temperature gradients, indicating that it captures the key microscopic processes underpinning soil respiration. We show that alongside thermal microbial adaptation, substrate heterogeneity and microbial turnover and carbon use efficiency, O2 dissolution and diffusion in water associated with soil pore space is another key explanation for the attenuated temperature response of soil respiration and should be considered in developing soil organic carbon models.

Reduction effect of individual N, P, K fertilization on antibiotic resistance genes in reclaimed water irrigated soil.

The transfer of antibiotic resistance genes (ARGs) in soil under reclaimed water irrigation poses a potential environmental risk. Regulation of NPK fertilizer could influence the behavior of bacterial communities, mobile genetic elements (MGEs), and soil properties, which determine the fate of ARGs. To identify the key element in NPK fertilizer and realize efficient regulation, we explored the effect of individual N, P, K fertilization on ARG variation in tomato rhizosphere and bulk soils. Compared with an unfertilized treatment, N fertilization resulted in greater decreases in the abundance of ARGs (decreases of 24.06%-73.09%) than did either P fertilization (increases of up to 35.84%, decreases of up to 58.80%) or K fertilization (decreases of 13.47%-72.47%). The influence of different forms of N (CO(NH2)2, NaNO3, and NH4HCO3), P (Ca(H2PO4)2 and CaMgO4P+), and K (KCl and K2(SO4)) fertilizers was also investigated in this study, and showed the influence of NaNO3, CaMgO4P+, and K2(SO4) on reducing ARGs abundance was greater in different types of N, P, K fertilizers. Bacterial communities showed the strongest response to N fertilization. The reduced bacterial diversity and abundance of ARG-host and non-host organisms explained the decline of total ARG abundance in soil. In soils fertilized with either P or K, the effect of soil properties, especially total nitrogen and pH, on ARG variation was greater than that of bacterial community and MGEs. These results suggest that N regulation of in NPK fertilizer may be an effective way to reduce the risks of ARGs in soil associated with reclaimed water irrigation.

Cropping system exerts stronger influence on antibiotic resistance gene assemblages in greenhouse soils than reclaimed wastewater irrigation.

The effects of reclaimed wastewater (RW) irrigation on the spread of antibiotic resistance genes (ARGs) in soil is modulated by a myriad of biotic and abiotic factors and their relative significance remains vague. We compared microbial communities, assemblages of genes associated with microbial resistance to antibiotics, biocides and metals, and insertion sequences (ISs) in soils following 16 years of irrigation with groundwater (GW), RW or alternately with GW and RW in two greenhouses with different cropping systems, using shotgun metagenome sequencing. The results showed that cropping system exerted greater influence than irrigation on the profile of ISs and resistance genes. This influence was most strongly associated with concentrations of copper, mercury and perfloxacin in the soils. There was no significant difference in soil ARG profiles between continuous RW irrigation and alternating GW and RW irrigation. Proteobacteria, Actinobacteria and Firmicutes and a limited number of ISs were closely associated with the detected ARGs. Most ARGs were found to co-occur with metal and biocide resistance genes through the mechanism of efflux pumps. These findings highlight the significance of understanding and improving crop management in mitigating the dissemination of ARGs in soils irrigated with RW.

Poor Competitiveness of Bradyrhizobium in Pigeon Pea Root Colonization in Indian Soils.

Pigeon pea, a legume crop native to India, is the primary source of protein for more than a billion people in developing countries. The plant can form symbioses with N2-fixing bacteria; however, reports of poor crop nodulation in agricultural soils abound. We report here a study of the bacterial community associated with pigeon pea, with a special focus on the symbiont population in different soils and vegetative and non-vegetative plant growth. Location with respect to the plant roots was determined to be the main factor controlling the bacterial community, followed by developmental stage and soil type. Plant genotype plays only a minor role. Pigeon pea roots have a reduced microbial diversity compared to the surrounding soil and select for Proteobacteria, especially for Rhizobium spp., during vegetative growth. While Bradyrhizobium, a native symbiont of pigeon pea, can be found associating with roots, its presence is dependent on plant variety and soil conditions. A combination of 16S rRNA gene amplicon survey, strain isolation, and co-inoculation with nodule-forming Bradyrhizobium spp. and non-N2-fixing Rhizobium spp. demonstrated that the latter is a much more successful colonizer of pigeon pea roots. Poor nodulation of pigeon pea in Indian soils may be caused by a poor Bradyrhizobium competitiveness against non-nodulating root colonizers such as Rhizobium. Hence, inoculant strain selection of symbionts for pigeon pea should be based not only on their nitrogen fixation potential but, more importantly, on their competitiveness in agricultural soils. IMPORTANCE Plant symbiosis with N2-fixing bacteria is a key to sustainable, low-input agriculture. While there are ongoing projects aiming to increase the yield of cereals using plant genetics and host-microbiota interaction engineering, the biggest potential lies in legume plants. Pigeon pea is a basic food source for a billion low-income people in India. Improving its interactions with N2-fixing rhizobia could dramatically reduce food poverty in India. Despite the Indian origin of this plant, pigeon pea nodulates only poorly in native soils. While there have been multiple attempts to select the best N2-fixing symbionts, there are no reliable strains available for geographically widespread use. In this article, using 16S rRNA gene amplicon, culturomics, and plant co-inoculation assays, we show that the native pigeon pea symbionts such as Bradyrhizobium spp. are able to nodulate their host, despite being poor competitors for colonizing roots. Hence, in this system, the establishment of effective symbiosis seems decoupled from microbial competition on plant roots. Thus, the effort of finding suitable symbionts should focus not only on their N2-fixing potential but also on their ability to colonize. Increasing pigeon pea yield is a low-hanging fruit to reduce world hunger and degradation of the environment through the overuse of synthetic fertilizers.

Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity.

How soil is managed, particularly for agriculture, exerts stresses upon soil microbiomes, resulting in altered community structures and functional states. Understanding how soil microbiomes respond to combined stresses is important for predicting system performance under different land use scenarios, aids in identification of the most environmentally benign managements, and provides insight into how system function can be recovered in degraded soils. We use a long-established field experiment to study the effects of combined chronic (press) disturbance of the magnitude of organic carbon inputs with acute (pulse) effects of physical disturbance by tillage and chemical disturbance due to inorganic fertilization and pesticide application. We show that because of the variety of ways it can be assessed, biodiversity-here based on microbial small subunit rRNA gene phylotypes-does not provide a consistent view of community change. In contrast, aggregated traits associated with soil microbiomes indicate general loss of function, measured as a reduction of average genome lengths, associated with chronic reduction of organic inputs in arable or bare fallow soils and altered growth strategies associated with rRNA operon copy number in prokaryotes, as well as a switch to pathogenicity in fungal communities. In addition, pulse disturbance by soil tillage is associated with an increased influence of stochastic processes upon prokaryote community assembly, but fungicide used in arable soils results in niche assembly of fungal communities compared to untilled grassland. Overall, bacteria, archaea, and fungi do not share a common response to land management change, and estimates of biodiversity do not capture important facets of community adaptation to stresses adequately. IMPORTANCE Changes in soil microbiome diversity and function brought about by land management are predicted to influence a range of environmental services provided by soil, including provision of food and clean water. However, opportunities to compare the long-term effects of combinations of stresses imposed by different management approaches are limited. We exploit a globally unique 50-year field experiment, demonstrating that soil management practices alter microbiome diversity, community traits, and assembly. Grassland soil microbiomes are dominated by fewer-but phylogenetically more diverse-prokaryote phylotypes which sustain larger genomes than microbiomes in arable or bare fallow soil maintained free of plants. Dominant fungi in grassland soils are less phylogenetically diverse than those in arable or fallow soils. Soil tillage increases stochastic processes in microbiome assembly: this, combined with reduced plant biomass, presents opportunities for organisms with a capacity for pathogenesis to become established in stressed soils.

Crop type exerts greater influence upon rhizosphere phosphohydrolase gene abundance and phylogenetic diversity than phosphorus fertilization.

Rock phosphate is an alternative form of phosphorus (P) fertilizer; however, there is no information regarding the influence of P fertilizer sources in Brazilian Cerrado soils upon microbial genes coding for phosphohydrolase enzymes in crop rhizospheres. Here, we analyze a field experiment comparing maize and sorghum grown under different P fertilization (rock phosphate and triple superphosphate) upon crop performance, phosphatase activity and rhizosphere microbiomes at three levels of diversity: small subunit rRNA marker genes of bacteria, archaea and fungi; a suite of alkaline and acid phosphatase and phytase genes; and ecotypes of individual genes. We found no significant difference in crop performance between the fertilizer sources, but the accumulation of fertilizer P into pools of organic soil P differed. Phosphatase activity was the only biological parameter influenced by P fertilization. Differences in rhizosphere microbiomes were observed at all levels of biodiversity due to crop type, but not fertilization. Inspection of phosphohydrolase gene ecotypes responsible for differences between the crops suggests a role for lateral genetic transfer in establishing ecotype distributions. Moreover, they were not reflected in microbial community composition, suggesting that they confer competitive advantage to individual cells rather than species in the sorghum rhizosphere.

The effects of long-term fertilizations on soil hydraulic properties vary with scales.

Soil structure is an indicator of soil quality and its alterations following cropping system conversion or fertilization change evolve slowly. How such alterations vary with scale remains elusive. We investigated this based on the Rothamsted long-term wheat experiment (since 1843) in the UK. Triplicate cores 7 cm high and 10 cm in diameter were taken from plots that have been under different fertilizations or returned to natural woodland for more than one century for imaging using X-ray computed tomography with the voxel size being 40 µm. We then broke each core and sampled three aggregates from it to scan with the voxel size being 1.5 µm. For each core and aggregate sample, we calculated its pore size distribution, permeability and tortuosity. The results showed that the fertilization change >170 years ago reshaped the soil structure differently between the core scale and the aggregate scale. Macro-porosity of the pores (>40 µm) in the cores unfertilized or fertilized with inorganic fertilizers was low and the pores were poorly connected in the top 10 cm of soil, compared to those given farmyard manure or in the woodland. In all treatments, the pores in the core images were hydraulically anisotropic with their permeability in the horizontal direction being higher than that in the vertical direction, whereas the aggregates were comparatively isotropic. The fertilization affected image porosity and permeability at core scale more significantly than at aggregate scale, and the aggregates fertilized with farmyard manure and in the woodland were more permeable than the aggregates in other treatments. It was also found that compared to no-fertilization or fertilization with complete fertilizers, fertilizing without phosphorus over the past 20 years increased the porosity and permeability of the aggregates but not of the cores. Fertilization with inorganic fertilizers increased the tortuosity of the macropores in the cores but not of the intra-aggregate pores, compared to no-fertilization. Porosity-permeability relationship for aggregates unfertilized or fertilized with inorganic fertilisers followed a power law with R 2 > 0.8. In contrast, the permeability of the aggregates in farmyard manure and in the woodland trended differently as their porosity increased. The results also revealed that the transport ability of the aggregates and cores responded differently to carbon in that with soil carbon increasing, the permeability of the aggregates increased asymptotically while the permeability of the cores, especially its horizontal component, increased exponentially.

Improved sensitivity, accuracy and prediction provided by a high-performance liquid chromatography screen for the isolation of phytase-harbouring organisms from environmental samples.

HPLC methods are shown to be of predictive value for classification of phytase activity of aggregate microbial communities and pure cultures. Applied in initial screens, they obviate the problems of 'false-positive' detection arising from impurity of substrate and imprecision of methodologies that rely on phytate-specific media. In doing so, they simplify selection of candidates for biotechnological applications. Combined with 16S sequencing and simple bioinformatics, they reveal diversity of the histidine phosphatase class of phytases most commonly exploited for biotechnological use. They reveal contribution of multiple inositol-polyphosphate phosphatase (MINPP) activity to aggregate soil phytase activity, and they identity Acinetobacter spp. as harbouring this prevalent soil phytase activity. Previously, among bacteria MINPP was described exclusively as an activity of gut commensals. HPLC methods have also identified, in a facile manner, a known commercially successful histidine (acid) phosphatase enzyme. The methods described afford opportunity for isolation of phytases for biotechnological use from other environments. They reveal the position of attack on phytate by diverse histidine phosphatases, something that other methods lack.

Key traits for ruminant livestock across diverse production systems in the context of climate change: perspectives from a global platform of research farms.

Ruminant livestock are raised under diverse cultural and environmental production systems around the globe. Ruminant livestock can play a critical role in food security by supplying high-quality, nutrient-dense food with little or no competition for arable land while simultaneously improving soil health through vital returns of organic matter. However, in the context of climate change and limited land resources, the role of ruminant-based systems is uncertain because of their reputed low efficiency of feed conversion (kilogram of feed required per kilogram of product) and the production of methane as a by-product of enteric fermentation. A growing human population will demand more animal protein, which will put greater pressure on the Earth's planetary boundaries and contribute further to climate change. Therefore, livestock production globally faces the dual challenges of mitigating emissions and adapting to a changing climate. This requires research-led animal and plant breeding and feeding strategies to optimise ruminant systems. This study collated information from a global network of research farms reflecting a variety of ruminant production systems in diverse regions of the globe. Using this information, key changes in the genetic and nutritional approaches relevant to each system were drawn that, if implemented, would help shape more sustainable future ruminant livestock systems.

Soil structure, nutrient status and water holding capacity shape Uruguayan grassland prokaryotic communities.

Soil microbial communities play critical roles in maintaining natural ecosystems such as the Campos biome grasslands of southern South America. These grasslands are characterized by a high diversity of soils, low available phosphorus (P) and limited water holding capacity. This work aimed to describe prokaryotic communities associated with different soil types and to examine the relationship among these soil communities, the parent material and the soil nutrient status. Five Uruguayan soils with different parent material and nutrient status, under natural grasslands, were compared. The structure and diversity of prokaryotic communities were characterized by sequencing 16S rRNA gene amplicons. Proteobacteria, Actinobacteria, Firmicutes,Verrucomicrobia, Acidobacteria, Planctomycetes and Chloroflexi were the predominant phyla. Ordination based on several distance measures was able to discriminate clearly between communities associated with different soil types. Edge-PCA phylogeny-sensitive ordination and differential relative abundance analyses identified Archaea and the bacterial phyla Firmicutes, Acidobacteria, Actinobacteria and Verrucomicrobia as those with significant differences among soil types. Canonical analysis of principal coordinates identified porosity, clay content, available P, soil organic carbon and water holding capacity as the main variables contributing to determine the characteristic prokaryotic communities of each soil type.

Soil as an extended composite phenotype of the microbial metagenome.

We use a unique set of terrestrial experiments to demonstrate how soil management practises result in emergence of distinct associations between physical structure and biological functions. These associations have a significant effect on the flux, resilience and efficiency of nutrient delivery to plants (including water). Physical structure, determining the air-water balance in soil as well as transport rates, is influenced by nutrient and physical interventions. Contrasting emergent soil structures exert selective pressures upon the microbiome metagenome. These selective pressures are associated with the quality of organic carbon inputs, the prevalence of anaerobic microsites and delivery of nutrients to microorganisms attached to soil surfaces. This variety results in distinctive gene assemblages characterising each state. The nature of the interactions provide evidence that soil behaves as an extended composite phenotype of the resident microbiome, responsive to the input and turnover of plant-derived organic carbon. We provide new evidence supporting the theory that soil-microbe systems are self-organising states with organic carbon acting as a critical determining parameter. This perspective leads us to propose carbon flux, rather than soil organic carbon content as the critical factor in soil systems, and we present evidence to support this view.

Development of a reproducible method of analysis of iron, zinc and phosphorus in vegetables digests by SEC-ICP-MS.

Vegetables contain iron, zinc and phosphorus as complexes with phytates limiting their availability from a vegetarian diet, meaning non-haem iron deficiency anaemia and zinc deficiency immune malfunction are a risk. Although these elements have been analysed previously in biological fluids and cereal using LC-ICP-MS, there is no method suitable for analysing iron, zinc and phosphorus simultaneously in vegetables because of their complex matrix. In this study, we analysed iron, zinc and phosphorus in cabbage, broccoli, pepper, spinach, kale and rocket after a simulated gastrointestinal digestion using a newly optimised SEC-ICP-MS method. Ammonium nitrate, as the mobile phase, and a suitable rinsing regime, allowed good reproducibility and maintenance of the equipment. The method showed good reproducibility and can be easily adapted to other vegetables, as required.

Calcium exerts a strong influence upon phosphohydrolase gene abundance and phylogenetic diversity in soil.

The mechanisms by which microbial communities maintain functions within the context of changing environments are key to a wide variety of environmental processes. In soil, these mechanisms support fertility. Genes associated with hydrolysis of organic phosphoesters represent an interesting set of genes with which to study maintenance of function in microbiomes. Here, we shown that the richness of ecotypes for each gene varies considerably in response to application of manure and various inorganic fertilizer combinations. We show, at unprecedented phylogenetic resolution, that phylogenetic diversity of phosphohydrolase genes are more responsive to soil management and edaphic factors than the taxonomic biomarker 16S rRNA gene. Available phosphorus - assessed by measuring Olsen-P - exerted some influence on alkaline phosphatase distribution: however, consistent and significant differences were observed in gene abundance between treatments that were inconsistent with bioavailable orthophosphate being the dominant factor determining gene abundance. Instead, we observed gene niche separation which was most strongly associated with soil exchangeable calcium. Our study suggests that the bioavailability of enzyme cofactors (exchangeable calcium in the case of phoD, phoX and ßPPhy studied here) influence the abundance of genes in soil microbial communities; in the absence of cofactors, genes coding for alternative enzyme families that do not require the limiting cofactor (for example, non-specific acid phosphatases which require vanadate) become more abundant.

Cover crop species have contrasting influence upon soil structural genesis and microbial community phenotype.

Cover crops (plants grown in an agricultural rotation between cash crops) can significantly improve soil quality via sequestering carbon, retaining nutrients, decreasing soil erosion, and maintaining belowground biodiversity. However, little is known about the effects of such plants upon soil structure. The aim of the study was to assess the impact of four species typically used as cover crops and which have contrasting root architecture (viz. clover, black oat, phacelia, tillage radish) on soil structural genesis and the associated modification of microbial community structure in a clay soil. The four plant species were grown in a replicated pot experiment with sieved soil (<2 mm), with unplanted soil as control for 8 weeks. X-ray Computed Tomography was used to quantify the formation of pore networks in 3D and phospholipid fatty acid analysis was performed to characterise the microbial community phenotype. Black oats developed a greater soil-pore connectivity than the other species throughout the growth period, whereas phacelia decreased both the porosity and pore-connectivity. The microbial community phenotype under phacelia was notably different from the other species, with a greater proportion of fungal markers. Thus, different plant species have differential effects upon soil structural genesis and microbial community phenotype, which provides evidence that certain species may be more suitable as cover crops in terms of soil structural conditioning depending upon specific contexts.

Reducing water use by alternate-furrow irrigation with livestock wastewater reduces antibiotic resistance gene abundance in the rhizosphere but not in the non-rhizosphere.

Livestock wastewater is rich in nutrients but may contain antibiotics and antibiotic resistance genes (ARGs). Their discharge to watercourses or soil may result in proliferation of ARGs. Irrigation with wastewater appears to be the most feasible option of disposing of it. One efficient irrigation technology used in arid regions is alternate-furrow irrigation (AFI) by alternately drying part of the plant roots for a prolonged period to physiologically reduce transpiration without compromising yield. However, the extent to which AFI with wastewater influences the concentration of antibiotics and spread of ARGs in soil is poorly understood. The purpose of this paper is to investigate how AFI using swine wastewater alters antibiotic kinetics and ARGs abundance under different irrigation rates, using pepper as the model plant. We examined three AFI treatments using 50%, 65% and 80% of the amount of water employed in sufficient conventional furrow irrigation. Each treatment had a groundwater irrigation control. The results showed that antibiotic concentrations and relative ARGs abundance in the top 20 cm of soil did not increase with the irrigation amount, although they were higher than those in the groundwater-irrigated soils. The relative ARGs abundance in the soil was modulated by irrigation amount and reducing the irrigation amount in AFI reduced ARGs dispersion only in rhizosphere. When the soil moisture was close to field capacity, ARGs were more abundant in rhizosphere than in non-rhizosphere, possibly because the rhizosphere is rich in microbes and increasing antibiotic concentrations due to an increase in irrigation rate favors antibiotic-resistant microbiome in competing for substrates. These, however, were not mirrored in the relative ARGs abundance in the roots. These results have important implications as it revealed that reducing the input of antibiotics and ARGs into soil with AFI does not necessarily reduce ARGs proliferation.

Effects of cropping systems upon the three-dimensional architecture of soil systems are modulated by texture.

Soil delivers fundamental ecosystem functions via interactions between physical and biological processes mediated by soil structure. The structure of soil is also dynamic and modified by natural factors and management intervention. The aim of this study was to investigate the effects of different cropping systems on soil structure at contrasting spatial scales. Three systems were studied in replicated plot field experiments involving varying degrees of plant-derived inputs to the soil, viz. perennial (grassland), annual (arable), and no-plant control (bare fallow), associated with two contrasting soil textures (clayey and sandy). We hypothesized the presence of plants results in a greater range (diversity) of pore sizes and that perennial cropping systems invoke greater structural heterogeneity. Accordingly, the nature of the pore systems was visualised and quantified in 3D by X-ray Computed Tomography at the mm and µm scale. Plants did not affect the porosity of clay soil at the mm scale, but at the µm scale, annual and perennial plant cover resulted in significantly increased porosity, a wider range of pore sizes and greater connectivity compared to bare fallow soil. However, the opposite occurred in the sandy soil, where plants decreased the porosity and pore connectivity at the mm scale but had no significant structural effect at the µm scale. These data reveal profound effects of different agricultural management systems upon soil structural modification, which are strongly modulated by the extent of plant presence and also contingent on the inherent texture of the soil.