Remediation methods for soil contaminated with poly- and perfluoroalkyl substances (PFAS) are needed to prevent their leaching into drinking water sources and to protect living organisms in the surrounding environment. In this study, the efficacy of processed and amended clays and carbons as soil amendments to sequester PFAS and prevent leaching was assessed using PFAS-contaminated soil and validated using sensitive ecotoxicological bioassays. Four different soil matrices including quartz sand, clay loam soil, garden soil, and compost were spiked with 4 PFAS congeners (PFOA, PFOS, GenX, and PFBS) at 0.01-0.2 μg/mL and subjected to a 3-step extraction method to quantify the leachability of PFAS from each matrix. The multistep extraction method showed that PFAS leaching from soil was aligned with the total carbon content in soil, and the recovery was dependent on concentration of the PFAS. To prevent the leaching of PFAS, several sorbents including activated carbon (AC), calcium montmorillonite (CM), acid processed montmorillonite (APM), and organoclays modified with carnitine, choline, and chlorophyll were added to the four soil matrices at 0.5-4 % /w, and PFAS was extracted using the LEAF method. Total PFAS bioavailability was reduced by 58-97 % by all sorbents in a dose-dependent manner, with AC being the most efficient sorbent with a reduction of 73-97 %. The water leachates and soil were tested for toxicity using an aquatic plant () and a soil nematode (), respectively, to validate the reduction in PFAS bioavailability. Growth parameters in both ecotoxicological models showed a dose-dependent reduction in toxicity with value-added growth promotion from the organoclays due to added nutrients. The kinetic studies at varying time intervals and varying pHs simulating acidic rain, fresh water, and brackish water suggested a stable sorption of PFAS on all sorbents that fit the pseudo-second-order for up to 21 days. Contaminated soil with higher than 0.1 μg/mL PFAS may require reapplication of soil amendments every 21 days. Overall, AC showed the highest sorption percentage of total PFAS from studies, while organoclays delivered higher protection in ecotoxicological models (). This study suggests that immobilization with soil amendments can reduce PFAS leachates and their bioavailability to surrounding organisms. A combination of sorbents may facilitate the most effective remediation of complex soil matrices containing mixtures of PFAS and prevent leaching and uptake into plants.

Soil microorganisms play critical roles in the degradation of micro-and nano-pollutants, and the corresponding proteins and enzymes play roles in pollutant recognition, transportation, and degradation. Our ability to study these pathways from soil samples is often complicated by the complex processes involved in extracting proteins from soil matrices. This study aimed to develop a new protein soil extraction protocol that yielded active, intracellular enzymes from the perchlorate degradation pathway, particularly perchlorate reductase. An indirect method, which focused on first separating the cells from the soil matrix, followed by cell lysis and enzyme extraction, was evaluated. The optimized indirect method achieved a final extraction efficiency of the active enzyme and total protein of 15.7 % and 3.3 %, respectively. The final step of separating enzymes from residual soil components resulted in the highest activity and protein losses of 67.7 % ± 14.8 % and 91.8 % ± 1.8 %, respectively. Five buffers, each at different concentrations (0.01 M, 0.05 M, and 0.1 M), were tested to enhance enzyme extraction efficiency. The best extractant requires careful consideration between the highest activity and the quality of the recovered enzymes. Coextraction of humic substances could be minimized by using 0.1 M as compared to 0.01 M and 0.05 M of sodium pyrophosphate; however, this resulted in less recovered activity compared to lower extractant concentrations.

Critical to the environmental sustainability of hard rock mining is the reclamation of disturbed lands following mine closure through revegetation. Improved understanding of associations between above- and belowground processes that characterize successful plant establishment is critical to the implementation of more efficient revegetation strategies for nutrient-poor mine waste materials. The specific objective of this five-year temporal study was to identify progressive biotic and abiotic indicators of primary soil development on mine waste rock (WR) on a slope hydroseeded with native plant species and to quantify comparative effects of plant lifeform on soil development. Aboveground plant diversity and belowground substrate properties were measured annually at 67 m intervals along transects following the slope contour. Seeded WR was compared to unseeded WR and the adjacent native ecosystem. A temporal increase in WR microbial biomass was observed in seeded WR relative to unseeded areas. Microbial community analysis found the unseeded WR to be defined by oligotrophic microbes, whereas targeted grass and shrub root zones samples demonstrated significant increases in specific cellulose and lignin degrading and N-cycling phylotypes. More extensive chemical and biological fertility development was observed in shrub root zones relative to grass. Ten chemical and biological indicators increased significantly in shrub WR relative to unseeded WR, whereas grass WR was only enriched in bacterial 16S rRNA gene copy number/g substrate and bacterial/archaeal and fungal diversity. In addition, the shrub root zone had significantly higher nitrogen-cycling potential than grass root zones or unseeded WR. Thus, both grasses and shrubs improve belowground WR development; however, shrub establishment had greater fertility outcomes. Concurrent belowground fertility development is critical to sustainable plant establishment. Coupled evaluation of above- and belowground metrics provides an improved quantitative assessment of revegetation progress and a valuable tool to guide management decisions.

Plant parasitic nematode (PPN) control has historically relied on the use of synthetic chemical nematicides, however many are toxic to both human health and the environment. The withdrawal of the more harmful nematicides coupled with increases in soil temperatures and increased occurrence of pests and diseases associated with climate change, may enable PPN to increase in numbers and spread globally. The need for sustainable and environmentally friendly management options is necessary while facing future food security scares in order to feed the ever-growing population. Seaweed extracts have been used for decades in agriculture and horticulture as soil biostimulants, however there is a growing body of evidence to suggest that they could be used to reduce the occurrence of damaging PPN infections. Using meta-analysis, we investigated whether seaweed extracts applied to soil could reduce root knot nematode (RKN) abundance and whether there could be confounding factors that influence their efficacy. We found that seaweed extracts reduce RKN performance and that various factors affected the efficacy of seaweed, including the seaweed species itself and the crop the seaweed was applied to. extracts were found to be the most effective. Particular RKN species were more sensitive than others to seaweed species used and, in some cases, specific seaweed species only affected particular RKN species Different life cycle stages were also differentially susceptible to seaweed application, where both egg hatching and population abundance could be reduced via seaweed use. This research indicates that seaweed extracts could potentially be used to help reduce RKN attack on plants.

Uganda faces a considerable challenge to match its food production to an annual population growth rate of 3%. Cooking bananas are the country's most produced staple crop but the annual national harvest is not increasing. The crop grows on infertile soils that are normally fertilised organically and often susceptible to erosion. Soil nematodes are well-established as bioindicators of soil quality that can support environmental monitoring and assessment of the sustainability of agricultural systems. These invertebrates are a highly ranked indicator of biodiversity with molecular approaches available. Consequently, we have applied next-generation DNA sequencing of soil nematodes to evaluate soil quality of Ugandan banana plantations. The aim is to establish a method for constructing an aspect of an environmental biosafety dossier with the future aim of assessing the impact of transgenic crops and improving current cropping systems. The soil samples did not differ significantly in any of the measured soil chemistry factors, soil texture or percentage of organic matter. Thirty taxons of soil nematodes other than the plant parasites were recovered from soil supporting nine banana plantations plus three each from coffee and banana-coffee interplants from East and West Uganda. Cluster analysis correctly allocated each plantation to the crop/intercrop being grown when based on the abundance of taxa rather than taxa presence or absence. This indicates that the host has considerable effects on the abundance of specific nematode species within the soil. Overall, nematodes were more abundant in soil from coffee plantations than from banana-coffee interplants with the lowest values being from fields supporting just banana. Only the basal and trophic diversity indices and the percentage of nematodes that are rapid colonisers varied between the three plantation types. The soil of all fifteen plantations can be classified as having a mature soil web condition with low physical disturbance, limited chemical stressors, moderately high nutrient enrichment and balanced decomposition channels.

Abandoned mine lands present persistent environmental challenges to ecosystems and economies; reclamation an important step for overcoming these challenges. Phytostabilization is an elegant and cost-effective reclamation strategy, however, establishing plants on severely degraded soils is problematic, often requiring soil amendment additions. We evaluated whether amendment mixtures composed of lime, biochar, biosolids, and locally effective microbes (LEM) could alleviate the constraints that hinder phytostabilization success. We hypothesized that 1) plants grown in tailings amended with lime, biochar, and biosolids (LBB) would establish faster and grow larger than plants grown in tailings amended with lime only, and 2) the LEM source would influence microbial community function and structure in amended mine tailings. We conducted a greenhouse study that simulated conditions to measure the influence of LBB-LEM amendment blends on plant growth, plant nutrients, metal concentrations, microbial function, and microbial community structure. Blue wildrye [ Buckley ssp (Burtt Davy) Gould] was grown in tailings collected from the Formosa mine site amended with various combinations of LBB-LEM. The above and below ground biomass of plants grown in mine tailings amended with LBB was 3 to 4 times larger than the biomass of plants grown in tailings amended only with lime. Although the LEM addition did not influence immediate plant growth, it did affect nutrient content and altered the rhizosphere community membership. As such, it is not yet clear if LEM-driven alterations in microbial membership will advance mine reclamation strategies by improving long-term growth.

Characterising spatial microbial community structure is important to understand and explain the consequences of continuous plantation of one crop species on the performance of subsequent crops, especially where this leads to reduced growth vigour and crop yield. We investigated the spatial structure, specifically distance-decay of similarity, of soil bacterial and fungal communities in two long-established orchards with contrasting agronomic characteristics. A spatially explicit sampling strategy was used to collect soil from under recently grubbed rows of apple trees and under the grassed aisles. Amplicon-based metabarcoding technology was used to characterise the soil microbial communities. The results suggested that (1) most of the differences in soil microbial community structure were due to large-scale differences (i.e. between orchards), (2) within-orchard, small-scale (1-5 m) spatial variability was also present, but spatial relationships in microbial community structure differed between orchards and were not predictable, and (3) vegetation type (i.e. trees or grass and their associated management) can significantly alter the structure of soil microbial communities, affecting a large proportion of microbial groups. The discontinuous nature of soil microbial community structure in the tree stations and neighbouring grass aisles within an orchard illustrate the importance of vegetation type and allied weed and nutrient management on soil microbial community structure.

The identification of locally-adapted rhizobia for effective inoculation of grain legumes in Africa's semiarid regions is strategic for developing and optimizing cheap nitrogen fixation technologies for smallholder farmers. This study was aimed at selecting and characterising effective native rhizobia, from Ghanaian soils for groundnut ( L.) inoculation. From surface-disinfected root nodules of cowpea and groundnut plants grown on farmers' fields, 150 bacterial isolates were obtained, 30 of which were eventually found to nodulate groundnut plants. After testing the symbiotic potential of these isolates on groundnut on sterilized substrate, seven of them, designated as KNUST 1001-1007, were evaluated in an open field pot experiment using N-labelled soil. Although N dilution analyses did not indicate differences among treatments in the proportion of nitrogen (N) derived from the atmosphere (%Ndfa), all seven strains increased total N derived from N fixation by inoculated groundnut plants as compared to the non-inoculated control. Inoculation with KNUST 1002 led to total N accumulation as high as that of the groundnut reference strain 32H1. Genetic characterisation of the isolates by sequence analysis of 16S rRNA gene, 16S - 23S rRNA intergenic transcribed spacer (ITS) region and gene revealed that isolates KNUST 1003 and 1007 were related to , a common bean symbiont. The other five isolates, including KNUST 1002 belonged to the genus, being closely related to . Therefore, this study revealed novel native Ghanaian rhizobia with potential for the development of groundnut inoculants.

Rhizobia play important roles in agriculture owing to their ability to fix nitrogen through a symbiosis with legumes. The specificity of rhizobia-legume associations means that underused legume species may depend on seed inoculation with their rhizobial partners. For black medic () and lucerne () little is known about the natural prevalence of their rhizobial partner in UK soils, so that the need for inoculating them is unclear. We analysed the site-dependence of rhizobial seed inoculation effects on the subsequent ability of rhizobial communities to form symbioses with four legume species (, , and ). At ten organic farms across the UK, a species-diverse legume based mixture (LBM) which included these four species was grown. The LBM seed was inoculated with a mix of commercial inocula specific for clover and lucerne. At each site, soil from the LBM treatment was compared to the soil sampled prior to the sowing of the LBM (the control). From each site and each of the two treatments, a suspension of soils was applied to seedlings of the four legume species and grown in axenic conditions for six weeks. Root nodules were counted and their rhizobia isolated. PCR and sequencing of a fragment of the B gene from rhizobial isolates allowed identification of strains. The number of nodules on each of the four legume species was significantly increased when inoculated with soil from the LBM treatment compared to the control. Both the proportion of plants forming nodules and the number of nodules formed varied significantly by site, with sites significantly affecting the species but not the species. These differences in nodulation were broadly reflected in plant biomass where site and treatment interacted; at some sites there was a significant advantage from inoculation with the commercial inoculum but not at others. In particular, this study has demonstrated the commercial merit of inoculation of lucerne with compatible rhizobia.

European earthworms were introduced to North America by European settlers about 400 years ago. Human-mediated introductions significantly contributed to the spread of European species, which commonly are used as fishing bait and are often disposed deliberately in the wild. We investigated the genetic structure of in a 100 km range south of Calgary, Canada, an area that likely was devoid of this species two decades ago. Genetic relationships among populations, gene flow, and migration events among populations were investigated using seven microsatellite markers and the mitochondrial 16S rDNA gene. Earthworms were collected at different distances from the city and included fishing baits from three different bait distributors. The results suggest that field populations in Alberta established rather recently and that bait and field individuals in the study area have a common origin. Genetic variance within populations decreased outside of the urban area, and the most distant populations likely originated from a single introduction event. The results emphasise the utility of molecular tools to understand the spatial extent and connectivity of populations of exotic species, in particular soil-delling species, that invade native ecosystems and to obtain information on the origin of populations. Such information is crucial for developing management and prevention strategies to limit and control establishment of non-native earthworms in North America.

Earthworms benefit agriculture by providing several ecosystem services. Therefore, strategies to increase earthworm abundance and activity in agricultural soils should be identified, and encouraged. earthworms primarily feed on organic inputs to soils but it is not known which organic amendments are the most effective for increasing earthworm populations. We conducted earthworm surveys in the field and carried out experiments in single-earthworm microcosms to determine the optimum food source for increasing earthworm biomass using a selection of crop residues and organic wastes available to agriculture. We found that although farmyard manure increased earthworm populations more than cereal straw in the field, straw increased earthworm biomass more than manures when milled and applied to microcosms. Earthworm growth rates were positively correlated with the calorific value of the amendment and straw had a much higher calorific value than farmyard manure, greenwaste compost, or anaerobic digestate. Reducing the particle size of straw by milling to <3 mm made the energy in the straw more accessible to earthworms. The benefits and barriers to applying milled straw to arable soils in the field are discussed.

In this study, three lytic phages (namely, PRSA-1, PRSA-2 and PRSA-26) were isolated and characterized for their morphology, host range, profile and restriction endonuclease banding pattern of genome size. The susceptible rhizobial isolates were identified by H and II sequence analysis. The results showed that all phages had polyhedral head with non-contractile tail which confirmed their relationship with the family. All the three phages produced highly distinct plaques on their host bradyrhizobial lawn, and were highly sensitive to chloroform. The phage genome sizes ranged from 34.7 to 53.1 kbp. The phages were tested against groundnut-nodulating bradyrhizobial strains TUTAHSA75, TUTAHSA155 and TUTAHSA126 isolated from South African soils. The results revealed different bacterial susceptibilities to phages. Bradyrhizobial isolate TUTAHSA126 was susceptible to all three phages (i.e. PRSA-1, PRSA-2 and PRSA-26), TUTAHSA155 to two phages (i.e. PRSA-1, PRSA-2), and TUTAHSA75 to only one phage (i.e. PRSA-1). Phylogenetic analysis of H and II gene sequences of the phage-susceptible bradyrhizobial isolates revealed their close relatedness to a diverse group of species. Phage PRSA-1 could parasitize on all three bradyrhizobial strains, which indicates its potential role in horizontal gene transfer through lysogenic conversion, and/or genetic transduction in soil microbial environments.

f.sp. (Fos) is an effective biocontrol agent (BCA) against the parasitic weed . It acts in the rhizosphere of several tropical cereals, where it may interfere with indigenous microbial populations. To test this impact, we assessed in a 2-season field experiment at two contrasting tropical agro-ecological sites the response of nitrifying and total indigenous prokaryotic communities in the rhizosphere of maize to the exposure of the Fos-BCA "Foxy-2". At early leaf development (EC30), flowering (EC60) and senescence (EC90) stage of maize, rhizosphere samples were obtained and subjected to community analysis of bacterial and archaeal (ammonia monooxigenase) (AOB, AOA) and 16S rRNA genes. Abundance and community composition of all studied genes were predominantly influenced by soil type, crop growth stage and seasonality. No major effect of "Foxy-2" was found. Notably, total archaeal community relative to bacteria dominated in the clayey soil which was linked to its strong soil organic carbon (SOC) background. Compared to bacterial nitrifiers, domination of nitrifying archaea increased towards senescence stage which was explained by biochemical differences in organic resource availability between the crop growth stages. During the short rain season, the higher archaeal abundance was mainly driven by increased availability of organic substrates, i.e., extractable organic carbon. Our findings suggested that archaea had greater rhizosphere competence than "Foxy-2" in soils with higher clay and SOC contents. We verified that "Foxy-2" in maize rhizospheres is compatible with nitrifying prokaryotes under the given environments, in particular in clayey soils dominated by archaea.

Different DNA extraction protocols were evaluated on a reference soil. A wide difference was found in the total extractable DNA as derived from different extraction protocols. Concerning the DNA yield phenol-chloroform-isomyl alcohol extraction resulted in high DNA yield but also in a remarkable co-extraction of contaminants making PCR from undiluted DNA extracts impossible. By comparison of two different extraction kits, the Macherey&Nagel SoilExtract II kit resulted in the highest DNA yields when buffer SL1 and the enhancer solution were applied. The enhancer solution not only significantly increased the DNA yield but also the amount of co-extracted contaminates, whereas additional disintegration strategies did not. Although a three times repeated DNA extraction increased the total amount of extracted DNA, microbial fingerprints were merely affected. However, with the 5th extraction this changed. A reduction of total DGGE band numbers was observed for archaea and fungi, whereas for bacteria the diversity increased. The application of ethidium monoazide (EMA) or propidium monoazide (PMA) treatment aiming on the selective removal of soil DNA derived from cells lacking cell wall integrity resulted in a significant reduction of total extracted DNA, however, the hypothesized effect on microbial fingerprints failed to appear indicating the need for further investigations.

The plant pathogen is very difficult to control due to its persistent, long-living sclerotial structures in soil. Sclerotia are the main source of infection for diseases, which cause high yield losses on a broad host range world-wide. Little is known about micro-organisms associated with sclerotia in soil. Therefore, microbial communities of greenhouse and field incubated sclerotia were analysed by a multiphasic approach. Using microbial fingerprints performed by PCR-SSCP, sclerotia-associated bacterial communities showed a high diversity, whereas only a few fungi could be detected. Statistical analysis of fingerprints revealed the influence of soil types, incubation conditions (greenhouse, field), and incubation time (5 and 12 weeks) on the bacterial as well as fungal community. No significant differences were found for the microbial community associated with different anastomosis sub-groups (AG 1-IB and AG 1-IC). sclerotia are an interesting bio-resource: high proportions of fungal cell-wall degrading isolates as well as those with antagonistic activity towards were found. While a fraction of 28.4% of sclerotia-associated bacteria (=40 isolates) with antagonistic properties was determined, only 4.4% (=6 isolates) of the fungal isolates were antagonistic. We identified strong antagonists of the genera , , , and , which can be used as biological control agents incorporated in soil or applied to host plants.

In Eastern Spain, almond trees have been cultivated in terraced orchards for centuries, forming an integral part of the Mediterranean forest scene. In the last decades, orchards have been abandoned due to changes in society. This study investigates effects of changes in land use from forest to agricultural land and the posterior land abandonment on soil microbial community, and the influence of soil physico-chemical properties on the microbial community composition (assessed as abundances of phospholipids fatty acids, PLFA). For this purpose, three land uses (forest, agricultural and abandoned agricultural) at four locations in SE Spain were selected. Multivariate analysis showed a substantial level of differentiation in microbial community structure according to land use. The microbial communities of forest soils were highly associated with soil organic matter content. However, we have not found any physical or chemical soil property capable of explaining the differences between agricultural and abandoned agricultural soils. Thus, it was suggested that the cessation of the perturbation caused by agriculture and shifts in vegetation may have led to changes in the microbial community structure. PLFAs indicative of fungi and ratio of fungal to bacterial PLFAs were higher in abandoned agricultural soils, whereas the relative abundance of bacteria was higher in agricultural soils. Actinomycetes were generally lower in abandoned agricultural soils, while the proportions of vesicular-arbuscular mycorrhyzal fungi were, as a general trend, higher in agricultural and abandoned agricultural soils than in forests. Total microbial biomass and richness increased as agricultural < abandoned agricultural < forest soils.

Livestock wastes contain many pathogenic microorganisms including bacteria, viruses and protozoa. Following the application of these wastes to land the potential exists for environmental contamination. Plants, soil and ultimately water courses which may subsequently be used as catchments for public water supplies may all be affected. Research attention is now being focused on this possibility, especially in the case of protozoan pathogens which may be the most important as they are often resistant to current methods used in public water treatment. In this review we highlight some of the many factors that are likely to influence the degree of pollution by their effect on both the vertical and horizontal transport of microorganisms through soil. Soil pH, temperature, the presence of plants, microbial surface properties, type of waste, soil type and soil water content and flow may all affect the rate and extent of vertical transport, with the latter two generally considered to be the most important. Lateral movement is a particular problem in soils with impermeable substrata or in waterlogged conditions and in these cases the major factors affecting movement include rainfall rate, topography of the land and the rate at which microorganisms partition into the runoff.