Zinc toxicity stimulates microbial production of extracellular polymers in a copiotrophic acid soil

The production of extracellular polymeric substances (EPS) is crucial for biofilm structure, microbial nutrition and proximal stability of habitat in a variety of environments. However, the production patterns of microbial EPS in soils as affected by heavy metal contamination remain uncertain. Here we investigate the extracellular response of the native microbial biomass in a grassland soil treated with refined glycerol or crude unrefined biodiesel co-product (BCP) with and without ZnCl2. We extracted microbial EPS and more readily soluble microbial products (SMP), and quantified total polysaccharide, uronic acid, and protein content in these respective extracts. Organic addition, especially BCP, significantly stimulated the production of EPS-polysaccharide and protein but had no impact on EPS-uronic acids, while in the SMP-fraction, polysaccharides and uronic acids were both significantly increased. In response to the inclusion of Zn2+, both EPS- and SMP-polysaccharides increased. This implies firstly that a tolerance mechanism of soil microorganisms against Zn2+ toxicity exists through the stimulation of SMP and EPS production, and secondly that co-products of biofuel industries may have value-added use in bioremediation efforts to support in-situ production of microbial biopolymers. Microbial films and mobile polymers are likely to impact a range of soil properties. The recent focus on EPS research in soils is anticipated to help contribute an improved understanding of biofilm dynamics in other complex systems - such as continuously operated bioreactors

Soil organic carbon, extracellular polymeric substances (EPS), and soil structural stability as affected by previous and current land-use

While soil microbial ecology, soil organic carbon (SOC) and soil physical quality are widely understood to be interrelated — the underlying drivers of emergent properties, from land management to biochemistry, are hotly debated. Biological binding agents, microbial exudates, or ‘extracellular polymeric substances’ (EPS) in soil are now receiving increased attention due to several of the existing methodological challenges having been overcome. We applied a recently developed approach to quantify soil EPS, as extracellular protein and extracellular polysaccharide, on the well-characterised soils of the Highfield Experiment, Rothamsted Research, UK. Our aim was to investigate the links between agricultural land use, SOC, transient binding agents known as EPS, and their impacts on soil physical quality (given by mean weight diameter of water stable aggregates; MWD). We compared the legacy effects from long-term previous land-uses (unfertilised grassland, fertilised arable, and fallow) which were established >50 years prior to investigation, crossed with the same current land-uses established for a duration of only 2.5 years prior to sampling. Continuously fallow and grassland soils represented the poorest and greatest states of structural integrity, respectively. Total SOC and %N were found to be affected by both previous and current land-uses, while extractable EPS and MWD were driven primarily by the current land-use. Land-use change between these two extremes (fallow→grass; grass→fallow) resulted in smaller SOC differences (64% increase or 37% loss) compared to MWD (125% increase or 78% loss). SOC concentration correlated well to MWD (adjusted R2 = 0.72) but the high SOC content from previous grassland was not found to contribute directly to the current stability (p < 0.05). Our work thus supports the view that certain distinct components of SOC, rather than the total pool, have disproportionately important effects on a soil’s structural stability. EPS-protein was more closely related to aggregate stability than EPS-polysaccharide (p values of 0.002 and 0.027, respectively), and ranking soils with the 5 highest concentrations of EPS-protein to their corresponding orders of stability (MWD) resulted in a perfect match. We confirmed that both EPS-protein and EPS-polysaccharide were transient fractions: supporting the founding models for aggregate formation. We suggest that management of transient binding agents such as EPS —as opposed to simply increasing the total SOC content— may be a more feasible strategy to improve soil structural integrity and help achieve environmental objectives

Biodiesel co-product (BCP) decreases soil nitrogen (N) losses to groundwater

This study compares a traditional agricultural approach to minimise N pollution of groundwater (incorporation of crop residues) with applications of small amounts of biodiesel co-product (BCP) to arable soils. Loss of N from soil to the aqueous phase was shown to be greatly reduced in the laboratory, mainly by decreasing concentrations of dissolved nitrate-N. Increases in soil microbial biomass occurred within 4 days of BCP application—indicating rapid adaptation of the soil microbial community. Increases in biomass-N suggest that microbes were partly mechanistic in the immobilisation of N in soil. Straw, meadow-grass and BCP were subsequently incorporated into experimental soil mesocosms of depth equal to plough layer (23 cm), and placed in an exposed netted tunnel to simulate field conditions. Leachate was collected after rainfall between the autumn of 2009 and spring of 2010. Treatment with BCP resulted in less total-N transferred from soil to water over the entire period, with 32.1, 18.9, 13.2 and 4.2 mg N kg(−1) soil leached cumulatively from the control, grass, straw and BCP treatments, respectively. More than 99 % of nitrate leaching was prevented using BCP. Accordingly, soils provided with crop residues or BCP showed statistically significant increases in soil N and C compared to the control (no incorporation). Microbial biomass, indicated by soil ATP concentration, was also highest for soils given BCP (p < 0.05). These results indicate that field-scale incorporation of BCP may be an effective method to reduce nitrogen loss from agricultural soils, prevent nitrate pollution of groundwater and augment the soil microbial biomass

Sequestration of C in soils under Miscanthus can be marginal and is affected by genotype-specific root distribution

AbstractMiscanthus is a low input energy crop suitable for low fertility marginal arable land and thought to provide carbon sequestration in soil. We analysed a long-term field experiment (14-year) to determine whether differences in genotype, growth habit, and root distribution affected soil carbon spatially under different Miscanthus genotypes. Soil cores were taken centrally and radially to a depth of 1m, and divided into six vertical segments. Total root length (TRL), root dry matter (RDM) and δ13C signature of soil organic carbon (SOC) were measured directly, and root length density (RLD), fractions of Miscanthus-derived soil organic C (SOCM), and residual soil carbon (SOCorig) were calculated. Genotype was found to exhibit a statistically significant influence on spatial allocation of SOC. Grouping varieties into ‘tuft-forming’ (T) and ‘non-tuft-forming’ (NT) phenotypes revealed that respective groups accumulated similar amounts of RDM over 14 years (11.4±3.3 vs. 11.9±4.8Mgha−1, respectively). However, phenotype T allocated more carbon to roots in the subsoil than NT (33% vs. 25%). Miscanthus genotypes sequestered between 4.2 and 7.1gC4-SOCkg−1 soil over the same period, which was more than the average loss of C3-derived SOC (3.25gkg−1). Carbon stocks in the ‘A horizon’ under Miscanthus increased by about 5Mgha−1 above the baseline, while the net increase in the subsoil was marginal. Amounts of Miscanthus root C in the subsoil were small (1.2–1.8MgCha−1) but could be important for sustainable sequestration as root density (RLD) explained a high percentage of SOCM (R2=0.66)

A comparison of two colorimetric assays, based upon Lowry and Bradford techniques, to estimate total protein in soil extracts

Soil extracts usually contain large quantities of dissolved humified organic material, typically reflected by high polyphenolic content. Since polyphenols seriously confound quantification of extracted protein, minimising this interference is important to ensure measurements are representative. Although the Bradford colorimetric assay is used routinely in soil science for rapid quantification protein in soil-extracts, it has several limitations. We therefore investigated an alternative colorimetric technique based on the Lowry assay (frequently used to measure protein and humic substances as distinct pools in microbial biofilms). The accuracies of both the Bradford assay and a modified Lowry microplate method were compared in factorial combination. Protein was quantified in soil-extracts (extracted with citrate), including standard additions of model protein (BSA) and polyphenol (Sigma H1675-2). Using the Lowry microplate assay described, no interfering effects of citrate were detected even with concentrations up to 5 times greater than are typically used to extract soil protein. Moreover, the Bradford assay was found to be highly susceptible to two simultaneous and confounding artefacts: 1) the colour development due to added protein was greatly inhibited by polyphenol concentration, and 2) substantial colour development was caused directly by the polyphenol addition. In contrast, the Lowry method enabled distinction between colour development from protein and non-protein origin, providing a more accurate quantitative analysis. These results suggest that the modified-Lowry method is a more suitable measure of extract protein (defined by standard equivalents) because it is less confounded by the high polyphenolic content which is so typical of soil extracts

Measuring the soil-microbial interface: extraction of extracellular polymeric substances (EPS) from soil biofilms

Many soil microbes exist in biofilms. These biofilms are typified by variable quantities of extracellular polymeric substances (EPS: predominantly polysaccharides, glycoconjugates, and proteins) and the embedded microbial cells. A method to measure soil-EPS (the biofilm exclusive of microbial cells) has not yet been described. The present work investigates the potential of five extraction methods to estimate changes in soil-EPS content. A rationale for selection of appropriate EPS extraction and methodology is discussed, including the crucial consideration of both intracellular and extracellular contamination. EPS was developed in situ by provision of labile C (glycerol) to the microbial biomass of a moist soil and then applying desiccation stress. Only two out of the five extraction methods showed statistically significant increases in polysaccharide production responding to substrate addition. Humified organic matter, estimated by its humic acid equivalent (HAE) was used to indicate the degree of extracellular contamination, and/or creation of humic artefacts – both of which affect detection of changes in EPS. The HAE concentration was very high when applying original and modified methods designed to extract glomalin related soil protein (GRSP). Extraction methods involving heating with dilute sulphuric acid appeared to overestimate EPS-polysaccharide. Using microbial ATP as an indicator of cell-lysis, confidence could only be ascribed to EPS extraction with cation exchange resin. Using this method, the expected increases in EPS-polysaccharide were clearly apparent. The HAE/protein ratios of EPS extracts were also lowest with cation exchange – indicating this method did not cause excessive contamination from humified soil organic matter or create related artefacts

Environmental horticulture for domestic and community gardens—An integrated and applied research approach

Societal Impact Statement Daunting global challenges of climate change and biodiversity loss may seem overwhelming. However, gardeners have a secret weapon—gardens, balconies, indoor planting, yards and allotments are mini-ecosystems that offer opportunities to counter perceptions of helplessness, inadequacy and resultant inaction by using those spaces to ‘Do what we can, with what we have, where we are’. Minimising gardening ‘footprints’ to mitigate harmful impacts, whilst maximising gardening ‘handprints’ to enhance benefits, is readily achievable. With this in mind, the Royal Horticultural Society is leading research into environmental horticulture for gardens, and benefits for individual wellbeing. Summary This article presents an integrated and applied research approach to the unique and multi-disciplinary area of science referred to here as environmental horticulture. It does this by: (a) providing an institutional perspective (The Royal Horticultural Society) on a research approach for this particular area, emphasising why domestic and community gardens are important in the context of global environmental threats; (b) presenting four primary research focus areas and project examples; and (c) highlighting interdisciplinary linkages, future research needs, public engagement/knowledge sharing opportunities, and ‘Green Skills’ development in the area of environmental horticulture. Research focus areas discussed are: (1) responding to the changing climate (adaptation, mitigation and resilience solutions in gardens); (2) ‘plants for purpose’ (harnessing the potential of horticultural plant diversity, and gardening, to help regulate environmental conditions); (3) sustainability and climate risk reduction through effective and efficient resource management (reduction, re-use, recycling and repurposing); and (4) gardening and cultivated plant choice for human health and wellbeing. We argue that a key research priority is improving our understanding of the linkages and interactions between soil, water, plants, weather and people. These crucial linkages affect above and below ground processes, for both outdoor and indoor plants. They impact the effectiveness with which water and nutrient cycling takes place, the extent to which ecosystem services may be delivered, and the resultant capacity of gardens and gardening to provide environmental and human health benefits