Enteropathogen survival in soil from different land-uses is predominantly regulated by microbial community composition

peer-reviewedMicrobial enteropathogens can enter the environment via landspreading of animal slurries and manures. Biotic interactions with the soil microbial community can contribute to their subsequent decay. This study aimed to determine the relative impact of biotic, specifically microbial community structure, and physico-chemical properties associated with soils derived from 12 contrasting land-uses on enteropathogen survival. Phenotypic profiles of microbial communities (via phospholipid fatty acid (PLFA) profiling), and total biomass (by fumigation-extraction), in the soils were determined, as well as a range of physicochemical properties. The persistence of Salmonella Dublin, Listeria monocytogenes, and Escherichia coli was measured over 110 days within soil microcosms. Physicochemical and biotic data were used in stepwise regression analysis to determine the predominant factor related to pathogen-specific death rates. Phenotypic structure, associated with a diverse range of constituent PLFAs, was identified as the most significant factor in pathogen decay for S. Dublin, L. monocytogenes, non-toxigenic E. coli O157 but not for environmentally-persistent E. coli. This demonstrates the importance of entire community-scale interactions in pathogen suppression, and that such interactions are context-specific

Impact of basidiomycete fungi on the wettability of soil contaminated with a hydrophobic polycyclic aromatic hydrocarbon

Polyaromatic hydrocarbons (PAHs) present a challenge to bioremediation because they are hydrophobic, thus influencing the water availability and repellency of soil. The addition of different concentrations of the PAH, anthracene, showed it to induce moderate levels of repellency. We investigated the efficacy of three basidiomycete fungal species on improving the wettability of soil by reducing repellency caused by contamination of soil with 7 ppm anthracene. A microcosm system was used that enabled determination of the impact of fungi on wettability at three locations down a 30 mm deep repacked soil core. Before incubation with fungi, the contaminated soil had a repellency of R = 3.12 ± 0.08 (s.e.). After 28 days incubation, Coriolus versicolor caused a significant reduction in repellency to R = 1.79 ± 0.35 (P <0.001) for the top section of the soil in a microcosm. Phanerochaete chrysosporium and Phlebia radiata did not influence repellency. None of the fungi had an effect at 20 mm depth

Effects of soil type and composition of rhizodeposits on rhizosphere priming phenomena

Inputs of fresh plant-derived C may stimulate microbially-mediated turnover of soil organic matter (SOM) in the rhizosphere. But studies of such ‘priming’ effects in artificial systems often produce conflicting results, depending on such variables as rates of substrate addition, substrate composition, whether pure compounds or mixtures of substrates are used, and whether the addition is pulsed or continuous. Studies in planted systems are less common, but also produce apparently conflicting results, and the mechanisms of these effects are poorly understood. To add to the evidence on these matters, we grew a C4 grass for 61 d in two contrasting soils – an acid sandy soil and a more fertile clay-loam – which had previously only supported C3 vegetation. We measured total soil respiration and its C isotope composition, and used the latter to partition the respiration between plant- and soil-C sources. We found SOM turnover was enhanced (i.e. positive priming) by plant growth in both soils. In treatments in which the grass was clipped, net growth was greatly diminished, and priming effects were correspondingly weak. In treatments without clipping, net plant growth, total soil respiration and SOM-derived respiration were all much greater. Further, SOM-derived respiration increased over time in parallel with increases in plant growth, but the increase was delayed in the less fertile soil. We conclude the observed priming effects were driven by microbial demand for N, fuelled by deposition of C substrate from roots and competition with roots for N. The extent of priming depended on soil type and plant growing conditions. In a further experiment, we simulated rhizodeposition of soluble microbial substrates in the same two soils with near-continuous additions for 19 d of either C4-labelled sucrose (i.e. a simple single substrate) or a maize root extract (i.e. a relatively diverse substrate), and we measured soil respiration and its C isotope signature. In the more fertile soil, sucrose induced increasingly positive priming effects over time, whereas the maize root extract produced declining priming effects over time. We suggest this was because N and other nutrients were provided from the mineralization of this more diverse substrate. In the less-fertile soil, microbial N demand was probably never satisfied by the combined mineralization from added substrate and soil organic matter. Therefore priming effects were approximately constant over time. We conclude that the chemical nature of putative priming compounds can greatly influence priming phenomena

Interactions between soil structure and fungi

The spatial organisation of soils is crucially important in affecting belowground function, and the associated delivery of ecosystem services. Fungi constitute an important part of the soil biomass. As well as playing key roles in nutrient cycling and biotic interactions, they are also intimately involved in soil structural dynamics. Fungi mediate the formation of soil structure at a variety of spatial scales via charge, adhesive and enmeshment mechanisms. They also produce large quantities of hydrophobic compounds that affect water infiltration properties of soils. Fungi can also destroy soil structure via decomposition of organic matter that affects soil aggregation. In turn, soil structure affects fungi. The filamentous growth-form of fungi is a very efficient spacefilling structure well adapted for life in a spatially heterogeneous environment such as soil, but the labyrinthine pore network ultimately regulates how fungal mycelia grow through and function within the soil. The distribution of water within soils plays a crucial role in governing fungal development and activity, as does the spatial distribution of nutrient resources. This article reviews the continual interplay that occurs between soil structure and fungi, and discusses how self-organisation mechanisms may operate in the soil system

Risk Assessment of E. coli Survival Up to the Grazing Exclusion Period After Dairy Slurry, Cattle Dung, and Biosolids Application to Grassland

peer-reviewedGrassland application of dairy slurry, cattle dung, and biosolids offers an opportunity to recycle valuable nutrients (N, P, and K), which may all introduce pathogens to the soil environment. Herein, a temporal risk assessment of the survival of Escherichia coli (E. coli) up to 40 days in line with the legislated grazing exclusion time points after application was examined across six scenarios: (1) soil and biosolids mixture, (2) biosolids amended soil, (3) dairy slurry application, (4) cattle dung on pasture, (5) comparison of scenario 2, 3, and 4, and (6) maximum legal vs. excess rate of application for scenario 2 and 3. The risk model input parameters were taken or derived from regressions within the literature and an uncertainty analysis (n = 1,000 trials for each scenario) was conducted. Scenario 1 results showed that E. coli survival was higher in the soil/biosolids mixture for higher biosolids portion, resulting in the highest 20 day value of residual E. coli concentration (i.e., C20, log10 CFU g−1 dw) of 1.0 in 100% biosolids or inoculated soil and the lowest C20 of 0.098 in 75/25 soil/biosolids ratio, respectively, in comparison to an average initial value of ~6.4 log10 CFU g−1 dw. The E. coli survival across scenario 2, 3, and 4 showed that the C20 value of biosolids (0.57 log10 CFU g−1 dw) and dairy slurry (0.74 log10 CFU ml−1) was 2.9–3.7 times smaller than that of cattle dung (2.12 log10 CFU g−1 dw). The C20 values of biosolids and dairy slurry associated with legal and excess application rates ranged from 1.14 to 1.71 log10 CFU ha−1, which is a significant reduction from the initial concentration range (12.99 to 14.83 log10 CFU ha−1). The E. coli survival in un-amended soil was linear with a very low decay rate resulting in a higher C20 value than that of biosolids or dairy slurry. The risk assessment and uncertainly analysis showed that the residual concentrations in biosolids/dairy slurry applied soil after 20 days would be 45–57% lower than that of the background soil E. coli concentration. This means the current practice of grazing exclusion times is safe to reduce the risk of E. coli transmission into the soil environment.This publication has emanated from research funded by the EU FP7 Environment theme–Grant no. 265269 Marketable sludge derivatives from a highly integrated wastewater treatment plant (END-O-SLUDG)

Land-Use Changes Associated with Oil Palm Plantations Impact PLFA Microbial Phenotypic Community Structure throughout the Depth of Tropical Peats

Tropical peatlands are complex and globally-important ecosystems that are increasingly threatened by anthropogenic disturbances, primarily via agricultural development. Microbes in peatlands play important roles in governing overall ecosystem functions and sustenance, with specific population dynamics governing carbon sink or source dynamics. We determined phenotypic microbial community structures under forest, drained, burned and oil palm plantation peatlands, using phospholipid fatty acid (PLFA) profiling. Communities were distinct under each land-use type, varied consistently with depth down to two metres, but with a distinct characteristic shift at circa one metre depth. There was bacterial dominance across all land-use types and depths. The burnt peatland showed the greatest contrast relative to forest, possibly due to the difference in water table level. Gram-positive bacteria was the most dominant group in surface layers under all land-use types except burnt, and their relative abundance decreased with depth, replaced by Gram-negative groups in deeper layers. Fungal relative abundance remained low across both land-use types and depth ranges. Our results shed light on a hitherto virtually unknown tropical peat microbial phenotypic community structure and indicate that anthropogenic disturbance in tropical peatlands severely alter microbial communities

Soil microbial community assembly precedes vegetation development after drastic techniques to mitigate effects of nitrogen deposition

Oligotrophic semi-natural systems are threatened by high levels of nitrogen deposition. To mitigate these effects, drastic techniques such as sod-cutting and topsoil removal are applied to reduce nitrogen loads in existing systems and expand their area on former agricultural fields. We assessed the effects of these techniques along with the influence of previous land-use, isolation and vegetation development on subsequent microbial community assembly in restored agricultural areas. Microbial community phenotypic structure was measured using PLFA-analysis, along with soil chemistry and vegetation development. Differences in soil nitrogen pools due to restoration techniques were the most differentiating factor for both microbial community assembly and vegetation development. Only after topsoil removal was resemblance of both below- and above-ground communities to well-developed heathlands increased within 10–15 years. After sod-cutting both microbial community and vegetation composition remained more similar to agricultural sites. The relative contribution of agricultural sites and heathlands in the direct vicinity had more pronounced effects on local microbial community composition than current land-use in all study sites including agricultural areas and heathlands. Vegetation development was apparently of minor importance for microbial community assembly, since characteristic belowground assembly preceded that of aboveground development in both restoration contexts

The heterogeneous soil environment:are there preferential pathways for fungal spread?

Most studies with soil-borne pathogenic fungi have been done with little explicit characterisation of soil structure within which fungi spread and biotic interactions occur. Soil, however, constitutes a framework of surfaces formed by old root channels, cracks or biopores in combination with aggregates. Using epidemiological and soil biological techniques in controlled environments we investigated the effect of soil heterogeneity on fungal growth dynamics. We show that cracks and larger pores can act either as preferential pathways or barriers for the spread of fungal plant pathogens through soil. Understanding the effect of soil structure on pathogen and antagonist dynamics is therefore critical for our understanding of epidemics and the development of control strategies in a heterogeneous environment

Nutrient and trace element concentrations influence greenhouse gas emissions from Malaysian tropical peatlands

Tropical peatlands are unique and globally important ecosystems for carbon storage that are generally considered nutrient poor. However, different nutrient and trace element concentrations in these complex ecosystems and their interactions with carbon emissions are largely unknown. The objective of this research was to explore the concentrations of macro- and micronutrients and othertrace elements in surface peats, and their relationship with greenhouse gas emissions in North Selangor peatlands subjected to different land use. All nutrient and trace element concentrations except chromium exhibited significant differences between sites. Most macronutrients and some micronutrients showed significant differences between seasons, typically with a reduction over time from wet to dry seasons, possibly due to leaching. CO2 emissions were positively related to organic matter content and manganese concentrations and negatively correlated with selenium. CH4 emissions were positively correlated with organic matter content, manganese, copper, barium, cobalt and aluminium, and negatively correlated with molybdenum, selenium, lithium and vanadium. This research has detected loss of essential nutrients over time, aiding to increase nutrient limitation in tropical peatlands due to drainage. The observed significant correlation between trace elements and greenhouse gas emissions strengthens the importance of including trace element analyses in understanding the biogeochemical functions of these understudied peatlands