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

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

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

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 holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots

Despite often being conceptualized as a thin layer of soil around roots, the rhizosphere is actually a dynamic system of interacting processes. Hiltner originally defined the rhizosphere as the soil influenced by plant roots. However, soil physicists, chemists, microbiologists, and plant physiologists have studied the rhizosphere independently, and therefore conceptualized the rhizosphere in different ways and using contrasting terminology. Rather than research-specific conceptions of the rhizosphere, the authors propose a holistic rhizosphere encapsulating the following components: microbial community gradients, macroorganisms, mucigel, volumes of soil structure modification, and depletion or accumulation zones of nutrients, water, root exudates, volatiles, and gases. These rhizosphere components are the result of dynamic processes and understanding the integration of these processes will be necessary for future contributions to rhizosphere science based upon interdisciplinary collaborations. In this review, current knowledge of the rhizosphere is synthesized using this holistic perspective with a focus on integrating traditionally separated rhizosphere studies. The temporal dynamics of rhizosphere activities will also be considered, from annual fine root turnover to diurnal fluctuations of water and nutrient uptake. The latest empirical and computational methods are discussed in the context of rhizosphere integration. Clarification of rhizosphere semantics, a holistic model of the rhizosphere, examples of integration of rhizosphere studies across disciplines, and review of the latest rhizosphere methods will empower rhizosphere scientists from different disciplines to engage in the interdisciplinary collaborations needed to break new ground in truly understanding the rhizosphere and to apply this knowledge for practical guidance

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

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