The Hydroponic Rockwool Root Microbiome: Under Control or Underutilised?

Land plants have an ancient and intimate relationship with microorganisms, which influences the composition of natural ecosystems and the performance of crops. Plants shape the microbiome around their roots by releasing organic nutrients into the soil. Hydroponic horticulture aims to protect crops from damaging soil-borne pathogens by replacing soil with an artificial growing medium, such as rockwool, an inert material made from molten rock spun into fibres. Microorganisms are generally considered a problem to be managed, to keep the glasshouse clean, but the hydroponic root microbiome assembles soon after planting and flourishes with the crop. Hence, microbe-plant interactions play out in an artificial environment that is quite unlike the soil in which they evolved. Plants in a near-ideal environment have little dependency on microbial partners, but our growing appreciation of the role of microbial communities is revealing opportunities to advance practices, especially in agriculture and human health. Hydroponic systems are especially well-suited to active management of the root microbiome because they allow complete control over the root zone environment; however, they receive much less attention than other host-microbiome interactions. Novel techniques for hydroponic horticulture can be identified by extending our understanding of the microbial ecology of this unique environment.

Cotton strip assay detects soil microbial degradation differences among crop rotation and tillage experiments on Vertisols.

The cotton strip assay (CSA) is a simple and inexpensive method of evaluating management effects on soil microbial decomposition. The average loss of tensile strength of cotton strips buried 3 to 35 days in soils from two long-term tillage and crop-rotation experiments was of the order: cotton-wheat rotation > minimum-tillage cotton monoculture > maximum-tillage cotton monoculture. The study suggests CSA can be an effective indicator to delineate microbial activity, soil organic carbon or crop biomass as influenced by agricultural practices in cotton fields.

Modelling polycyclic aromatic hydrocarbon bioavailability in historically contaminated soils with six in-vitro chemical extractions and three earthworm ecotypes.

Accurate prediction of organic contaminant bioavailability for risk assessment in ecological applications is hindered by limited validation on relevant bioassay species. Here, six in-vitro chemical extraction methods (butanol, non-buffered and buffered hydroxypropyl-ß-cyclodextrin (HPCD, Buf-HPCD), Tenax, potassium persulfate oxidation, polyoxymethylene solid phase extraction (POM)) were tested for PAH bioaccumulation prediction in three earthworm ecotypes with dissimilar exposures, Amynthas sp., Eisenia fetida, and Lumbricus terrestris, in historically contaminated soils from manufactured gas plant (MGP) sites. Extractions were compared directly and modelled in a calculation approach using equilibrium partitioning theory (EqPT) with a novel combination of different organic carbon/octanol-water partitioning parameters (KOC and KOW). In the direct comparison approach Buf-HPCD showed the closest prediction of accumulation for burrowing Amynthas sp. and L. terrestris (within 1.5 and 3.1, respectively), but Tenax and POM showed the closest approximation for E. fetida (within 1.1 and 0.9, respectively). The optimum method for predicting PAH bioaccumulation in the calculation approach depended on earthworm species and the partitioning parameters used in equations of the four models, but overall POM, which was independent of KOC, showed the closest approximation of accumulation, within a factor of 2.5 across all species. This work effectively identifies the optimum in-vitro based approaches for PAH bioavailability prediction in earthworms as a model soil health indicator for ecological risk assessment within regulatory and remediation decision frameworks.

Advancing prediction of polycyclic aromatic hydrocarbon bioaccumulation in plants for historically contaminated soils using Lolium multiflorum and simple chemical in-vitro methodologies.

This study compared chemical extraction methods for the prediction of PAH bioaccumulation in ryegrass (Lolium multiflorum) roots in four Manufactured Gas Plant (MGP) historically (>50 years) contaminated soils. The in-vitro methods compared were butanol (BuOH), non-buffered and buffered 2-hydroxypropyl-ß-cyclodextrin extractions (HPCD, Buf-HPCD), potassium persulfate oxidation (KPS), solid phase extraction using Tenax resin (Tenax), and polyoxymethylene solid-phase extraction (POM). Extractions were directly compared with bioaccumulation and modelled using equilibrium partitioning theory (EqPT) with a combination of different partitioning parameters (KOC and KOW values) that aimed to improve predictions. The PAH accumulation in plant roots showed good correlation with concentrations in soils, and higher concentrations of the 4-6 ring PAHs compared with 2-3 ring PAHs. Plant accumulation of 16 PAHs in L. multiflorum was estimated within a factor of 5 using direct comparison for all bioaccessibility extraction methods. Accumulation values predicted using the calculation approach depended on the combination of KOC, KOW parameters and root components (total lipid vs total dry weight) used in calculations. Using KOC values derived from historically contaminated soils improved accuracy of predicted total root accumulation although precision was low. The combined contribution of PAH in lipid and carbohydrate root components (total dry weight) overestimated accumulation and a lipid only approach using generic partitioning parameters provided more accurate and precise approximation of bioaccumulation in roots of L. multiflorum in the soils. Overall, Tenax, POM and HPCD-based extractions showed promising results for predicting L. multiflorum root accumulation using the different approaches. This work significantly extends current knowledge for integrating simple chemical extractions into ecological risk assessment frameworks for the prediction of plant PAH bioavailability in historically contaminated soils.

Coring lubricants can increase soil microbial activity in Vertisols.

It is essential that sampling procedures for biological measurements are done in a way that reflects the soil processes, whilst limiting sampling artefacts. In heavy clay Vertisol soils, coring lubricants are often considered necessary in order to extract and recover soil for quality and health assessments. Previous reports into the use of coring lubricants have found soil carbon measurements to be inflated but to date, a study to evaluate the effects of these lubricants on soil microbial activity, has not been forthcoming. We measured soil carbon dioxide (CO2) evolution in response to the addition of common coring lubricants, to determine the effects upon soil microbial activity to the depth of 100 cm. Application of coring lubricants to the surface soil layers of field collected cores did not significantly influence CO2 evolution however, microbial activity increased in deeper soil layers (30-100 cm) with the use of WD-40, mould stripper and silicone oil. When the ratio of coring lubricant to soil was increased to ~5 g coring lubricant to 100 g-1 soil, there was a significant (P = .001) effect on microbial activity, with silicone oil and mould stripper inflating measurements by at least 5%, whilst olive oil and WD-40 were similar to the control. The results imply that when using coring rigs to recover soil for microbial functional analysis in Vertisols, the use of coring lubricants is best avoided, with further research recommended.

The impact of carbon addition on the organisation of rhizosheath of chickpea.

Spatio-temporal development of the rhizosheath during root elongation has the potential to modify the function of the rhizosphere under abiotic stress. We quantified the impact of carbon (i.e. glucose) addition on the development and function of rhizosheath of drought tolerant and sensitive chickpea (Cicer arietinum L.) by integrating soil pore volume obtained from X-ray microtomography (µCT), soil physical and microbial respiration measures, and measurements of root traits. Structural equation modelling indicated the feedback mechanisms between added carbon, root traits, pore geometry, and soil functions differed between the cultivars in a fashion congruent with the concept of soil as a self-organising system that interacts with an introduced root system. The drought tolerant cultivar partitioned more photosynthetically fixed carbon to the roots, had more root hairs and more porous rhizosheath, as compared with the sensitive cultivar.

Capitalizing on deliberate, accidental, and GM-driven environmental change caused by crop modification.

The transgenic traits associated with the majority of commercial genetically modified crops are focused on improving herbicide and insecticide management practices. The use of the transgenic technology in these crops and the associated chemistry has been the basis of studies that provide evidence for occasional improvement in environmental benefits due to the use of less residual herbicides, more targeted pesticides, and reduced field traffic. This is nicely exemplified through studies using Environmental Impact Quotient (EIQ) assessments. Whilst EIQ evaluations may sometimes illustrate environmental benefits they have their limitations. EIQ evaluations are not a surrogate for Environmental Risk Assessments and may not reflect real environmental interactions between crops and the environment. Addressing the impact cultivated plants have on the environment generally attracts little public attention and research funding, but the introduction of GM has facilitated an expansion of research to address potential environmental concerns from government, NGOs, industry, consumers, and growers. In this commentary, some evidence from our own research and several key papers that highlight EIQ assessments of the impact crops are having on the environment are presented. This information may be useful as an education tool on the potential benefits of GM and conventional farming. In addition, other deliberate, accidental, and GM-driven benefits derived from the examination of GM cropping systems is briefly discussed.

Effect of nematodes on rhizosphere colonization by seed-applied bacteria.

There is much interest in the use of seed-applied bacteria for biocontrol and biofertilization, and several commercial products are available. However, many attempts to use this strategy fail because the seed-applied bacteria do not colonize the rhizosphere. Mechanisms of rhizosphere colonization may involve active bacterial movement or passive transport by percolating water or plant roots. Transport by other soil biota is likely to occur, but this area has not been well studied. We hypothesized that interactions with soil nematodes may enhance colonization. To test this hypothesis, a series of microcosm experiments was carried out using two contrasting soils maintained under well-defined physical conditions where transport by mass water flow could not occur. Seed-applied Pseudomonas fluorescens SBW25 was capable of rhizosphere colonization at matric potentials of -10 and -40 kPa in soil without nematodes, but colonization levels were substantially increased by the presence of nematodes. Our results suggest that nematodes can have an important role in rhizosphere colonization by bacteria in soil.

Comparison of the spectral emission of lux recombinant and bioluminescent marine bacteria.

The purpose of the present paper was to study the influence of bacteria harbouring the luciferase-encoding Vibrio harveyi luxAB genes upon the spectral emission during growth in batch-culture conditions. In vivo bioluminescence spectra were compared from several bioluminescent strains, either naturally luminescent (Vibrio fischeri and Vibrio harveyi) or in recombinant strains (two Gram-negative Escherichia coli::luxAB strains and a Gram-positive Bacillus subtilis::luxAB strain). Spectral emission was recorded from 400 nm to 750 nm using a highly sensitive spectrometer initially devoted to Raman scattering. Two peaks were clearly identified, one at 491-500 nm (+/- 5 nm) and a second peak at 585-595 (+/- 5 nm) with the Raman CCD. The former peak was the only one detected with traditional spectrometers with a photomultiplier detector commonly used for spectral emission measurement, due to their lack of sensitivity and low resolution in the 550-650 nm window. When spectra were compared between all the studied bacteria, no difference was observed between natural or recombinant cells, between Gram-positive and Gram-negative strains, and growth conditions and growth medium were not found to modify the spectrum of light emission.