Establishment of a transparent soil system to study Bacillus subtilis chemical ecology

Bacterial secondary metabolites are structurally diverse molecules that drive microbial interaction by altering growth, cell differentiation, and signaling. Bacillus subtilis, a Gram-positive soil-dwelling bacterium, produces a wealth of secondary metabolites, among them, lipopeptides have been vastly studied by their antimicrobial, antitumor, and surfactant activities. However, the natural functions of secondary metabolites in the lifestyles of the producing organism remain less explored under natural conditions, i.e. in soil. Here, we describe a hydrogel-based transparent soil system to investigate B. subtilis chemical ecology under controllable soil-like conditions. The transparent soil matrix allows the growth of B. subtilis and other isolates gnotobiotically and under nutrient-controlled conditions. Additionally, we show that transparent soil allows the detection of lipopeptides production and dynamics by HPLC-MS and MALDI-MS imaging, along with fluorescence imaging of 3-dimensional bacterial assemblages. We anticipate that this affordable and highly controllable system will promote bacterial chemical ecology research and help to elucidate microbial interactions driven by secondary metabolites.

Archaeal and Bacterial Diversity and Distribution Patterns in Mediterranean-Climate Vernal Pools of Mexico and the Western USA

Biogeographic patterns in microorganisms are poorly understood, despite the importance of microbial communities for a range of ecosystem processes. Our knowledge of microbial ecology and biogeography is particularly deficient in rare and threatened ecosystems. We tested for three ecological patterns in microbial community composition within ephemeral wetlands—vernal pools—located across Baja California (Mexico) and California (USA): (1) habitat filtering; (2) a latitudinal diversity gradient; and (3) distance decay in community composition. Paired water and soil samples were collected along a latitudinal transect of vernal pools, and bacterial and archaeal communities were characterized using 16S rDNA sequencing. We identified two main microbial communities, with one community present in the soil matrix that included archaeal and bacterial soil taxa, and another community present in the overlying water that was dominated by common freshwater bacterial taxa. Aquatic microbial communities were more diverse in the north, and displayed a significant but inverted latitudinal diversity pattern. Aquatic communities also exhibited a significant distance-decay pattern, with geographic proximity, and precipitation explaining part of the community variation. Collectively these results indicate greater sensitivity to spatial and environmental variation in vernal pool aquatic microbial communities than in soil microbial communities. We conclude that vernal pool aquatic microbial communities can display distribution patterns similar to those exhibited by larger organisms, but differ in some key aspects, such as the latitudinal gradient in diversity.

The effect of the use of a soil improver based on waste brown coal on the enzymatic activity of soil in the cultivation of Paulownia hybrids (Paulownia Siebold & Zuccarini, 1835)

The effect of the use of a soil improver based on waste brown coal on the enzymatic activity of soil in the cultivation of Paulownia hybrids (Paulownia Siebold & Zuccarini, 1835). An important element in controlling the condition of the soil and the plants grown on it are tests of the enzymatic activity of the soil matrix. One of the greatest advantages of using enzyme tests is the ability to make an assessment that also includes other non-measurable factors that affect soil health and condition. The diagnosed changes in soil enzymatic activity are the best parameter for determining the biochemical processes taking place there. This article describes the enzymatic activity of lessive soils on which the Paulownia hybrid variety is cultivated and a soil improver based on waste brown coal is used

Stepping beyond perfectly mixed conditions in soil hydrological modelling using a Lagrangian approach

A recent experiment of Bowers et al. (2020) revealed that diffusive mixing of water isotopes (δ2H, δ18O) over a fully saturated soil sample of a few centimetres in length required several days to equilibrate completely. In this study, we present an approach to simulate such time-delayed diffusive mixing processes on the pore scale beyond instantaneously and perfectly mixed conditions. The diffusive pore mixing (DIPMI) approach is based on a Lagrangian perspective on water particles moving by diffusion over the pore space of a soil volume and carrying concentrations of solutes or isotopes. The idea of DIPMI is to account for the self-diffusion of water particles across a characteristic length scale of the pore space using pore-size-dependent diffusion coefficients. The model parameters can be derived from the soil-specific water retention curve and no further calibration is needed. We test our DIPMI approach by simulating diffusive mixing of water isotopes over the pore space of a saturated soil volume using the experimental data of Bowers et al. (2020). Simulation results show the feasibility of the DIPMI approach to reproduce measured mixing times and concentrations of isotopes at different tensions over the pore space. This result corroborates the finding that diffusive mixing in soils depends on the pore size distribution and the specific soil water retention properties. Additionally, we perform a virtual experiment with the DIPMI approach by simulating mixing and leaching processes of a solute in a vertical, saturated soil column and comparing results against simulations with the common perfect-mixing assumption. Results of this virtual experiment reveal that the frequently observed steep rise and long tailing of breakthrough curves, which are typically associated with non-uniform transport in heterogeneous soils, may also occur in homogeneous media as a result of imperfect subscale mixing in a macroscopically homogeneous soil matrix.

Internal Instability in Soils: A Critical Review of the Fundamentals and Ramifications

Seepage-induced fine-particle migration that leads to a change in the conductivity of a soil matrix is referred to as internal instability. This could jeopardize the structural integrity of the soil matrix by initiating suffusion (or suffosion), a form of internal erosion. Susceptibility to suffusion has been studied mostly under extreme laboratory conditions to develop empirical design criteria, which are typically based on the particle size distribution. The physics governing the process have not been comprehensively uncovered in the classical studies because of experimental limitations. Mainstream evaluation methods often over-idealize the suffusion process, holding a probabilistic perspective for estimating constriction sizes and fines migration. Prospective studies on constitutive modeling techniques and modern computational techniques have allowed a more representative evaluation and deeper insight into the problem. Recent advances in sensing technologies, visualization, and tracking techniques have equally enriched the quality of the data on suffusion. This paper sets out to present the long-standing knowledge on the internal instability phenomenon in soils. An attempt is made to pinpoint ambiguities and underscore research gaps. The classical empirical studies and modern visualizing techniques are integrated with particle-based numerical simulations to strengthen the theoretical understanding of the phenomenon.

Direct evidence for the role of microbial community composition in the formation of soil organic matter composition and persistence

The largest terrestrial carbon sink on earth is soil carbon stocks. As the climate changes, the rate at which the Earth’s climate warms depends in part on the persistence of soil organic carbon. Microbial turnover forms the backbone of soil organic matter (SOM) formation and it has been recently proposed that SOM molecular complexity is a key driver of stability. Despite this, the links between microbial diversity, chemical complexity and biogeochemical nature of SOM remain missing. Here we tested the hypotheses that distinct microbial communities shape the composition of SOM, and microbial-derived SOM has distinct decomposition potential depending on its community of origin. We inoculated microbial communities of varying diversities into a model soil matrix amended with simple carbon (cellobiose) and measured the thermal stability of the resultant SOM. Using a Rock-Eval® ramped thermal analysis, we found that microbial community composition drives the chemical fingerprint of soil carbon. While diversity was not a driver of SOM composition, bacteria-only communities lead to more thermally labile soil C pools than communities with bacteria and fungi. Our results provide direct evidence for a link between microbial community structure, SOM composition, and thermal stability. This evidence demonstrates the relevance of soil microorganisms in building persistent SOM stocks.

Variation in root exudate composition influences soil microbiome membership and function

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix. Previous research has shown that plant root exudate profiles vary between species and genotypes which can likely support different microbial associations. Here, utilizing distinct sorghum genotypes as a model system, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolisms. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments, a High Organic acid Treatment (HOT) and a High Sugar Treatment (HST). Root exudate treatments were added to laboratory soil reactors and 16S rRNA gene profiling illustrated distinct microbial membership in response to HST or HOT amendments. Alpha and beta diversity metrics were significantly different between treatments, (Shannon’s, p < 0.0001, mrpp = 0.01, respectively). Exometabolite production was highest in the HST, with increased production of key organic acids, non-proteinogenic amino acids, and three plant growth-promoting phytohormones (benzoic acid, salicylic acid, indole-3-acetic acid), suggesting plant-derived sugars fuel microbial carbon metabolism and contribute to phytohormone production. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified potential plant growth-promoting microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multi-omics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production.

The Geo-Hydro-Mechanical Properties of a Turbiditic Formation as Internal Factors of Slope Failure Processes

Similar to many inner areas of Southern Europe, the Daunia Apennines are affected by widespread landsliding, often consisting of slow, deep-seated movements. Recurrent acceleration of these landslides causes damage to buildings and infrastructures, severely biasing the socio-economic development of the region. Most landslides in the area of study occur within clayey units of turbiditic flysch formations, often severely disturbed by tectonic thrust and previous landsliding. The Faeto Flysch (FAE) is one of the most widespread turbiditic formations in the Daunia Apennines and is representative of the tectonised geological formations involved in slope failure. This work, by examining the landslide processes occurring at four pilot sites, aims at connecting the observed mechanisms to the geo-hydro-mechanical setup of FAE in the slopes. It is found that the soil portion of FAE consists of highly plastic clays, resulting in low intrinsic shear strength, and hence controls the initiation and progression of failure in the slopes, as such representing an internal predisposing factor to landsliding. In addition, the presence of fractured rock strata confers a high permeability at the slope scale, with respect to that of the soil matrix. This results in severe piezometric levels in the slope, which represent another internal predisposing factor to failure, and in the ability to induce significant seasonal pore water pressure oscillations down to great depths, connected to rainfall infiltration, thus triggering the recurrent acceleration of the landslides.

Antibiotics in the soil and their effect on the soil microbiot

Antibiotics have been crucial in the fight against infectious diseases for the past 50 years. In agriculture they are widely used in the treatment of animals, birds and aquaculture, to prevent spoilage of feed, as stimulators of growth and productivity of livestock, in the production of essential amino acids as impurities in feed, and so on. At present, the use of antibiotics in animal husbandry has become excessive due to the prevention of global epidemics. In turn, the ingress of antibiotics into water and soil, in particular through organic fertilizers, poses a potential threat to these environments. Thus, a variety of antibiotic resistance genes (GRAs) are spreading in soil microorganisms, which is currently a global health problem. It is believed that the stability of antibiotics after entering the soil is mainly due to their rate of decomposition and sorption to the organic soil matrix. A wide range of values of the half-life (DT50) of these compounds in soils indicates that their stability depends on a number of factors: soil properties, climatic conditions (temperature, precipitation, and humidity), physicochemical characteristics of antibiotics. High antimicrobial activity of antibiotics in the soil differentially inhibits the development of soil microorganisms, affects their species composition, which can cause changes in the ecological functionality of the soil. Thus, even low concentrations of antibiotics significantly reduce soil respiration. This phenomenon is especially noticeable in the presence of sulfamethoxazole, sulfamethazine, sulfadiazine and trimethoprim in the soil. The presence of antibiotics in the soil affects the processes of nitrification and / or denitrification, and the inhibition of these processes depends on the duration of exposure and the type of compound. Monensin and chlortetracycline at concentrations of 0.01–0.1 and 0.0003–0.3 mg/kg of soil do not affect nitrification at all. Antibiotics also affect the rate of iron transformation in the soil. Thus, sulfadiazine and monensin block the reduction of iron (Fe (III)) in the soil from a few days to 50 days. It should be noted that the lack of standardized tests hinders research that would lead to generalized conclusions about the effects of antibiotics on biogeochemical cycles, in particular on iron circulation. An important indicator of the response to antibiotics in the soil is considered to be the change in the enzymatic activity of dehydrogenase, phosphatase and urease of soil microorganisms, which may be associated with growth inhibition or death of sensitive microorganisms. In addition, the presence of some antibiotics in the soil can cause over-population of fungal populations, which are generally less sensitive to antibiotics than bacteria. There is evidence that antibiotics alter the enzymatic activity of soil microorganisms, especially they affect the ability to metabolize carbon of various origins. In addition, antibiotics not only affect the total number of microbiota, but also the relative content of different groups (gram-negative and gram-positive bacteria, fungi) in microbial populations. The importance of GRA studies of soil microorganisms is that they have led to the discovery of new genes responsible for bacterial resistance to antibiotics.

A constitutive model for gassy clay

Fine-grained marine sediments often contain gas bubbles that can cause many geotechnical problems. This soil has a composite structure with gas bubbles fitting within the saturated soil matrix. The gas cavity has a detrimental effect on the soil stiffness and strength when they are filled with undissolved gas only. The gas cavity can be filled with gas and pore water due to ‘bubble flooding’. Bubble flooding has a beneficial effect on the soil stiffness and undrained shear strength because it makes the saturated soil matrix partially drained under a globally undrained condition. A critical state constitutive model for gassy clay is presented which accounts for the composite structure of the soil and bubble flooding. The gas cavity is assumed to have a detrimental effect on the plastic hardening of the saturated soil matrix. Some of the bubbles can be flooded by pore water from the saturated soil matrix which leads to higher mean effective stress of the saturated soil matrix. Consequently, both soil stiffness and strength increase. Only one new parameter is introduced to model the detrimental effect of gas bubbles on plastic hardening. The model has been validated by the results of three gassy clays.