Monilinia spp., which causes brown rot, is one of the most damaging pathogens in stone fruits. Researchers are exploring epiphytic and endophytic microorganisms with the potential to suppress pathogens, control pathogenic microorganisms, and/or promote plant growth. In this study, microorganisms with antagonistic activity against three Monilinia species were isolated from plum orchard soil and plum fruits. Antagonism tests in vitro showed strong antagonistic properties of six strains of bacteria and two yeast-like fungi against M. fructigena, M. fructicola, and M. laxa, with growth inhibition from 45.5 to 84.6%. The antagonists were identified and characterized at the genetic level using whole genome sequencing (WGS). Genes involved in antibiotic resistance, virulence, secondary metabolite synthesis, and plant growth promotion were identified and characterized through genome mapping, gene prediction, and annotation. None of the microorganisms studied were predicted to be pathogenic to humans. The results of this study indicate that the bacteria Bacillus pumilus, B. velezensis, two strains of Lysinibacillus agricola, Pseudomonas chlororaphis isolated from stone fruit orchard soil, and the yeast-like fungus Aureobasidium pullulans, isolated from plums, are promising candidates for the biological control of Monilinia spp.

Whole-life geotechnical design accounts for the evolution of geotechnical properties due to the actions imparted on the infrastructure during the design life to improve design outcomes. In fine-grained soils, geotechnical properties evolve as a result of cyclic softening from excess pore pressure generation under undrained cyclic loading, and hardening during subsequent dissipation. Traditionally geotechnical design has focused on reduced strength and stiffness from softening, overlooking beneficial effects of hardening leading to increases in strength and stiffness. This paper presents a surrogate model that can capture the evolution of geotechnical properties of normally and lightly over consolidated clays through episodes of undrained pre-failure cyclic loading with intervening consolidation, validated against laboratory element test results. The surrogate model is shown to capture the essential elements of the whole-life soil-structure interaction, which include: (i) the excess pore pressure generated during undrained cyclic loading and the associated soil softening; (ii) the reduction in void ratio caused by the dissipation of excess pore pressured during the consolidation process; and (iii) the evolution of undrained shear strength and stiffness through these processes. The surrogate model allows rapid estimation of evolving soil properties in design, enabling automated optimization of geotechnical design calculations (such as required size of foundations or anchors), and use in probabilistic analyses such as Monte Carlo approaches, to quantify the influence of uncertainty in loading history and geotechnical parameters on system reliability.

For the safe use of microbiome-based solutions in agriculture, the genome sequencing of strains composing the inoculum is mandatory to avoid the spread of virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Moreover, the annotated genomes can enable the design of specific primers to trace the inoculum into the soil and provide insights into the molecular and genetic mechanisms of plant growth promotion and biocontrol activity. In the present work, the genome sequences of some members of beneficial microbial consortia that have previously been tested in greenhouse and field trials as promising biofertilizers for maize, tomato and wheat crops have been determined. Strains belong to well-known plant-growth-promoting bacterial genera such as Bacillus, Burkholderia, Pseudomonas and Rahnella. The genome size of strains ranged from 4.5 to 7.5 Mbp, carrying many genes spanning from 4402 to 6697, and a GC content of 0.04% to 3.3%. The annotation of the genomes revealed the presence of genes that are implicated in functions related to antagonism, pathogenesis and other secondary metabolites possibly involved in plant growth promotion and gene clusters for protection against oxidative damage, confirming the plant-growth-promoting (PGP) activity of selected strains. All the target genomes were found to possess at least 3000 different PGP traits, belonging to the categories of nitrogen acquisition, colonization for plant-derived substrate usage, quorum sensing response for biofilm formation and, to a lesser extent, bacterial fitness and root colonization. No genes putatively involved in pathogenesis were identified. Overall, our study suggests the safe application of selected strains as plant probiotics for sustainable agriculture.

The exopolysaccharide (EPS) produced by Pantoea alhagi NX-11, referred to as alhagan, enhances plant stress resistance, improves soil properties, and exhibits notable rheological properties. Despite these benefits, the exact bio-synthetic process of alhagan by P. alhagi NX-11 remains unclear. This study focused on sequencing the complete genome of P. alhagi NX-11 and identifying an alhagan synthesis gene cluster (LQ939_RS12550 to LQ939_RS12700). Gene annotation revealed that alhagan biosynthesis in P. alhagi NX-11 follows the Wzx/Wzy-dependent pathway. Furthermore, transcriptome analysis of P. alhagi NX-11 highlighted significant upregulation of four glycosyltransferase genes (alhH, wcaJ, alhK, and alhM) within the alhagan synthesis gene cluster. These glycosyltransferases are crucial for alhagan synthesis. To delve deeper into this process, two upregulated and uncharacterized glycosyltransferase genes, alhH and alhK, were knocked out. The resulting mutants, Delta alhH and Delta alhK, showed a notable decrease in EPS yield, reduced molecular weight, and altered monosaccharide compositions. These findings contribute to a better understanding of the alhagan biosynthesis mechanism in P. alhagi NX-11.

Phosphonates (PHTs), organic compounds with a stable C-P bond, are widely distributed in nature. Glyphosate (GP), a synthetic PHT, is extensively used in agriculture and has been linked to various human health issues and environmental damage. Given the prevalence of GP, developing cost-effective, on-site methods for GP detection is key for assessing pollution and reducing exposure risks. We adopted Agrobacterium tumefaciens CHLDO, a natural GP degrader, as a host and the source of genetic parts for constructing PHT biosensors. In this bacterial species, the phn gene cluster, encoding the C-P lyase pathway, is regulated by the PhnF transcriptional repressor. We selected the phnG promoter, which displays a dose-dependent response to GP, to build a set of whole-cell biosensors. Through stepwise genetic optimization of the transcriptional cascade, we created a whole-cell biosensor capable of detecting GP in the 0.25-50 mu M range in various samples, including soil and water.

The accurate quantification of the temporal changes in seabed strength allows for more reliable and less conservative geotechnical design. A recently developed effective stress framework, established within a one-dimensional computational domain to quantify changes in soil strength due to pore pressure generation and dissipation, has been extended to a twodimensional (2D) computational domain to allow for consideration of boundary value problems that are too complex to be simplified to one-dimensional conditions. The work to implement the 2D framework is reported across two companion papers. The first of the two papers utilises large deformation finite element analyses to quantify the spatial distribution of accumulated plastic shear strain. These distributions are encapsulated within a strain influence function that is used within the new 2D framework in this paper to calculate the extent and magnitude of excess pore pressure, and in turn the mobilised soil strength for a number of boundary value problems that represent typical offshore geotechnical processes. The merit of the new 2D framework is explored via retrospective simulations of existing experimental and numerical data. The resulting comparisons demonstrate the potential of the new framework, which is in quantifying the reliability of a range of geotechnical structures under complex loading conditions.

The undrained shear strength of contractive fine-grained soils changes with time, reducing due to pore pressure generation and increasing during consolidation. There is an increasing appetite to recognise these temporal soil strength changes in offshore geotechnical design, as it provides a basis for potentially less conservative designs. Contributions to this endeavour are reported across two companion papers. This first paper extends an existing effective stress framework that relates the generation of pore pressure to accumulated plastic shear strain, allowing undrained shear strength to be calculated within the context of critical-state soil mechanics. The main development is the extension of the computational domain to two dimensions, allowing calculations to be made for boundary value problems that cannot be satisfactorily simplified to onedimensional conditions. The magnitude and distribution of accumulated shear strain surrounding objects buried in soil are quantified through a series of large deformation finite element analyses. These spatial distributions are described using a strain influence function in the new 2D framework to calculate the extent and magnitude of excess pore pressure, and in turn the mobilised soil strength around the buried object. The performance of the 2D framework is examined in the companion paper through retrospective simulations of experimental and numerical data.

Vanillic acid (VA) is a phenolic compound frequently present in wastewater and agricultural soil. High concentrations of VA will increase the burden of sewage treatment and pose toxicity to crop plants. Although advanced oxidation has been successfully used to remove VA, green and sustainable treatments for VA pollution with efficient VA-degrading microbes, especially about the full pathways of VA degradation, are not well documented. In this study, a full investigation of VA degradation ability and associated metabolic mechanisms in the new VA-degrading bacterium Herbaspirillum aquaticum KLS-1 was performed. Results showed that strain KLS1 completely removed 500 mg/L VA within 36 h following a zero-order degradation kinetic model with a degradation half-time of 15.01 h. An efficient VA degradation occurred under the conditions with pH values of 7-9, temperatures of 30-40 degrees C, and shaking speeds of 150-200 rpm. A fed-batch experiment and SEM analysis showed that strain KLS-1 exhibited a good ability to remove up to 46.8 mg VA without cellular damage. The protocatechuate ortho-cleavage pathway was probably associated with efficient VA degradation in strain KLS-1 according to the whole genome sequencing and transcriptomic analysis. This study has offered a comprehensive understanding of full VA degradation mechanisms in microbes by using genomic sequencing coupled with transcriptomic analysis and provided a new VA-degrading bacterium for potential bioremediation of VA pollution.

Heavy metals are dangerous contaminants that constitute a threat to human health because they persist in soils and are easily transferred into the food chain, causing damage to human health. Among heavy metals, nickel appears to be one of the most dangerous, being responsible for different disorders. Public health protection requires nickel detection in the environment and food chains. Biosensors represent simple, rapid, and sensitive methods for detecting nickel contamination. In this paper, we report on the setting up a whole-cell-based system, in which protoplasts, obtained from Nicotiana tabacum leaves, were used as transducers to detect the presence of heavy metal ions and, in particular, nickel ions. Protoplasts were genetically modified with a plasmid containing the Green Fluorescent Protein reporter gene (GFP) under control of the promoter region of a sunflower gene coding for a small Heat Shock Protein (HSP). Using this device, the presence of heavy metal ions was detected. Thus, the possibility of using this whole-cell system as a novel tool to detect the presence of nickel ions in food matrices was assessed.

Pesticides and fertilizers used in agriculture can negatively affect the soil, increasing its toxicity. In this work, a battery of whole-cell bacterial lux-biosensors based on the E. coli MG1655 strain with various inducible promoters, as well as the natural luminous Vibrio aquamarinus VKPM B-11245 strain, were used to assess the effects of agrochemical soil treatments. The advantages of using biosensors are sensitivity, specificity, low cost of analysis, and the ability to assess the total effect of toxicants on a living cell and the type of their toxic effect. Using the V. aquamarinus VKPM B-11245 strain, the synergistic effect of combined soil treatment with pesticides and mineral fertilizers was shown, which led to an increase in the overall (integral) toxicity of soils higher than that of the individual application of substances. Several probable implementation mechanisms of agrochemical toxic effects have been discovered. DNA damage caused by both SOS response induction and alkylation, oxidative stress due to increased superoxide levels, and damage to cellular proteins and membranes are among them. Thus, the usage of biosensors makes it possible to assess the cumulative effect of various toxicants on living organisms without using expensive chemical analyses.