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Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.

Listeria monocytogenes is a ubiquitous, opportunistic pathogenic organism. Environmental adaptation requires constant regulation of gene expression. Among transcriptional regulators, AgrA is part of an auto-induction system. Temperature is an environmental cue critical for in vivo adaptation. In order to investigate how temperature may affect AgrA-dependent transcription, we compared the transcriptomes of the parental strain L. monocytogenes EGD-e and its ΔagrA mutant at the saprophytic temperature of 25°C and in vivo temperature of 37°C. Variations of transcriptome were higher at 37°C than at 25°C. Results suggested that AgrA may be involved in the regulation of nitrogen transport, amino acids, purine and pyrimidine biosynthetic pathways and phage-related functions. Deregulations resulted in a growth advantage at 37°C, but affected salt tolerance. Finally, our results suggest overlaps with PrfA, σB, σH and CodY regulons. These overlaps may suggest that through AgrA, Listeria monocytogenes integrates information on its biotic environment.

Background For ten years, CRISPR/cas9 system has become a very useful tool for obtaining site-specific mutations on targeted genes in many plant organisms. This technology opens up a wide range of possibilities for improved plant breeding in the future. In plants, the CRISPR/Cas9 system is mostly used through stable transformation with constructs that allow for the expression of the Cas9 gene and sgRNA. Numerous studies have shown that site-specific mutation efficiency can vary greatly between different plant species due to factors such as plant transformation efficiency, Cas9 expression, Cas9 nucleotide sequence, the addition of intronic sequences, and many other parameters. Since 2016, when the first edited grapevine was created, the number of studies using functional genomic approaches in grapevine has remained low due to difficulties with plant transformation and gene editing efficiency. In this study, we optimized the process to obtain site-specific mutations and generate knock-out mutants of grapevine ( Vitis vinifera cv. ‘Chardonnay’). Building on existing methods of grapevine transformation, we improved the method for selecting transformed plants at chosen steps of the developing process using fluorescence microscopy. Results By comparison of two different Cas9 gene and two different promoters, we increased site-specific mutation efficiency using a maize-codon optimized Cas9 containing 13 introns (zCas9i), achieving up to 100% biallelic mutation in grapevine plantlets cv. ‘Chardonnay’. These results are directly correlated with Cas9 expression level. Conclusions Taken together, our results highlight a complete methodology for obtaining a wide range of homozygous knock-out mutants for functional genomic studies and future breeding programs in grapevine.

Current knowledge about effects of disturbance on the fate of invaders in complex microbial ecosystems is still in its infancy. In order to investigate this issue, we compared the fate of Klebsiella pneumoniae (Kp) and Listeria monocytogenes (Lm) in soil microcosms. We then used environmental disturbances (freeze–thaw or heat cycles) to compare the fate of both invaders and manipulate soil microbial diversity. Population dynamics of the two pathogens was assessed over 50 days of invasion while microbial diversity was measured at times 0, 20 and 40 days. The outcome of invasion was strain-dependent and the response of the two invaders to disturbance differed. Resistance to Kp invasion was higher under the conditions where resident microbial diversity was the highest while a significant drop of diversity was linked to a higher persistence. In contrast, Lm faced stronger resistance to invasion in heat-treated microcosms where diversity was the lowest. Our results show that diversity is not a universal proxy of resistance to microbial invasion, indicating the need to properly assess other intrinsic properties of the invader, such as its metabolic repertoire, or the array of interactions between the invader and resident communities.

Soil DNA extraction has become a critical step in describing microbial biodiversity. Historically, ascertaining overarching microbial ecological theories has been hindered as independent studies have used numerous custom and commercial DNA extraction procedures. For that reason, a standardized soil DNA extraction method (ISO-11063) was previously published. However, although this ISO method is suited for molecular tools such as quantitative PCR and community fingerprinting techniques, it has only been optimized for examining soil bacteria. Therefore, the aim of this study was to assess an appropriate soil DNA extraction procedure for examining bacterial, archaeal and fungal diversity in soils of contrasting land-use and physico-chemical properties. Three different procedures were tested: the ISO-11063 standard; a custom procedure (GnS-GII); and a modified ISO procedure (ISOm) which includes a different mechanical lysis step (a FastPrep ®-24 lysis step instead of the recommended bead-beating). The efficacy of each method was first assessed by estimating microbial biomass through total DNA quantification. Then, the abundances and community structure of bacteria, archaea and fungi were determined using real-time PCR and terminal restriction fragment length polymorphism approaches. Results showed that DNA yield was improved with the GnS-GII and ISOm procedures, and fungal community patterns were found to be strongly dependent on the extraction method. The main methodological factor responsible for differences between extraction procedure efficiencies was found to be the soil homogenization step. For integrative studies which aim to examine bacteria, archaea and fungi simultaneously, the ISOm procedure results in higher DNA recovery and better represents microbial communities.

AbstractBackground Microbial communities are of tremendous importance for ecosystem functioning and yet we know little about the ecological processes driving the assembly of these communities in the environment. Here, we used an unprecedented experimental approach based on the manipulation of physical distance between neighboring cells during soil colonization to determine the role of bacterial interactions in soil community assembly. We hypothesized that experimentally manipulating the physical distance between bacterial cells will modify the interaction strengths leading to differences in microbial community composition, with increasing distance between neighbors favoring poor competitors.Results We found significant differences in both bacterial community diversity, composition and co-occurrence networks after soil colonization that were related to physical distancing. We show that reducing distances between cells resulted in a loss of bacterial diversity, with at least 41% of the dominant OTUs being significantly affected by physical distancing. Our results suggest that physical distancing may differentially modulate competitiveness between neighboring species depending on the taxa present in the community. The mixing of communities that assembled at high and low cell densities did not reveal any “home field advantage” during coalescence. This confirms that the observed differences in competitiveness were due to biotic rather than abiotic filtering.Conclusions Our study demonstrates that the competitiveness of bacteria strongly depends on cell density and community membership, therefore highlighting the fundamental role of microbial interactions in the assembly of soil communities.

In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism–soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.In this Review, Philippot et al. explore how soil microorganisms can affect the physical and chemical properties of soil and discuss the ecological and evolutionary consequences of these microbially driven shifts in soil properties. They also explore how microbially mediated changes in soil properties can be used to combat threats to soil health and other environmental challenges.

Pesticides affect a diverse range of non-target species and may be linked to global biodiversity loss. The magnitude of this hazard remains only partially understood. We present a synthesis of pesticide (insecticide, herbicide and fungicide) impacts on multiple non-target organisms across trophic levels based on 20,212 effect sizes from 1,705 studies. For non-target plants, animals (invertebrate and vertebrates) and microorganisms (bacteria and fungi), we show negative responses of the growth, reproduction, behaviour and other physiological biomarkers within terrestrial and aquatic systems. Pesticides formulated for specific taxa negatively affected non-target groups, e.g. insecticidal neonicotinoids affecting amphibians. Negative effects were more pronounced in temperate than tropical regions but were consistent between aquatic and terrestrial environments, even after correcting for field-realistic terrestrial and environmentally relevant exposure scenarios. Our results question the sustainability of current pesticide use and support the need for enhanced risk assessments to reduce risks to biodiversity and ecosystems.

Arbuscular mycorrhizal symbiosis occurs between obligate biotrophic fungi of the phylum Glomeromycota and most of land plants. The exchange of nutrients between host plants and arbuscular mycorrhizal fungi is presumed to be the main benefit for the two symbiotic partners. In this review article, we outline the current concepts of nutrient exchanges within this symbiosis (mechanisms and regulation). First, we focus on phosphorus and nitrogen transfer from the fungal partner to the host plant and on the reciprocal transfer of carbon compounds, with a highlight on a possible interplay between nitrogen and phosphorus nutrition during arbuscular mycorrhizal symbiosis. We further discuss potential mechanisms of regulation of these nutrient exchanges linked to membrane dynamics. The review finally addresses the common mycorrhizal networks formed by arbuscular mycorrhizal fungi, which inter-connect plants from similar and/or different species. Then the best way to integrate this knowledge and the ensuing potential benefits of arbuscular mycorrhiza in a sustainable agriculture is discussed. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

1. Nitrogen is the major nutrient limiting plant growth in terrestrial ecosystems, and the transformation of inert nitrogen to forms that can be assimilated by plants is mediated by soil micro-organisms. 2 The last decade has witnessed many significant advances in our understanding of plant-microbe interactions with evidence that plants have evolved multiple strategies to cope with nitrogen limitation by shaping and recruiting nitrogen-cycling microbial communities. However, most studies have typically focused on the impact of plants on only one, or relatively few, processes within the nitrogen cycle. 3 This review synthesizes recent advances in our understanding of the various routes by which plants influence the availability of nitrogen via an array of interactions with different guilds of nitrogen-cycling micro-organisms. We also propose a plant trait-based framework for linking plant nitrogen acquisition strategies to the activities of nitrogen-cycling microbial guilds. In doing so, we provide a more comprehensive picture of the ecological relationships between plants and nitrogen-cycling micro-organisms in terrestrial ecosystems. 4 Finally, we identify previously overlooked processes within the nitrogen cycle that could be targeted in future research and be of interest for plant health or for improving plant nitrogen acquisition, while minimizing nitrogen inputs and losses in sustainable agricultural systems.