sp. nov., a novel species isolated from the beech rhizosphere.

Bacterial strain H4R21 was isolated from beech rhizosphere soil sampled in the forest experimental site of Montiers (Meuse, France). It effectively weathers minerals, hydrolyses chitin and produces quorum sensing signal molecules. The strain is aerobic and Gram-stain-negative.

Re-Envisioning the Plant Disease Triangle: Full Integration of the Host Microbiota and a Focal Pivot to Health Outcomes.

The disease triangle is a structurally simple but conceptually rich model that is used in plant pathology and other fields of study to explain infectious disease as an outcome of the three-way relationship between a host, a pathogen, and their environment. It also serves as a guide for finding solutions to treat, predict, and prevent such diseases. With the omics-driven, evidence-based realization that the abundance and activity of a pathogen are impacted by proximity to and interaction with a diverse multitude of other microorganisms colonizing the same host, the disease triangle evolved into a tetrahedron shape, which features an added fourth dimension representing the host-associated microbiota.

Applied microbiology of the phyllosphere.

The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics.

Characterization of Seed Mycobiota Using Culture-Dependent and Culture-Independent Approaches.

Seed fungi are potentially important for their roles in seedling microbiome assembly and seedling health, but surveys of full seed fungal communities remain limited. While culture-dependent methods have been used to characterize some members of the seed mycobiota, recent culture-independent studies have improved the ease in identifying and characterizing full seed fungal communities. In this chapter, we describe how to survey seed fungi using both traditional culture-based methods and culture-free metabarcoding.

Genomic and transcriptomic characterization of the Collimonas quorum sensing genes and regulon.

Collimonads are well-adapted to nutrient-poor environments. They are known to hydrolyse chitin, produce antifungal metabolites, weather minerals, and are effective biocontrol agents protecting plants from fungal diseases. The production of N-acyl homoserine lactones (AHLs) was suggested to be a conserved trait of collimonads, but little is known about the genes that underlie this production or the genes that are controlled by AHLs.

A metacommunity ecology approach to understanding microbial community assembly in developing plant seeds.

Microorganisms have the potential to affect plant seed germination and seedling fitness, ultimately impacting plant health and community dynamics. Because seed-associated microbiota are highly variable across individual plants, plant species, and environments, it is challenging to identify the dominant processes that underlie the assembly, composition, and influence of these communities. We propose here that metacommunity ecology provides a conceptually useful framework for studying the microbiota of developing seeds, by the application of metacommunity principles of filtering, species interactions, and dispersal at multiple scales.

Comparison of bacterial diversity, root exudates and soil enzymatic activities in the rhizosphere of AVP1-transgenic and nontransgenic wheat (Triticum aestivum L.).

Aims: Soil microbial communities are among the most diverse communities that might be affected due to transgenic crops. Therefore, risk assessment studies on transgenes are essentially required as any adverse effects may depend not only on the specific gene and crop involved but also on soil conditions.

Methods And Results: The present study deals with the comparison of bacterial populations, root exudates and activities of soil enzymes in nontransgenic and AVP1-transgenic wheat rhizosphere, overexpressing vacuolar H + pyrophosphatase for salinity and drought stress tolerance.

It's the Economy, Stupid: Applying (Micro)economic Principles to Microbiome Science.

A key challenge in microbiome science is the scale mismatch problem, which arises when the scale at which microbial communities are sampled, interrogated, and averaged is different from the scale at which individual microorganisms within those communities interact with each other and with their environment. Profiling the microbial communities in a teaspoon of soil, from a scoop of fecal matter, or along a plant leaf surface represents a scale mismatch of multiple orders of magnitude, which may limit our ability to interpret or predict species interactions and community assembly within such samples. In this Perspective, we explore how economists, who are historically and topically split along the lines of micro- and macroeconomics, deal with the scale mismatch problem, and how taking clues from (micro)economists could benefit the field of microbiomics.

Optimizing viability and yield and improving stability of Gram-negative, non-spore forming plant-beneficial bacteria encapsulated by spray-drying.

This study investigates methods to commercialize safer alternatives to chemical pesticides that pose risks to human safety and the environment. Spray-drying encapsulation of the plant-protective, antifungal bacterium Collimonas arenae Cal35 in in situ cross-linked alginate microcapsules (CLAMs) was optimized to minimize losses during spray-drying and maximize yield of spray-dried powder. Only inlet temperature significantly affected survival during spray-drying, while inlet temperature, spray rate, and alginate concentration significantly affected yield of spray-dried powder.

Sporulation is dispensable for the vegetable-associated life cycle of the human pathogen Bacillus cereus.

Bacillus cereus is a common food-borne pathogen that is responsible for important outbreaks of food poisoning in humans. Diseases caused by B. cereus usually exhibit two major symptoms, emetic or diarrheic, depending on the toxins produced.

Repeated Exposure of Aspergillus niger Spores to the Antifungal Bacterium Collimonas fungivorans Ter331 Selects for Delayed Spore Germination.

The bacterial strain Collimonas fungivorans Ter331 (CTer331) inhibits mycelial growth and spore germination in Aspergillus niger N402 (N402). The mechanisms underlying this antagonistic bacterial-fungal interaction have been extensively studied, but knowledge on the long-term outcome of this interaction is currently lacking. Here, we used experimental evolution to explore the dynamics of fungal adaptation to recurrent exposure to Ter331.

Identification of Collimonas gene loci involved in the biosynthesis of a diffusible secondary metabolite with broad-spectrum antifungal activity and plant-protective properties.

In greenhouse and field trials, a bacterial mixture of Collimonas arenae Cal35 and Bacillus velezensis FZB42, but not Cal35 alone or FZB42 alone, was able to protect tomato plants from challenge with the soilborne fungal pathogen Fusarium oxysporum f.sp. lycopersici (Fol).

Bacterial catabolism of indole-3-acetic acid.

Indole-3-acetic acid (IAA) is a molecule with the chemical formula CHNO, with a demonstrated presence in various environments and organisms, and with a biological function in several of these organisms, most notably in plants where it acts as a growth hormone. The existence of microorganisms with the ability to catabolize or assimilate IAA has long been recognized. To date, two sets of gene clusters underlying this property in bacteria have been identified and characterized: one (iac) is responsible for the aerobic degradation of IAA into catechol, and another (iaa) for the anaerobic conversion of IAA to 2-aminobenzoyl-CoA.

Interruption of Aspergillus niger spore germination by the bacterially produced secondary metabolite collimomycin.

Collimonas fungivorans Ter331 (CfTer331) is a soil bacterium that produces collimomycin, a secondary metabolite that inhibits the vegetative growth of fungi. Here we show that CfTer331 can also interfere with fungal spore germination and that collimomycin biosynthesis is required for this activity. More specifically, in co-cultures of Aspergillus niger N402 (AnN402) co-nidiospores with CfTer331, the rate of transition from the isotropic to polarized stage of the germination process was reduced and the relatively few AnN402 conidiospores that completed the germination process were less likely to survive than those that were arrested in the isotropic phase.

A brief from the leaf: latest research to inform our understanding of the phyllosphere microbiome.

The plant leaf surface, or phyllosphere, represents a unique and challenging microbial biome with a diverse and dynamic community of commensal, parasitic, and mutualistic agents of microscopic proportions. This mini-review offers a digest of recently published research dedicated to the study of phyllosphere microbiota, framed in the context of processes and outcomes of microbial community assembly, structure, and (inter)activity in the phyllosphere, with particular focus on the contributions of environment, plant, and microbe, and on the potential benefits of interrogating those contributions at finer resolutions.

Abundance, diversity and plant-specific adaptations of plant-associated lactic acid bacteria.

Lactic acid bacteria (LAB) are essential for many fruit, vegetable and grain food and beverage fermentations. However, the numbers, diversity and plant-specific adaptions of LAB found on plant tissues prior to the start of those fermentations are not well understood. When measured, these bacteria have been recovered from the aerial surfaces of plants in a range from <10 CFU g to over 10 CFU g of plant tissue and in lower quantities from the soil and rhizosphere.

An roGFP2-Based Bacterial Bioreporter for Redox Sensing of Plant Surfaces.

The reduction-oxidation (redox) environment of the phytobiome (i.e., the plant-microbe interface) can strongly influence the outcome of the interaction between microbial pathogens, commensals, and their host.

Metabolome and Microbiome Signatures in the Roots of Citrus Affected by Huanglongbing.

Huanglongbing (HLB) is a severe, incurable citrus disease caused by the bacterium ' Liberibacter asiaticus' (CLas). Although citrus leaves serve as the site of initial infection, CLas is known to migrate to and colonize the root system; however, little is known about the impact of CLas infection on root metabolism and resident microbial communities. Scions of 'Lisbon' lemon and 'Washington Navel' orange grafted onto 'Carrizo' rootstock were grafted with either CLas-infected citrus budwood or uninfected budwood.

Finished Genome Sequence of the Indole-3-Acetic Acid-Catabolizing Bacterium Pseudomonas putida 1290.

Use of indole-3-acetic acid (IAA) as a carbon, nitrogen, and energy source by 1290 is linked to the possession of a gene cluster that codes for conversion to catechol. Here, we present the genomic context of this gene cluster, which includes genes for IAA chemotaxis/transport and catechol catabolism.

Persistence of f. sp. in Soil Through Asymptomatic Colonization of Rotation Crops.

Asymptomatic plant colonization is hypothesized to enhance persistence of pathogenic forms of . However, a correlation between pathogen populations on living, asymptomatic plant tissues and soilborne populations after tillage has not been demonstrated. Living and dead tissues of broccoli, lettuce, spinach, wheat, cilantro, raspberry, and strawberry plants grown in soil infested with f.

Gene Expression in the Indole-3-Acetic Acid-Degrading Soil Bacterium Enterobacter soli LF7.

We show for soil bacterium LF7 that the possession of an ndole-3-cetic acid atabolic () gene cluster is causatively linked to the ability to utilize the plant hormone indole-3-acetic acid (IAA) as a carbon and energy source. Genome-wide transcriptional profiling by mRNA sequencing revealed that these genes, chromosomally arranged as and coding for the transformation of IAA to catechol, were the most highly induced (>29-fold) among the relatively few (<1%) differentially expressed genes in response to IAA. Also highly induced and immediately downstream of the cluster were genes for a major facilitator superfamily protein () and enzymes of the β-ketoadipate pathway (), which channels catechol into central metabolism.

Impact of soil pedogenesis on the diversity and composition of fungal communities across the California soil chronosequence of Mendocino.

Understanding how soil pedogenesis affects microbial communities and their in situ activities according to ecosystem functioning is a central issue in soil microbial ecology, as soils represent essential nutrient reservoirs and habitats for the biosphere. To address this question, soil chronosequences developed from a single, shared mineralogical parent material and having the same climate conditions are particularly useful, as they isolate the factor of time from other factors controlling the character of soils. In our study, we considered a natural succession of uplifted marine terraces in Mendocino, CA, ranging from highly fertile in the younger terrace (about 100,000 years old) to infertile in the older terraces (about 300,000 years old).

From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality.

Models are important tools in microbial ecology. They can be used to advance understanding by helping to interpret observations and test hypotheses, and to predict the effects of ecosystem management actions or a different climate. Over the past decades, biological knowledge and ecosystem observations have advanced to the molecular and in particular gene level.