Unravelling the impact of environmental factors in shaping plant microbiomes.

This article emphasizes the significant role of environmental factors in shaping the plant microbiome, highlighting how bacterial and fungal communities influence plant responses to water stress, and how environmental factors shape fungal communities in crops. Furthermore, recent studies describe how different genotypes and levels of water stress affect the composition of bacterial communities associated with quinoa plants, as well as the relationship between environmental factors and the structure of fungal communities in apple fruit. These findings underscore the importance of understanding plant microbiome dynamics in developing effective crop protection strategies and improving agricultural sustainability with the objective of advance towards a microbiome-based strategy which allows us to improve crop tolerance to abiotic stresses.

Sporulation Activated via σW Protects Bacillus from a Tse1 Peptidoglycan Hydrolase Type VI Secretion System Effector.

Within bacterial communities, community members engage in interactions employing diverse offensive and defensive tools to reach coexistence. Extracellular-matrix production and sporulation are defensive mechanisms used by Bacillus subtilis cells when they interact with Pseudomonas chlororaphis strains expressing a type VI secretion system (T6SS). Here, we define Tse1 as the main toxin mobilized by the Pseudomonas chlororaphis T6SS that triggers sporulation in Bacillus subtilis. We characterize Tse1 as a peptidoglycan hydrolase that indirectly alters the dynamics and functionality of the Bacillus cell membrane. We also delineate the response of Bacillus cells to Tse1, which through the coordinated actions of the extracellular sigma factor σW and the cytoplasmic histidine kinases KinA and KinB, culminates in activation of the sporulation cascade. We propose that this cellular developmental response permits bacilli to defend against the toxicity of T6SS-mobilized Tse1 effector. IMPORTANCE The study of bacterial interactions is helping to define species-specific strategies used to modulate the competition dynamics underlying the development of community compositions. In this study, we deciphered the role of Pseudomonas T6SS when competing with Bacillus and the mechanism by which a T6SS-toxin modifies Bacillus physiology. We found that Pseudomonas triggers Bacillus sporulation by injecting through T6SS a toxin that we called Tse1. We found that Tse1 is a hydrolase that degrades Bacillus peptidoglycan and indirectly damages Bacillus membrane functionality. In addition, we demonstrated the mechanism by which Bacillus cells increase the sporulation rate upon recognition of the presence of Tse1. Interestingly, asporogenic Bacillus cells are more sensitive to T6SS activity, which led us to propose sporulation as a last resort of bacilli to overcome this family of toxins.

Native metabolomics identifies the rivulariapeptolide family of protease inhibitors.

The identity and biological activity of most metabolites still remain unknown. A bottleneck in the exploration of metabolite structures and pharmaceutical activities is the compound purification needed for bioactivity assignments and downstream structure elucidation. To enable bioactivity-focused compound identification from complex mixtures, we develop a scalable native metabolomics approach that integrates non-targeted liquid chromatography tandem mass spectrometry and detection of protein binding via native mass spectrometry. A native metabolomics screen for protease inhibitors from an environmental cyanobacteria community reveals 30 chymotrypsin-binding cyclodepsipeptides. Guided by the native metabolomics results, we select and purify five of these compounds for full structure elucidation via tandem mass spectrometry, chemical derivatization, and nuclear magnetic resonance spectroscopy as well as evaluation of their biological activities. These results identify rivulariapeptolides as a family of serine protease inhibitors with nanomolar potency, highlighting native metabolomics as a promising approach for drug discovery, chemical ecology, and chemical biology studies.

A Noninvasive Method for Time-Lapse Imaging of Microbial Interactions and Colony Dynamics.

Complex interactions between microbial populations can greatly affect the overall properties of a microbial community, sometimes leading to cooperation and mutually beneficial coexistence, or competition and the death or displacement of organisms or subpopulations. Interactions between different biofilm populations are highly relevant in diverse scientific areas, from antimicrobial resistance to microbial ecology. The utilization of modern microscopic techniques has provided a new and interesting insight into how bacteria interact at the cellular level to form and maintain microbial biofilms. However, our ability to follow complex intraspecies and interspecies interactions in vivo at the microscopic level has remained somewhat limited. Here, we detailed BacLive, a novel noninvasive method for tracking bacterial growth and biofilm dynamics using high-resolution fluorescence microscopy and an associated ImageJ processing macro (https://github.com/BacLive) for easier data handling and image analysis. Finally, we provided examples of how BacLive can be used in the analysis of complex bacterial communities. IMPORTANCE Communication and interactions between single cells are continuously defining the structure and composition of microbial communities temporally and spatially. Methods routinely used to study these communities at the cellular level rely on sample manipulation which makes microscopic time-lapse experiments impossible. BacLive was conceived as a method for the noninvasive study of the formation and development of bacterial communities, such as biofilms, and the formation dynamics of specialized subpopulations in time-lapse experiments at a colony level. In addition, we developed a tool to simplify the processing and analysis of the data generated by this method.

Chemical Proportionality within Molecular Networks.

Molecular networking of non-targeted tandem mass spectrometry data connects structurally related molecules based on similar fragmentation spectra. Here, we report the Chemical Proportionality (ChemProp) contextualization of molecular networks. ChemProp scores the changes of abundance between two connected nodes over sequential data series (e.g., temporal or spatial relationships), which can be displayed as a direction within the network to prioritize potential biological and chemical transformations or proportional changes of (biosynthetically) related compounds. We tested the ChemProp workflow on a ground truth data set of a defined mixture and highlighted the utility of the tool to prioritize specific molecules within biological samples, including bacterial transformations of bile acids, human drug metabolism, and bacterial natural products biosynthesis. The ChemProp workflow is freely available through the Global Natural Products Social Molecular Networking (GNPS) environment.

Chemical interplay and complementary adaptative strategies toggle bacterial antagonism and co-existence.

Bacterial communities are in a continuous adaptive and evolutionary race for survival. In this work we expand our knowledge on the chemical interplay and specific mutations that modulate the transition from antagonism to co-existence between two plant-beneficial bacteria, Pseudomonas chlororaphis PCL1606 and Bacillus amyloliquefaciens FZB42. We reveal that the bacteriostatic activity of bacillaene produced by Bacillus relies on an interaction with the protein elongation factor FusA of P. chlororaphis and how mutations in this protein lead to tolerance to bacillaene and other protein translation inhibitors. Additionally, we describe how the unspecific tolerance of B. amyloliquefaciens to antimicrobials associated with mutations in the glycerol kinase GlpK is provoked by a decrease of Bacillus cell membrane permeability, among other pleiotropic responses. We conclude that nutrient specialization and mutations in basic biological functions are bacterial adaptive dynamics that lead to the coexistence of two primary competitive bacterial species rather than their mutual eradication.

Bacterial extracellular matrix as a natural source of biotechnologically multivalent materials.

The extracellular matrix (ECM) is an intricate megastructure made by bacterial cells to form architecturally complex biostructures called biofilms. Protection of cells, modulation of cell-to-cell signalling, cell differentiation and environmental sensing are functions of the ECM that reflect its diverse chemical composition. Proteins, polysaccharides and eDNA have specific functionalities while cooperatively interacting to sustain the architecture and biological relevance of the ECM. The accumulated evidence on the chemical heterogeneity and specific functionalities of ECM components has attracted attention because of their potential biotechnological applications, from agriculture to the water and food industries. This review compiles information on the most relevant bacterial ECM components, the biophysical and chemical features responsible for their biological roles, and their potential to be further translated into biotechnological applications.

More than words: the chemistry behind the interactions in the plant holobiont.

Plants and microbes have evolved sophisticated ways to communicate and coexist. The simplest interactions that occur in plant-associated habitats, i.e., those involved in disease detection, depend on the production of microbial pathogenic and virulence factors and the host's evolved immunological response. In contrast, microbes can also be beneficial for their host plants in a number of ways, including fighting pathogens and promoting plant growth. In order to clarify the mechanisms directly involved in these various plant-microbe interactions, we must still deepen our understanding of how these interkingdom communication systems, which are constantly modulated by resident microbial activity, are established and, most importantly, how their effects can span physically separated plant compartments. Efforts in this direction have revealed a complex and interconnected network of molecules and associated metabolic pathways that modulate plant-microbe and microbe-microbe communication pathways to regulate diverse ecological responses. Once sufficiently understood, these pathways will be biotechnologically exploitable, for example, in the use of beneficial microbes in sustainable agriculture. The aim of this review is to present the latest findings on the dazzlingly diverse arsenal of molecules that efficiently mediate specific microbe-microbe and microbe-plant communication pathways during plant development and on different plant organs.

Dual functionality of the amyloid protein TasA in Bacillus physiology and fitness on the phylloplane.

Bacteria can form biofilms that consist of multicellular communities embedded in an extracellular matrix (ECM). In Bacillus subtilis, the main protein component of the ECM is the functional amyloid TasA. Here, we study further the roles played by TasA in B. subtilis physiology and biofilm formation on plant leaves and in vitro. We show that ΔtasA cells exhibit a range of cytological symptoms indicative of excessive cellular stress leading to increased cell death. TasA associates to the detergent-resistant fraction of the cell membrane, and the distribution of the flotillin-like protein FloT is altered in ΔtasA cells. We propose that, in addition to a structural function during ECM assembly and interactions with plants, TasA contributes to the stabilization of membrane dynamics as cells enter stationary phase.

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages.

In our daily lives, we consume foods that have been transported, stored, prepared, cooked, or otherwise processed by ourselves or others. Food storage and preparation have drastic effects on the chemical composition of foods. Untargeted mass spectrometry analysis of food samples has the potential to increase our chemical understanding of these processes by detecting a broad spectrum of chemicals. We performed a time-based analysis of the chemical changes in foods during common preparations, such as fermentation, brewing, and ripening, using untargeted mass spectrometry and molecular networking. The data analysis workflow presented implements an approach to study changes in food chemistry that can reveal global alterations in chemical profiles, identify changes in abundance, as well as identify specific chemicals and their transformation products. The data generated in this study are publicly available, enabling the replication and re-analysis of these data in isolation, and serve as a baseline dataset for future investigations.

Chemical fertilization: a short-term solution for plant productivity?

The effect of long-term chemical fertilization on plant-microorganisms and microbe-microbe interactions.

The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization.

Bacteria of the genera Pseudomonas and Bacillus can promote plant growth and protect plants from pathogens. However, the interactions between these plant-beneficial bacteria are understudied. Here, we explore the interaction between Bacillus subtilis 3610 and Pseudomonas chlororaphis PCL1606. We show that the extracellular matrix protects B. subtilis colonies from infiltration by P. chlororaphis. The absence of extracellular matrix results in increased fluidity and loss of structure of the B. subtilis colony. The P. chlororaphis type VI secretion system (T6SS) is activated upon contact with B. subtilis cells, and stimulates B. subtilis sporulation. Furthermore, we find that B. subtilis sporulation observed prior to direct contact with P. chlororaphis is mediated by histidine kinases KinA and KinB. Finally, we demonstrate the importance of the extracellular matrix and the T6SS in modulating the coexistence of the two species on melon plant leaves and seeds.

Ruminal metagenomic libraries as a source of relevant hemicellulolytic enzymes for biofuel production.

The success of second-generation (2G) ethanol technology relies on the efficient transformation of hemicellulose into monosaccharides and, particularly, on the full conversion of xylans into xylose for over 18% of fermentable sugars. We sought new hemicellulases using ruminal liquid, after enrichment of microbes with industrial lignocellulosic substrates and preparation of metagenomic libraries. Among 150 000 fosmid clones tested, we identified 22 clones with endoxylanase activity and 125 with ß-xylosidase activity. These positive clones were sequenced en masse, and the analysis revealed open reading frames with a low degree of similarity with known glycosyl hydrolases families. Among them, we searched for enzymes that were thermostable (activity at > 50°C) and that operate at high rate at pH around 5. Upon a wide series of assays, the clones exhibiting the highest endoxylanase and ß-xylosidase activities were identified. The fosmids were sequenced, and the corresponding genes cloned, expressed and proteins purified. We found that the activity of the most active ß-xylosidase was at least 10-fold higher than that in commercial enzymatic fungal cocktails. Endoxylanase activity was in the range of fungal enzymes. Fungal enzymatic cocktails supplemented with the bacterial hemicellulases exhibited enhanced release of sugars from pretreated sugar cane straw, a relevant agricultural residue.

The race for antimicrobials in the multidrug resistance era.

The appearance of multidrug-resistant pathogens is a major threat to human health with the reemergence of fatal and untreatable diseases. In addition to a rational use of the well-known and available antibiotics, two complementary ways to overcome this public health issue are (i) the discovery of new antimicrobials and (ii) the chemical modification of pre-existing potent antibiotics. In this article, we highlight some of the strategies to generate new and promising antimicrobials for use in the management of these so-called 'superbugs'.

Interspecies cross-talk between co-cultured Pseudomonas putida and Escherichia coli.

Pseudomonas putida and Escherichia coli are ubiquitous microorganisms that can be isolated from soil rhizosphere, the surface of vegetables, fresh waters and wastewaters - environments in which they likely co-exist. Despite this, the potential interactions between these microbes have not been studied in detail. To analyse these interactions, we carried out RNA-seq transcriptomic analysis of these microbes as monocultures and as co-cultures. Our results show that co-culture of these microbes significantly alters transcriptional profiles. The most dramatic transcriptional changes in both microorganisms were involved in central carbon metabolism, as well as adhesion to surfaces and the activation of drug efflux pumps. We also found that acetate production was one of the mechanisms used by E. coli K-12 MG1655 in response to the presence of P. putida DOT-T1E.