Stability of a Pseudomonas putida KT2440 bacteriophage-carried genomic island and its impact on rhizosphere fitness

Bacteriophage-driven microbial phenotypic heterogeneity: ecological and biogeochemical importance

Bacteriophages (phages) reprogram host metabolism and generate phenotypic heterogeneity, yet the mechanisms and ecological implications remain poorly understood representing a major knowledge gap in microbial ecology. This review explores how phage infection alters microbial physiology, contributes to single-cell variation, and influences population dynamics. We highlight the potential consequences of phage-driven heterogeneity for microbial community structure and biogeochemical cycling, underscoring the importance of integrating phage-host interactions into ecological and ecosystem models.

Rational Design Assisted by Evolutionary Engineering Allows (De)Construction and Optimization of Complex Phenotypes in Pseudomonas putida KT2440

Beyond the rational construction of genetic determinants to encode target functions, complex phenotype engineering requires the contextualisation of their expression within the metabolic and genetic background of the host strain. Furthermore, wherever metabolic complexity is involved, phenotype engineering demands standard, reliable, plug-and-play tools. We introduce GENIO (GENome Integration and fitness Optimization platform for Pseudomonas putida), a framework to optimise genetic circuit performance by means of (i) chromosome-location-based differential gene expression and (ii) subsequent fitness improvement through evolutionary engineering if needed. Using gene expression strength and cell-to-cell variation, we characterised 10 P. putida chromosomal loci (ppLPS) to show that genome context rather than distance to ORI is the main factor driving differential expression performance. We further contextualised ppLPS gene expression against well-known chromosomal integration sites and plasmids displaying different copy numbers. GENIO supports comprehensive exploration of the gene expression space across P. putida's genome while unlocking performance optimization of complex heterologous metabolic pathways through evolutionary engineering. To demonstrate the usability of GENIO, we restored P. putida's aromatic hydrocarbon metabolism by (de)constructing the toluene/m-xylene catabolic pathway coded in the pWW0 plasmid. We also showed that engineering complex phenotypes requires accurate contextualisation of the synthetic pathways involved, a process that benefits from biological robustness.

Genotypic and Phenotypic Characterization of Pseudomonas atacamensis EMP42 a PGPR Strain Obtained from the Rhizosphere of Echinocactus platyacanthus (Sweet Barrel)

Plant growth-promoting rhizobacteria (PGPR) are a group of bacteria that associate with the rhizosphere of plants; one of the most abundant bacterial genera in this ecological niche is Pseudomonas, which is constantly expanding due to the emergence of new species such as Pseudomonas atacamensis, whose discovery in 2019 has led to the characterization of several strains from different environments but taxonomically related. The objective of this work was to phenotypically and molecularly characterize P. atacamensis strain EMP42, isolated from the rhizosphere of Echinocactus platyacanthus. The strain EMP42 is able to use different substrates and reduce oxidative stress in plants. It is capable of improving growth parameters such as the number of inflorescences and the height of the aerial body of Arabidopsis thaliana, as well as the germination and seedling survival of the cacti Echinocactus platyacanthus and Astrophytum capricorne. The genetic structure of P. atacamensis EMP42 consists of a closed chromosome of 6.14 Mbp, and 61.1% GC content. It has 5572 genes, including those associated with PGPR activities, such as the trpABCDE, SAP, phoABPRU and acsABC genes, among others, and three ncRNA loci, nine regulatory regions, five complete rRNA operons and three CRISPR-Cas loci, showing phylogenomic similarities with the reference strain P. atacamensis B21-026. Therefore, this study contributes to the understanding of genomic diversity within P. atacamensis and, particularly, highlights the potential application of strain EMP42 as a PGPR.

Soil viral diversity, ecology and climate change

Soil viruses are highly abundant and have important roles in the regulation of host dynamics and soil ecology. Climate change is resulting in unprecedented changes to soil ecosystems and the life forms that reside there, including viruses. In this Review, we explore our current understanding of soil viral diversity and ecology, and we discuss how climate change (such as extended and extreme drought events or more flooding and altered precipitation patterns) is influencing soil viruses. Finally, we provide our perspective on future research needs to better understand how climate change will impact soil viral ecology.

Gene mobility in microbiomes of the mycosphere and mycorrhizosphere -role of plasmids and bacteriophages

Microbial activity in soil, including horizontal gene transfer (HGT), occurs in soil hot spots and at "hot moments". Given their capacities to explore soil for nutrients, soil fungi (associated or not with plant roots) can act as (1) selectors of myco(rrhizo)sphere-adapted organisms and (2) accelerators of HGT processes across the cell populations that are locally present. This minireview critically examines our current understanding of the drivers of gene mobility in the myco(rrhizo)sphere. We place a special focus on the role of two major groups of gene mobility agents, i.e. plasmids and bacteriophages. With respect to plasmids, there is mounting evidence that broad-host-range (IncP-1β and PromA group) plasmids are prominent drivers of gene mobility across mycosphere inhabitants. A role of IncP-1β plasmids in Fe uptake processes has been revealed. Moreover, a screening of typical mycosphere-inhabiting Paraburkholderia spp. revealed carriage of integrated plasmids, next to prophages, that presumably confer fitness enhancements. In particular, functions involved in biofilm formation and nutrient uptake were thus identified. The potential of the respective gene mobility agents to promote the movement of such genes is critically examined.

Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration

Theories in soil biology, such as plant-microbe interactions and microbial cooperation and antagonism, have guided the practice of ecological restoration (ecorestoration). Below-ground biodiversity (bacteria, fungi, invertebrates, etc.) influences the development of above-ground biodiversity (vegetation structure). The role of rhizosphere bacteria in plant growth has been largely investigated but the role of phages (bacterial viruses) has received a little attention. Below the ground, phages govern the ecology and evolution of microbial communities by affecting genetic diversity, host fitness, population dynamics, community composition, and nutrient cycling. However, few restoration efforts take into account the interactions between bacteria and phages. Unlike other phages, filamentous phages are highly specific, nonlethal, and influence host fitness in several ways, which make them useful as target bacterial inocula. Also, the ease with which filamentous phages can be genetically manipulated to express a desired peptide to track and control pathogens and contaminants makes them useful in biosensing. Based on ecology and biology of filamentous phages, we developed a hypothesis on the application of phages in environment to derive benefits at different levels of biological organization ranging from individual bacteria to ecosystem for ecorestoration. We examined the potential applications of filamentous phages in improving bacterial inocula to restore vegetation and to monitor changes in habitat during ecorestoration and, based on our results, recommend a reorientation of the existing framework of using microbial inocula for such restoration and monitoring. Because bacterial inocula and biomonitoring tools based on filamentous phages are likely to prove useful in developing cost-effective methods of restoring vegetation, we propose that filamentous phages be incorporated into nature-based restoration efforts and that the tripartite relationship between phages, bacteria, and plants be explored further. Possible impacts of filamentous phages on native microflora are discussed and future areas of research are suggested to preclude any potential risks associated with such an approach.

Multifaceted Impacts of Bacteriophages in the Plant Microbiome

Plant-associated bacteria face multiple selection pressures within their environments and have evolved countless adaptations that both depend on and shape bacterial phenotype and their interaction with plant hosts. Explaining bacterial adaptation and evolution therefore requires considering each of these forces independently as well as their interactions. In this review, we examine how bacteriophage viruses (phages) can alter the ecology and evolution of plant-associated bacterial populations and communities. This includes influencing a bacterial population's response to both abiotic and biotic selection pressures and altering ecological interactions within the microbiome and between the bacteria and host plant. We outline specific ways in which phages can alter bacterial phenotype and discuss when and how this might impact plant-microbe interactions, including for plant pathogens. Finally, we highlight key open questions in phage-bacteria-plant research and offer suggestions for future study.

Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element

Integrative and conjugative elements (ICEs) comprise ubiquitous large mobile regions in prokaryotic chromosomes that transmit vertically to daughter cells and transfer horizontally to distantly related lineages. Their evolutionary success originates in maximized combined ICE-host fitness trade-offs, but how the ICE impacts on the host metabolism and physiology is poorly understood. Here we investigate global changes in the host genetic network and physiology of Pseudomonas putida with or without an integrated ICEclc, a model ICE widely distributed in proteobacterial genomes. Genome-wide gene expression differences were analyzed by RNA-seq using exponentially growing or stationary phase-restimulated cultures on 3-chlorobenzoate, an aromatic compound metabolizable thanks to specific ICEclc-located genes. We found that the presence of ICEclc imposes a variety of changes in global pathways such as cell cycle and amino acid metabolism, which were more numerous in stationary-restimulated than exponential phase cells. Unexpectedly, ICEclc stimulates cellular motility and leads to more rapid growth on 3-chlorobenzoate than cells carrying only the integrated clc genes. ICEclc also concomitantly activates the P. putida Pspu28-prophage, but this in itself did not provoke measurable fitness effects. ICEclc thus interferes in a number of cellular pathways, inducing both direct benefits as well as indirect costs in P. putida.

The 'Neglected' Soil Virome - Potential Role and Impact

Bacteriophages are among the most abundant and diverse biological units in the biosphere. They have contributed to our understanding of the central dogma of biology and have been instrumental in the evolutionary success of bacterial pathogens. In contrast to our current understanding of marine viral communities, the soil virome and its function in terrestrial ecosystems has remained relatively understudied. Here, we examine, in a comparative fashion, the knowledge gathered from studies performed in soil versus marine settings. We address the information with respect to the abundance, diversity, ecological significance, and effects of, in particular, bacteriophages on their host's evolutionary trajectories. We also identify the main challenges that soil virology faces and the studies that are required to accompany the current developments in marine settings.

Temperate bacteriophages as regulators of host behavior

Bacteriophages are ubiquitous and affect most facets of life, from evolution of bacteria, through ecology and global biochemical cycling to human health. The interactions between phages and bacteria often lead to biological novelty and an important milestone in this process is the ability of phages to regulate their host's behavior. In this review article, we will focus on newly reported cases that demonstrate how temperate phages regulate bacterial gene expression and behavior in a variety of bacterial species, pathogenic and environmental. This regulation is mediated by diverse mechanisms such as transcription factors, sRNAs, DNA rearrangements, and even controlled bacterial lysis. The outcome is mutualistic relationships that enable adaptively enhanced communal phage-host fitness under specific conditions.

Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species

Many metagenomic sequencing studies have observed the presence of closely related bacterial species or genotypes in the same microbiome. Previous attempts to explain these patterns of microdiversity have focused on the abiotic environment, but few have considered how biotic interactions could drive patterns of microbiome diversity. We dissected the patterns, processes, and mechanisms shaping the ecological distributions of three closely related Staphylococcus species in cheese rind biofilms. Paradoxically, the most abundant species (S. equorum) is the slowest colonizer and weakest competitor based on growth and competition assays in the laboratory. Through in vitro community reconstructions, we determined that biotic interactions with neighboring fungi help resolve this paradox. Species-specific stimulation of the poor competitor by fungi of the genus Scopulariopsis allows S. equorum to dominate communities in vitro as it does in situ. Results of comparative genomic and transcriptomic experiments indicate that iron utilization pathways, including a homolog of the S. aureus staphyloferrin B siderophore operon pathway, are potential molecular mechanisms underlying Staphylococcus-Scopulariopsis interactions. Our integrated approach demonstrates that fungi can structure the ecological distributions of closely related bacterial species, and the data highlight the importance of bacterium-fungus interactions in attempts to design and manipulate microbiomes.

Decades of culture-based studies and more recent metagenomic studies have demonstrated that bacterial species in agriculture, medicine, industry, and nature are unevenly distributed across time and space. The ecological processes and molecular mechanisms that shape these distributions are not well understood because it is challenging to connect in situ patterns of diversity with mechanistic in vitro studies in the laboratory. Using tractable cheese rind biofilms and a focus on coagulase-negative Staphylococcus (CNS) species, we demonstrate that fungi can mediate the ecological distributions of closely related bacterial species. One of the Staphylococcus species studied, S. saprophyticus, is a common cause of urinary tract infections. By identifying processes that control the abundance of undesirable CNS species, cheese producers will have more precise control on the safety and quality of their products. More generally, Staphylococcus species frequently co-occur with fungi in mammalian microbiomes, and similar bacterium-fungus interactions may structure bacterial diversity in these systems.

CDI Systems Are Stably Maintained by a Cell-Contact Mediated Surveillance Mechanism

Contact-dependent growth inhibition (CDI) systems are widespread amongst Gram-negative bacteria where they play important roles in inter-cellular competition and biofilm formation. CDI+ bacteria use cell-surface CdiA proteins to bind neighboring bacteria and deliver C-terminal toxin domains. CDI+ cells also express CdiI immunity proteins that specifically neutralize toxins delivered from adjacent siblings. Genomic analyses indicate that cdi loci are commonly found on plasmids and genomic islands, suggesting that these Type 5 secretion systems are spread through horizontal gene transfer. Here, we examine whether CDI toxin and immunity activities serve to stabilize mobile genetic elements using a minimal F plasmid that fails to partition properly during cell division. This F plasmid is lost from Escherichia coli populations within 50 cell generations, but is maintained in ~60% of the cells after 100 generations when the plasmid carries the cdi gene cluster from E. coli strain EC93. By contrast, the ccdAB "plasmid addiction" module normally found on F exerts only a modest stabilizing effect. cdi-dependent plasmid stabilization requires the BamA receptor for CdiA, suggesting that plasmid-free daughter cells are inhibited by siblings that retain the CDI+ plasmid. In support of this model, the CDI+ F plasmid is lost rapidly from cells that carry an additional cdiI immunity gene on a separate plasmid. These results indicate that plasmid stabilization occurs through elimination of non-immune cells arising in the population via plasmid loss. Thus, genetic stabilization reflects a strong selection for immunity to CDI. After long-term passage for more than 300 generations, CDI+ plasmids acquire mutations that increase copy number and result in 100% carriage in the population. Together, these results show that CDI stabilizes genetic elements through a toxin-mediated surveillance mechanism in which cells that lose the CDI system are detected and eliminated by their siblings.

In vivo gene expression of Pseudomonas putida KT2440 in the rhizosphere of different plants

Pseudomonas putida KT2440 has the ability to colonize the rhizosphere of a wide range of plants and can reach cell densities in the range of 10⁵–10⁶ cfu g soil⁻¹. Using the IVET technology we investigated which KT2440 genes were expressed in the rhizosphere of four different plants: pine, cypress, evergreen oak and rosemary. We identified 39 different transcriptional fusions containing the promoters of annotated genes that were preferentially expressed in the rhizosphere. Six of them were expressed in the rhizosphere of all the plant types tested, 11 were expressed in more than one plant and the remaining 22 fusions were found to be expressed in only one type of plant. Another 40 fusions were found to correspond to likely promoters that encode antisense RNAs of unknown function, some of which were isolated as fusions from the bacteria recovered in the rhizosphere from all of the plants, while others were specific to one or several of the plants. The results obtained in this study suggest that plant-specific signals are sensed by KT2440 in the rhizosphere and that the signals and consequent gene expression are related to the bacteria's successful establishment in this niche.