Chromatic Bacteria - A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria

Microfluidic Platform with Precisely Controlled Hydrodynamic Parameters and Integrated Features for Generation of Microvortices to Accurately Form and Monitor Biofilms in Flow

Microorganisms often live in habitats characterized by fluid flow, and their adhesion to surfaces in industrial systems or clinical settings may lead to pipe clogging, microbially influenced corrosion, material deterioration, food spoilage, infections, and human illness. Here, a novel microfluidic platform was developed to investigate biofilm formation under precisely controlled (i) cell concentration, (ii) temperature, and (iii) flow conditions. The developed platform central unit is a single-channel microfluidic flow cell designed to ensure ultrahomogeneous flow and condition in its central area, where features, e.g., with trapping properties, can be incorporated. In comparison to static and macroflow chamber assays for biofilm studies, microfluidic chips allow in situ monitoring of biofilm formation under various flow regimes and have better environment control and smaller sample requirements. Flow simulations and experiments with fluorescent particles were used to simulate bacteria flow in the platform cell for calculating flow velocity and direction at the microscale level. The combination of flow analysis and fluorescent strain injection in the cell showed that microtraps placed at the center of the channel were efficient in capturing bacteria at determined positions and to study how flow conditions, especially microvortices, can affect biofilm formation. The microfluidic platform exhibited improved performances in terms of homogeneity and robustness for in vitro biofilm formation. We anticipate the presented platform to be suitable for broad, versatile, and high-throughput biofilm studies at the microscale level.

Stable, fluorescent markers for tracking synthetic communities and assembly dynamics

BACKGROUND

After two decades of extensive microbiome research, the current forefront of scientific exploration involves moving beyond description and classification to uncovering the intricate mechanisms underlying the coalescence of microbial communities. Deciphering microbiome assembly has been technically challenging due to their vast microbial diversity but establishing a synthetic community (SynCom) serves as a key strategy in unravelling this process. Achieving absolute quantification is crucial for establishing causality in assembly dynamics. However, existing approaches are primarily designed to differentiate a specific group of microorganisms within a particular SynCom.

RESULTS

To address this issue, we have developed the differential fluorescent marking (DFM) strategy, employing three distinguishable fluorescent proteins in single and double combinations. Building on the mini-Tn7 transposon, DFM capitalises on enhanced stability and broad applicability across diverse Proteobacteria species. The various DFM constructions are built using the pTn7-SCOUT plasmid family, enabling modular assembly, and facilitating the interchangeability of expression and antibiotic cassettes in a single reaction. DFM has no detrimental effects on fitness or community assembly dynamics, and through the application of flow cytometry, we successfully differentiated, quantified, and tracked a diverse six-member SynCom under various complex conditions like root rhizosphere showing a different colonisation assembly dynamic between pea and barley roots.

CONCLUSIONS

DFM represents a powerful resource that eliminates dependence on sequencing and/or culturing, thereby opening new avenues for studying microbiome assembly. Video Abstract.

Hitching a Ride in the Phyllosphere: Surfactant Production of Pseudomonas spp. Causes Co-swarming of Pantoea eucalypti 299R

Here, we demonstrate the beneficial effect of surfactant-producing pseudomonads on Pantoea eucalypti 299R. We conducted a series of experiments in environments of increasing complexity. P. eucalypti 299R (Pe299R), and Pseudomonas sp. FF1 (Pff1) or Pe299R and surfactant-production deficient Pseudomonas sp. FF1::ΔviscB (Pff1ΔviscB) were co-inoculated in broth, on swarming agar plates, and on plants. In broth, there were no differences in the growth dynamics of Pe299R when growing in the presence of Pff1 or Pff1ΔviscB. By contrast, on swarming agar plates, Pe299R was able to co-swarm with Pff1 which led to a significant increase in Pe299R biomass compared to Pe299R growing with Pff1ΔviscB or in monoculture. Finally in planta, and using the single-cell bioreporter for reproductive success (CUSPER), we found a temporally distinct beneficial effect of Pff1 on co-inoculated Pe299R subpopulations that did not occur in the presence of Pff1ΔviscB. We tested three additional surfactant-producing pseudomonads and their respective surfactant knockout mutants on PE299R on swarming agar showing similar results. This led us to propose a model for the positive effect of surfactant production during leaf colonization. Our results indicate that co-motility might be common during leaf colonization and adds yet another facet to the already manyfold roles of surfactants.

Diverse and abundant phages exploit conjugative plasmids

Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 65 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the evolutionarily promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.

Selective Quantification of Bacteria in Mixtures by Using Glycosylated Polypyrrole/Hydrogel Nanolayers

Here, we present a covalent nanolayer system that consists of a conductive and biorepulsive base layer topped by a layer carrying biorecognition sites. The layers are built up by electropolymerization of pyrrole derivatives that either carry polyglycerol brushes (for biorepulsivity) or glycoside moieties (as biorecognition sites). The polypyrrole backbone makes the resulting nanolayer systems conductive, opening the opportunity for constructing an electrochemistry-based sensor system. The basic concept of the sensor exploits the highly selective binding of carbohydrates by certain harmful bacteria, as bacterial adhesion and infection are a major threat to human health, and thus, a sensitive and selective detection of the respective bacteria by portable devices is highly desirable. To demonstrate the selectivity, two strains of Escherichia coli were selected. The first strain carries type 1 fimbriae, terminated by a lectin called FimH, which recognizes α-d-mannopyranosides, which is a carbohydrate that is commonly found on endothelial cells. The otherE. coli strain was of a strain that lacked this particular lectin. It could be demonstrated that hybrid nanolayer systems containing a very thin carbohydrate top layer (2 nm) show the highest discrimination (factor 80) between the different strains. Using electrochemical impedance spectroscopy, it was possible to quantify in vivo the type 1-fimbriated E. coli down to an optical density of OD600 = 0.0004 with a theoretical limit of 0.00005. Surprisingly, the selectivity and sensitivity of the sensing remained the same even in the presence of a large excess of nonbinding bacteria, making the system useful for the rapid and selective detection of pathogens in complex matrices. As the presented covalent nanolayer system is modularly built, it opens the opportunity to develop a broad band of mobile sensing devices suitable for various field applications such as bedside diagnostics or monitoring for bacterial contamination, e.g., in bioreactors.

Label-free functional analysis of root-associated microbes with dynamic quantitative oblique back-illumination microscopy

The increasing global demand for food, coupled with concerns about the environmental impact of synthetic fertilizers, underscores the urgency of developing sustainable agricultural practices. Nitrogen-fixing bacteria, known as diazotrophs, offer a potential solution by converting atmospheric nitrogen into bioavailable forms, reducing the reliance on synthetic fertilizers. However, a deeper understanding of their interactions with plants and other microbes is needed. In this study, we introduce a recently developed label-free 3D quantitative phase imaging technology called dynamic quantitative oblique back-illumination microscopy (DqOBM) to assess the functional dynamic activity of diazotrophs in vitro and in situ. Our experiments involved three different diazotrophs (Sinorhizobium meliloti, Azotobacter vinelandii, and Rahnella aquatilis) cultured on media with amendments of carbon and nitrogen sources. Over 5 days, we observed increased dynamics in nutrient-amended media. These results suggest that the observed bacterial dynamics correlate with their metabolic activity. Furthermore, we applied qOBM to visualize microbial dynamics within the root cap and elongation zone of Arabidopsis thaliana primary roots. This allowed us to identify distinct areas of microbial infiltration in plant roots without the need for fluorescent markers. Our findings demonstrate that DqOBM can effectively characterize microbial dynamics and provide insights into plant-microbe interactions in situ, offering a valuable tool for advancing our understanding of sustainable agriculture.

Phylogenomic, structural, and cell biological analyses reveal that Stenotrophomonas maltophilia replicates in acidified Rab7A-positive vacuoles of Acanthamoeba castellanii

Acanthamoeba species are clinically relevant free-living amoebae (FLA) ubiquitously found in soil and water bodies. Metabolically active trophozoites graze on diverse microbes via phagocytosis. However, functional studies on Rab GTPases (Rabs), which are critical for controlling vesicle trafficking and maturation, are scarce for this FLA. This knowledge gap can be partly explained by the limited genetic tools available for Acanthamoeba cell biology. Here, we developed plasmids to generate fusions of A. castellanii strain Neff proteins to the N- or C-termini of mEGFP and mCherry2. Phylogenomic and structural analyses of the 11 Neff Rab7 paralogs found in the RefSeq assembly revealed that eight of them had non-canonical sequences. After correcting the gene annotation for the Rab7A ortholog, we generated a line stably expressing an mEGFP-Rab7A fusion, demonstrating its correct localization to acidified macropinocytic and phagocytic vacuoles using fluorescence microscopy live cell imaging (LCI). Direct labeling of live Stenotrophomonas maltophilia ESTM1D_MKCAZ16_6a (Sm18) cells with pHrodo Red, a pH-sensitive dye, demonstrated that they reside within acidified, Rab7A-positive vacuoles. We constructed new mini-Tn7 delivery plasmids and tagged Sm18 with constitutively expressed mScarlet-I. Co-culture experiments of Neff trophozoites with Sm18::mTn7TC1_Pc_mScarlet-I, coupled with LCI and microplate reader assays, demonstrated that Sm18 underwent multiple replication rounds before reaching the extracellular medium via non-lytic exocytosis. We conclude that S. maltophilia belongs to the class of bacteria that can use amoeba as an intracellular replication niche within a Stenotrophomonas-containing vacuole that interacts extensively with the endocytic pathway.IMPORTANCEDiverse Acanthamoeba lineages (genotypes) are of increasing clinical concern, mainly causing amoebic keratitis and granulomatous amebic encephalitis among other infections. S. maltophilia ranks among the top 10 most prevalent multidrug-resistant opportunistic nosocomial pathogens and is a recurrent member of the microbiome hosted by Acanthamoeba and other free-living amoebae. However, little is known about the molecular strategies deployed by Stenotrophomonas for an intracellular lifestyle in amoebae and other professional phagocytes such as macrophages, which allow the bacterium to evade the immune system and the action of antibiotics. Our plasmids and easy-to-use microtiter plate co-culture assays should facilitate investigations into the cellular microbiology of Acanthamoeba interactions with Stenotrophomonas and other opportunistic pathogens, which may ultimately lead to the discovery of new molecular targets and antimicrobial therapies to combat difficult-to-treat infections caused by these ubiquitous microbes.

Rediversification following ecotype isolation reveals hidden adaptive potential

Microbial communities play a critical role in ecological processes, and their diversity is key to their functioning. However, little is known about whether communities can regenerate ecological diversity following ecotype removal or extinction and how the rediversified communities would compare to the original ones. Here, we show that simple two-ecotype communities from the E. coli long-term evolution experiment (LTEE) consistently rediversified into two ecotypes following the isolation of one of the ecotypes, coexisting via negative frequency-dependent selection. Communities separated by more than 30,000 generations of evolutionary time rediversify in similar ways. The rediversified ecotype appears to share a number of growth traits with the ecotype it replaces. However, the rediversified community is also different from the original community in ways relevant to the mechanism of ecotype coexistence-for example, in stationary phase response and survival. We found substantial variation in the transcriptional states between the two original ecotypes, whereas the differences within the rediversified community were comparatively smaller, although the rediversified community showed unique patterns of differential expression. Our results suggest that evolution may leave room for alternative diversification processes even in a maximally reduced community of only two strains. We hypothesize that the presence of alternative evolutionary pathways may be even more pronounced in communities of many species where there are even more potential niches, highlighting an important role for perturbations, such as species removal, in evolving ecological communities.

Deciphering the interaction of bacteria inoculants with the recipient endophytic community in grapevine micropropagated plants

Engineering the plant microbiome with beneficial endophytic bacteria can improve the growth, health, and productivity of the holobiont. Here, we administered two beneficial bacterial strains, Kosakonia VR04 sp. and Rhizobium GR12 sp., to micropropagated grapevine cuttings obtained via somatic embryogenesis. While both strains colonized the plant endosphere, only Rhizobium GR12 sp. increased root biomass under nutritional-deficit conditions, as supported by the plant growth promotion traits detected in its genome. Phylogenetic and co-occurrence analyses revealed that the plant native bacterial community, originally dominated by Streptococcaceae and Micrococcaceae, dramatically changed depending on the inoculation treatments, as invading strains differently affected the relative abundance and the interactions of pre-existing taxa. After 30 days of plantlets' growth, Pantoea became a predominant taxon, and considering untreated plantlets as references, Rhizobium sp. GR12 showed a minor impact on the endophytic bacterial community. On the other hand, Kosakonia sp. VR04 caused a major change in community composition, suggesting an opportunistic colonization pattern. Overall, the results corroborate the importance of preserving the native endophytic community structure and functions during plant microbiome engineering.IMPORTANCEA better comprehension of bacterial colonization processes and outcomes could benefit the use of plant probiotics in the field. In this study, we applied two different beneficial bacteria to grapevine micropropagated plantlets and described how the inoculation of these strains impacts endophytic microbiota assembly. We showed that under nutritional deficit conditions, the response of the receiving endophytic bacterial communities to the invasion of the beneficial strains related to the manifestation of plant growth promotion effects by the inoculated invading strains. Rhizobium sp. GR12 was able to preserve the native microbiome structure despite its effective colonization, highlighting the importance of the plant-endophyte associations for the holobiont performance. Moreover, our approach showed that the use of micropropagated plantlets could be a valuable strategy to study the interplay among the plant, its native microbiota, and the invader on a wider portfolio of species besides model plants, facilitating the application of new knowledge in agriculture.

DA, Roberts AG, Puri AW. A widespread methylotroph acyl-homoserine lactone synthase produces a new quorum sensing signal that regulates swarming in Methylobacterium fujisawaense

IMPORTANCE

Bacteria known as pink-pigmented facultative methylotrophs colonize many diverse environments on earth, play an important role in the carbon cycle, and in some cases promote plant growth. However, little is known about how these organisms interact with each other and their environment. In this work, we identify one of the chemical signals commonly used by these bacteria and discover that this signal controls swarming motility in the pink-pigmented facultative methylotroph Methylobacterium fujisawaense DSM5686. This work provides new molecular details about interactions between these important bacteria and will help scientists predict these interactions and the group behaviors they regulate from genomic sequencing information.

Influence of Co-occurring Weakly Pathogenic Bacterial Species on Bacterial Spot Disease Dynamics on Tomato

Mixed infections caused by multiple pathogenic and weakly pathogenic strains inhabiting the same host plants are common in nature and may modify pathogen dynamics. However, traditional plant pathogen studies have mostly focused on the binary interaction between a single host and a single pathogen. In this study, we have looked beyond this binary interaction and evaluated the impact of coinfection on disease dynamics on tomato using the bacterial spot pathogen Xanthomonas perforans (Xp), the co-occurring weakly pathogenic strain of X. arboricola (Xa), and the co-occurring potential weak pathogenic strain of Pseudomonas capsici (Pc). Time-series coinfection experiments monitoring disease severity and within-host population dynamics revealed higher disease severity in coinfection by three species compared with infection by Xp alone. However, coinfection by dual species, Xp and Pc, or Xa resulted in lower disease severity compared with Xp alone. Thus, coinfection outcomes depend on interacting species. Weak pathogens could exploit Xp to colonize the host plant as indicated by their higher populations in coinfection. However, Xp population dynamics were dependent on the coinfecting partner. While resource competition might be a possible explanation for lower Xp population in dual coinfection, interaction of Pc with the host was found to influence Xp population. Interestingly, Xp population was higher in the presence of three-species interaction compared with Xp and Xa coinfection, suggesting potential modulation of cooperative interactions among Xp and Xa in three-species coinfection rather than competitive interactions. Humidity played a significant role in population dynamics of the three species. Overall, this study highlighted the importance of coinfection dynamics in studying plant disease outbreaks.

Diverse and abundant phages exploit conjugative plasmids

Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally-encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 64 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.

Label-Free Functional Analysis of Root-Associated Microbes with Dynamic Quantitative Oblique Back-illumination Microscopy

The increasing global demand for food, coupled with concerns about the environmental impact of synthetic fertilizers, underscores the urgency of developing sustainable agricultural practices. Nitrogen-fixing bacteria, known as diazotrophs, offer a potential solution by converting atmospheric nitrogen into bioavailable forms, reducing the reliance on synthetic fertilizers. However, a deeper understanding of their interactions with plants and other microbes is needed. In this study, we introduce a recently developed label-free 3D quantitative phase imaging technology called dynamic quantitative oblique back-illumination microscopy (DqOBM) to assess the dynamic activity of diazotrophs in vitro and in situ. Our experiments involved three different diazotrophs (Sinorhizobium meliloti, Azotobacter vinelandii, and Rahnella aquatilis) cultured on media with amendments of carbon and nitrogen sources. Over five days, we observed increased dynamic activity in nutrient-amended media. These results suggest that the observed bacterial dynamics correlate with their metabolic activity. Furthermore, we applied qOBM to visualize bacterial activity within the root cap and elongation zone of Arabidopsis thaliana primary roots. This allowed us to identify distinct areas of microbial infiltration in plant roots without the need for fluorescent markers. Our findings demonstrate that DqOBM can effectively characterize microbial activity and provide insights into plant-microbe interactions in situ, offering a valuable tool for advancing our understanding of sustainable agriculture.

The Use of Synthetic Microbial Communities to Improve Plant Health

Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now, it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites, and ability to induce plant resistance are some of the microbial traits to consider when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors as compared with the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability is still one of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health, focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.

Barcoding Populations of Pseudomonas fluorescens SBW25

In recent years, evolutionary biologists have developed an increasing interest in the use of barcoding strategies to study eco-evolutionary dynamics of lineages within evolving populations and communities. Although barcoded populations can deliver unprecedented insight into evolutionary change, barcoding microbes presents specific technical challenges. Here, strategies are described for barcoding populations of the model bacterium Pseudomonas fluorescens SBW25, including the design and cloning of barcoded regions, preparation of libraries for amplicon sequencing, and quantification of resulting barcoded lineages. In so doing, we hope to aid the design and implementation of barcoding methodologies in a broad range of model and non-model organisms.

Phyllosphere symbiont promotes plant growth through ACC deaminase production

Plant growth promoting bacteria can confer resistance to various types of stress and increase agricultural yields. The mechanisms they employ are diverse. One of the most important genes associated with the increase in plant biomass and stress resistance is acdS, which encodes a 1-aminocyclopropane-1-carboxylate- or ACC-deaminase. The non-proteinogenic amino acid ACC is the precursor and means of long-distance transport of ethylene, a plant hormone associated with growth arrest. Expression of acdS reduces stress induced ethylene levels and the enzyme is abundant in rhizosphere colonizers. Whether ACC hydrolysis plays a role in the phyllosphere, both as assembly cue and in growth promotion, remains unclear. Here we show that Paraburkholderia dioscoreae Msb3, a yam phyllosphere symbiont, colonizes the tomato phyllosphere and promotes plant growth by action of its ACC deaminase. We found that acdS is required for improved plant growth but not for efficient leaf colonization. Strain Msb3 readily proliferates on the leaf surface of tomato, only occasionally spreading to the leaf endosphere through stomata. The strain can also colonize the soil or medium around the roots but only spreads into the root if the plant is wounded. Our results indicate that the degradation of ACC is not just an important trait of plant growth promoting rhizobacteria but also one of leaf dwelling phyllosphere bacteria. Manipulation of the leaf microbiota by means of spray inoculation may be more easily achieved than that of the soil. Therefore, the application of ACC deaminase containing bacteria to the phyllosphere may be a promising strategy to increasing plant stress resistance, pathogen control, and harvest yields.

Rediversification Following Ecotype Isolation Reveals Hidden Adaptive Potential

Microbial communities play a critical role in ecological processes, and their diversity is key to their functioning. However, little is known about if communities can regenerate ecological diversity following species removal or extinction, and how the rediversified communities would compare to the original ones. Here we show that simple two-ecotype communities from the E. coli Long Term Evolution Experiment (LTEE) consistently rediversified into two ecotypes following the isolation of one of the ecotypes, coexisting via negative frequency-dependent selection. Communities separated by more than 30,000 generations of evolutionary time rediversify in similar ways. The rediversified ecotype appears to share a number of growth traits with the ecotype it replaces. However, the rediversified community is also different compared to the original community in ways relevant to the mechanism of ecotype coexistence, for example in stationary phase response and survival. We found substantial variation in the transcriptional states between the two original ecotypes, whereas the differences within the rediversified community were comparatively smaller, but with unique patterns of differential expression. Our results suggest that evolution may leave room for alternative diversification processes even in a maximally reduced community of only two strains. We hypothesize that the presence of alternative evolutionary pathways may be even more pronounced in communities of many species, highlighting an important role for perturbations, such as species removal, in evolving ecological communities.

Characterizing Biofilm Interactions between Ralstonia insidiosa and Chryseobacterium gleum

Ralstonia insidiosa and Chryseobacterium gleum are bacterial species commonly found in potable water systems, and these two species contribute to the robustness of biofilm formation in a model six-species community from the International Space Station (ISS) potable water system. Here, we set about characterizing the interaction between these two ISS-derived strains and examining the extent to which this interaction extends to other strains and species in these two genera. The enhanced biofilm formation between the ISS strains of R. insidiosa and C. gleum is robust to starting inoculum and temperature and occurs in some but not all tested growth media, and evidence does not support a soluble mediator or coaggregation mechanism. These findings shed light on the ISS R. insidiosa and C. gleum interaction, though such enhancement is not common between these species based on our examination of other R. insidiosa and C. gleum strains, as well as other species of Ralstonia and Chryseobacterium. Thus, while the findings presented here increase our understanding of the ISS potable water model system, not all our findings are broadly extrapolatable to strains found outside of the ISS. IMPORTANCE Biofilms present in drinking water systems and terminal fixtures are important for human health, pipe corrosion, and water taste. Here, we examine the enhanced biofilm of cocultures for two very common bacteria from potable water systems: Ralstonia insidiosa and Chryseobacterium gleum. While strains originally isolated on the International Space Station show enhanced dual-species biofilm formation, terrestrial strains do not show the same interaction properties. This study contributes to our understanding of these two species in both dual-culture and monoculture biofilm formation.

Polyamine metabolizing rhizobacteria Pseudomonas sp. GBPI_506 modulates hormone signaling to enhance lateral roots and nicotine biosynthesis in Nicotiana benthamiana

Beneficial rhizobacteria in the soil are important drivers of plant health and growth. In this study, we provide the draft genome of a root colonizing and auxin-producing Pseudomonas sp. strain GBPI_506. The bacterium was investigated for its contribution in the growth of Nicotiana benthamiana (Nb) and biosynthesis of nicotine. The bacterium showed chemotaxis towards root exudates potentially mediated by putrescine, a polyamine compound, to colonize the roots of Nb. Application of the bacterium with the roots of Nb, increased plant biomass and total soluble sugars in the leaves, and promoted lateral root (LR) development as compared to the un-inoculated plants. Confocal analysis using transgenic (DR5:GFP) Arabidopsis showed increased auxin trafficking in the LR of inoculated plants. Upregulation of nicotine biosynthesis genes and genes involved in salicylic acid (SA) and jasmonic acid (JA) signaling in the roots of inoculated plants suggested increased nicotine biosynthesis as a result of bacterial application. An increased JA content in roots and nicotine accumulation in leaves provided evidence on JA-mediated upregulation of nicotine biosynthesis in the bacterized plants. The findings suggested that the bacterial root colonization triggered networking between auxin, SA, and JA to facilitate LR development leading to enhanced plant growth and nicotine biosynthesis in Nb.

Conjugative RP4 Plasmid-Mediated Transfer of Antibiotic Resistance Genes to Commensal and Multidrug-Resistant Enteric Bacteria In Vitro

Many antibiotic-resistant bacteria carry resistance genes on conjugative plasmids that are transferable to commensals and pathogens. We determined the ability of multiple enteric bacteria to acquire and retransfer a broad-host-range plasmid RP4. We used human-derived commensal Escherichia coli LM715-1 carrying a chromosomal red fluorescent protein gene and green fluorescent protein (GFP)-labeled broad-host-range RP4 plasmid with ampR, tetR, and kanR in in vitro matings to rifampicin-resistant recipients, including Escherichia coli MG1655, Dec5α, Vibrio cholerae, Pseudomonas putida, Pseudomonas aeruginosa, Klebsiella pneumoniae, Citrobacter rodentium, and Salmonella Typhimurium. Transconjugants were quantified on selective media and confirmed using fluorescence microscopy and PCR for the GFP gene. The plasmid was transferred from E. coli LM715-1 to all tested recipients except P. aeruginosa. Transfer frequencies differed between specific donor-recipient pairings (10^-2 to 10^-8). Secondary retransfer of plasmid from transconjugants to E. coli LM715-1 occurred at frequencies from 10^-2 to 10^-7. A serial passage plasmid persistence assay showed plasmid loss over time in the absence of antibiotics, indicating that the plasmid imposed a fitness cost to its host, although some plasmid-bearing cells persisted for at least ten transfers. Thus, the RP4 plasmid can transfer to multiple clinically relevant bacterial species without antibiotic selection pressure.

Development of a set of novel binary expression vectors for plant gene function analysis and genetic transformation

With the advent of multiple omics and Genome-Wide Association Studies (GWAS) technology, genome-scale functional analysis of candidate genes is to be conducted in diverse plant species. Construction of plant binary expression vectors is the prerequisite for gene function analysis. Therefore, it is of significance to develop a set of plant binary expression vectors with highly efficient, inexpensive, and convenient cloning method, and easy-to-use in screening of positive recombinant in Escherichia coli. In this study, we developed a set of plant binary expression vectors, termed pBTR vectors, based on Golden Gate cloning using BsaI restriction site. Foreign DNA fragment of interest (FDI) can be cloned into the destination pBTR by one-step digestion-ligation reaction in a single tube, and even the FDI contains internal BsaI site(s). Markedly, in one digestion-ligation reaction, multiple FDIs (exemplified by cloning four soybean Glyma.02g025400, Glyma.05g201700, Glyma.06g165700, and Glyma.17g095000 genes) can be cloned into the pBTR vector to generate multiple corresponding expression constructs (each expression vector carrying an FDI). In addition, the pBTR vectors carry the visual marker, a brightness monomeric red fluorescent protein mScarlet-I, that can be observed with the unaided eye in screening of positive recombinants without the use of additional reagents/equipment. The reliability of the pBTR vectors was validated in plants by overexpression of AtMyb75/PAP1 in tomato and GUSPlus in soybean roots via Agrobacterium rhizogenes-mediated transformation, promoter activity analysis of AtGCSpro in Arabidopsis via A. tumefaciens-mediated transformation, and protein subcellular localization of the Vitis vinifera VvCEB1_opt in tobacco, respectively. These results demonstrated that the pBTR vectors can be used in analysis of gene (over)expression, promoter activity, and protein subcellular localization. These vectors will contribute to speeding up gene function analysis and the process of plant molecular breeding.

A conserved glutamate residue in RPM1-INTERACTING PROTEIN4 is ADP-ribosylated by the Pseudomonas effector AvrRpm2 to activate RPM1-mediated plant resistance

Gram-negative bacterial plant pathogens inject effectors into their hosts to hijack and manipulate metabolism, eluding surveillance at the battle frontier on the cell surface. The effector AvrRpm1Pma from Pseudomonas syringae pv. maculicola functions as an ADP-ribosyl transferase that modifies RESISTANCE TO P. SYRINGAE PV MACULICOLA1 (RPM1)-INTERACTING PROTEIN4 (RIN4), leading to the activation of Arabidopsis thaliana (Arabidopsis) resistance protein RPM1. Here we confirmed the ADP-ribosyl transferase activity of another bacterial effector, AvrRpm2Psa from P. syringae pv. actinidiae, via sequential inoculation of Pseudomonas strain Pto DC3000 harboring avrRpm2Psa following Agrobacterium-mediated transient expression of RIN4 in Nicotiana benthamiana. We conducted mutational analysis in combination with mass spectrometry to locate the target site in RIN4. A conserved glutamate residue (Glu156) is the most likely target for AvrRpm2Psa, as only Glu156 could be ADP-ribosylated to activate RPM1 among candidate target residues identified from the MS/MS fragmentation spectra. Soybean (Glycine max) and snap bean (Phaseolus vulgaris) RIN4 homologs without glutamate at the positions corresponding to Glu156 of Arabidopsis RIN4 are not ADP-ribosylated by bacterial AvrRpm2Psa. In contrast to the effector AvrB, AvrRpm2Psa does not require the phosphorylation of Thr166 in RIN4 to activate RPM1. Therefore, separate biochemical reactions by different pathogen effectors may trigger the activation of the same resistance protein via distinct modifications of RIN4.

The effect of bacterial growth strategies on plasmid transfer and naphthalene degradation for bioremediation

Mobilizable plasmids are extra-chromosomal, circular DNA that have contributed to the rapid evolution of bacterial genomes and have been used in environmental, biotechnological, and medicinal applications. Degradative plasmids with genetic capabilities to degrade organic contaminants, such as polycyclic aromatic hydrocarbons (PAHs), have the potential to be useful for more environmentally friendly and cost-effective remediation technologies compared to existing physical remediation methods. Genetic bioaugmentation, the addition of catabolic genes into well-adapted communities via plasmid transfer (conjugation), is being explored as a remediation approach that is sustainable and long-lasting. Here, we explored the effect of the ecological growth strategies of plasmid donors and recipients on conjugation and naphthalene degradation of two PAH-degrading plasmids, pNL1 and NAH7. Overall, both pNL1 and NAH7 showed conjugation preferences towards a slow-growing ecological growth strategy, except when NAH7 was in a mixed synthetic community. These conjugation preferences were partially described by a combination of growth strategy, GC content, and phylogenetic relatedness. Further, removal of naphthalene via plasmid-mediated degradation was consistently higher in a community consisting of recipients with a slow-growing ecological growth strategy compared to a mixed community or a community consisting of fast-growing ecological growth strategy. Understanding plasmid conjugation and degradative preferences has the capacity to influence future remediation technology design and has broad implications in biomedical, environmental, and health fields.

Cross-feeding niches among commensal leaf bacteria are shaped by the interaction of strain-level diversity and resource availability

Leaf microbiomes play crucial roles in plant health, making it important to understand the origins and functional relevance of their diversity. High strain-level leaf bacterial genetic diversity is known to be relevant for interactions with hosts, but little is known about its relevance for interactions with the multitude of diverse co-colonizing microorganisms. In leaves, nutrients like amino acids are major regulators of microbial growth and activity. Using metabolomics of leaf apoplast fluid, we found that different species of the plant genus Flaveria considerably differ in the concentrations of high-cost amino acids. We investigated how these differences affect bacterial community diversity and assembly by enriching leaf bacteria in vitro with only sucrose or sucrose + amino acids as possible carbon sources. Enrichments from F. robusta were dominated by Pantoea sp. and Pseudomonas sp., regardless of carbon source. The latter was unable to grow on sucrose alone but persisted in the sucrose-only enrichment thanks to exchange of diverse metabolites from Pantoea sp. Individual Pseudomonas strains in the enrichments had high genetic similarity but still displayed clear niche partitioning, enabling distinct strains to cross-feed in parallel. Pantoea strains were also closely related, but individuals enriched from F. trinervia fed Pseudomonas more poorly than those from F. robusta. This can be explained in part by the plant environment, since some cross-feeding interactions were selected for, when experimentally evolved in a poor (sucrose-only) environment but selected against in a rich (sucrose + amino acids) one. Together, our work shows that leaf bacterial diversity is functionally relevant in cross-feeding interactions and strongly suggests that the leaf resource environment can shape these interactions and thereby indirectly drive bacterial diversity.

A Pseudomonas aeruginosa PQS quorum-sensing system inhibitor with anti-staphylococcal activity sensitizes polymicrobial biofilms to tobramycin

As single- and mixed-species biofilms, Staphylococcus aureus and Pseudomonas aeruginosa cause difficult-to-eradicate chronic infections. In P. aeruginosa, pseudomonas quinolone (PQS)-dependent quorum sensing regulates virulence and biofilm development that can be attenuated via antagonists targeting the transcriptional regulator PqsR (MvfR). Here, we exploited a quinazolinone (QZN) library including PqsR agonists and antagonists for their activity against S. aureus alone, when co-cultured with P. aeruginosa, and in combination with the aminoglycoside tobramycin. The PqsR inhibitor, QZN 34 killed planktonic Gram-positives but not Gram-negatives. QZN 34 prevented S. aureus biofilm formation, severely damaged established S. aureus biofilms, and perturbed P. aeruginosa biofilm development. Although P. aeruginosa protected S. aureus from tobramycin in mixed biofilms, the combination of aminoglycoside antibiotic with QZN 34 eradicated the mixed-species biofilm. The mechanism of action of QZN 34 toward Gram-positive bacteria is shown to involve membrane perturbation and dissipation of transmembrane potential.

Dual-expression system for blue fluorescent protein optimization

Spectrally diverse fluorescent proteins (FPs) provide straightforward means for multiplexed imaging of biological systems. Among FPs fitting standard color channels, blue FPs (BFPs) are characterized by lower brightness compared to other spectral counterparts. Furthermore, available BFPs were not systematically characterized for imaging in cultured mammalian cells and common model organisms. Here we introduce a pair of new BFPs, named Electra1 and Electra2, developed through hierarchical screening in bacterial and mammalian cells using a novel dual-expression vector. We performed systematic benchmarking of Electras against state-of-art BFPs in cultured mammalian cells and demonstrated their utility as fluorescent tags for structural proteins. The Electras variants were validated for multicolor neuroimaging in Caenorhabditis elegans, zebrafish larvae, and mice in comparison with one of the best in the class BFP mTagBFP2 using one-photon and two-photon microscopy. The developed BFPs are suitable for multicolor imaging of cultured cells and model organisms in vivo. We believe that the described dual-expression vector has a great potential to be adopted by protein engineers for directed molecular evolution of FPs.

The Cell Membrane of a Novel Rhizobium phaseoli Strain Is the Crucial Target for Aluminium Toxicity and Tolerance

Soils with low pH and high aluminium (Al) contamination restrict common bean production, mainly due to adverse effects on rhizobia. We isolated a novel rhizobium strain, B3, from Kenyan soil which is more tolerant to Al stress than the widely used commercial strain CIAT899. B3 was resistant to 50 µM Al and recovered from 100 µM Al stress, while CIAT899 did not. Calcein labeling showed that less Al binds to the B3 membranes and less ATP and mScarlet-1 protein, a cytoplasmic marker, leaked out of B3 than CIAT899 cells in Al-containing media. Expression profiles showed that the primary targets of Al are genes involved in membrane biogenesis, metal ions binding and transport, carbohydrate, and amino acid metabolism and transport. The identified differentially expressed genes suggested that the intracellular γ-aminobutyric acid (GABA), glutathione (GSH), and amino acid levels, as well as the amount of the extracellular exopolysaccharide (EPS), might change during Al stress. Altered EPS levels could also influence biofilm formation. Therefore, these parameters were investigated in more detail. The GABA levels, extracellular EPS production, and biofilm formation increased, while GSH and amino acid level decreased. In conclusion, our comparative analysis identified genes that respond to Al stress in R. phaseoli. It appears that a large portion of the identified genes code for proteins stabilizing the plasma membrane. These genes might be helpful for future studies investigating the molecular basis of Al tolerance and the characterization of candidate rhizobial isolates that perform better in Al-contaminated soils than commercial strains.

Strategies for Improving Small-Molecule Biosensors in Bacteria

In recent years, small-molecule biosensors have become increasingly important in synthetic biology and biochemistry, with numerous new applications continuing to be developed throughout the field. For many biosensors, however, their utility is hindered by poor functionality. Here, we review the known types of mechanisms of biosensors within bacterial cells, and the types of approaches for optimizing different biosensor functional parameters. Discussed approaches for improving biosensor functionality include methods of directly engineering biosensor genes, considerations for choosing genetic reporters, approaches for tuning gene expression, and strategies for incorporating additional genetic modules.

Slow expanders invade by forming dented fronts in microbial colonies

Living organisms never cease to evolve, so there is a significant interest in predicting and controlling evolution in all branches of life sciences. The most basic question is whether a trait should increase or decrease in a given environment. The answer seems to be trivial for traits such as the growth rate in a bioreactor or the expansion rate of a tumor. Yet, it has been suggested that such traits can decrease, rather than increase, during evolution. Here, we report a mutant that outcompeted the ancestor despite having a slower expansion velocity when in isolation. To explain this observation, we developed and validated a theory that describes spatial competition between organisms with different expansion rates and arbitrary competitive interactions.

Most organisms grow in space, whether they are viruses spreading within a host tissue or invasive species colonizing a new continent. Evolution typically selects for higher expansion rates during spatial growth, but it has been suggested that slower expanders can take over under certain conditions. Here, we report an experimental observation of such population dynamics. We demonstrate that mutants that grow slower in isolation nevertheless win in competition, not only when the two types are intermixed, but also when they are spatially segregated into sectors. The latter was thought to be impossible because previous studies focused exclusively on the global competitions mediated by expansion velocities, but overlooked the local competitions at sector boundaries. Local competition, however, can enhance the velocity of either type at the sector boundary and thus alter expansion dynamics. We developed a theory that accounts for both local and global competitions and describes all possible sector shapes. In particular, the theory predicted that a slower on its own, but more competitive, mutant forms a dented V-shaped sector as it takes over the expansion front. Such sectors were indeed observed experimentally, and their shapes matched quantitatively with the theory. In simulations, we further explored several mechanisms that could provide slow expanders with a local competitive advantage and showed that they are all well-described by our theory. Taken together, our results shed light on previously unexplored outcomes of spatial competition and establish a universal framework to understand evolutionary and ecological dynamics in expanding populations.

Positive interactions are common among culturable bacteria

Interspecies interactions shape the structure and function of microbial communities. In particular, positive, growth-promoting interactions can substantially affect the diversity and productivity of natural and engineered communities. However, the prevalence of positive interactions and the conditions in which they occur are not well understood. To address this knowledge gap, we used kChip, an ultrahigh-throughput coculture platform, to measure 180,408 interactions among 20 soil bacteria across 40 carbon environments. We find that positive interactions, often described to be rare, occur commonly and primarily as parasitisms between strains that differ in their carbon consumption profiles. Notably, nongrowing strains are almost always promoted by strongly growing strains (85%), suggesting a simple positive interaction–mediated approach for cultivation, microbiome engineering, and microbial consortium design.

Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites

Recombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. Here we show that the accessibility of translation initiation sites modelled using the mRNA base-unpairing across the Boltzmann's ensemble significantly outperforms alternative features. This approach accurately predicts the successes or failures of expression experiments, which utilised Escherichia coli cells to express 11,430 recombinant proteins from over 189 diverse species. On this basis, we develop TIsigner that uses simulated annealing to modify up to the first nine codons of mRNAs with synonymous substitutions. We show that accessibility captures the key propensity beyond the target region (initiation sites in this case), as a modest number of synonymous changes is sufficient to tune the recombinant protein expression levels. We build a stochastic simulation model and show that higher accessibility leads to higher protein production and slower cell growth, supporting the idea of protein cost, where cell growth is constrained by protein circuits during overexpression.

Monitoring the growth, survival and phenol utilization of the fluorescent-tagged Pseudomonas oleovorans immobilized and free cells

Bioaugmentation in wastewater treatment plants (WWTPs) is challenging due to low survival and persistence of applied microbes. This study aimed to track the capacity and survival of fluorescent-tagged Pseudomonas oleovoransICTN13 as a model organism applicable in bioaugmentation of phenol-containing wastewater. The isolate was immobilized in alginate biopolymer, and enhanced efficacy and survival for biodegradation of phenol against free cells were studied. Encapsulated cells resulted in enhanced phenol removal efficiency (~94%) compared to free cells (~72%). Encapsulation of cells facilitated an extended storage time of 30 days. Remarkably, phenol and COD removal efficacy of encapsulated cells was sustained up to ~ 92-93% in a reactor after 45 days, while free cells could produce ~ 80-84% removal efficiency. Fluorescence microscopy showed high survival of the encapsulated cells, whereas gradual deterioration of free cells was observed. Thus, the findings highlight the importance of bio augmented strain in WWTPs where encapsulation is a crucial factor.

Fluorescent Protein Expression as a Proxy for Bacterial Fitness in a High-Throughput Assay

Bacterial growth is classically assessed by measuring the increases in optical density of pure cultures in shaken liquid media. Measuring growth using optical density has severe limitations when studying multistrain interactions, as it is not possible to measure the growth of individual strains within mixed cultures. Here, we demonstrated that constitutively expressed fluorescent proteins can be used to track the growth of individual strains in different liquid media. Fluorescence measurements were highly correlated with optical density measurements and cell counts. This allowed us to assess bacterial growth not only in pure cultures but also in mixed bacterial cultures and determine the impact of a competitor on a focal strain, thereby assessing relative fitness. Furthermore, we were able to track the growth of two different strains simultaneously by using fluorescent proteins with differential excitation and emission wavelengths. Bacterial densities measured by fluorescence yielded more consistent data between technical replicates than optical density measurements. Our setup employs fluorescence microplate readers that allow high throughput and replication. IMPORTANCE We expand on an important limitation of the concept of measuring bacterial growth, which is classically limited to one strain at a time. By adopting our approach, it is possible to measure the growth of several bacterial strains simultaneously with high temporal resolution and in a high-throughput manner. This is important to investigate bacterial interactions, such as competition and facilitation.

SorTn-seq: a high-throughput functional genomics approach to discovering regulators of bacterial gene expression

We recently developed a high-throughput functional genomics approach, named 'SorTn-seq', to identify factors affecting expression of any gene of interest in bacteria. Our approach facilitates high-throughput screening of complex mutant pools, a task previously hindered by a lack of suitable techniques. SorTn-seq combines high-density, Tn5-like transposon mutagenesis with fluorescence-activated cell sorting of a strain harboring a promoter-fluorescent reporter fusion, to isolate mutants with altered gene expression. The transposon mutant pool is sorted into different bins on the basis of fluorescence, and mutants are deep-sequenced to identify transposon insertions. DNA is prepared for sequencing by using commercial kits augmented with custom primers, enhancing ease of use and reproducibility. Putative regulators are identified by comparing the number of insertions per genomic feature in the different sort bins, by using existing bioinformatic pipelines and software packages. SorTn-seq can be completed in 1-2 weeks and requires general microbiology skills and basic flow cytometry experience.

Deciphering bacterial mechanisms of root colonization

Bacterial colonization of the rhizosphere is critical for the establishment of plant-bacteria interactions that represent a key determinant of plant health and productivity. Plants influence bacterial colonization primarily through modulating the composition of their root exudates and mounting an innate immune response. The outcome is a horizontal filtering of bacteria from the surrounding soil, resulting in a gradient of reduced bacterial diversity coupled with a higher degree of bacterial specialization towards the root. Bacteria-bacteria interactions (BBIs) are also prevalent in the rhizosphere, influencing bacterial persistence and root colonization through metabolic exchanges, secretion of antimicrobial compounds and other processes. Traditionally, bacterial colonization has been examined under sterile laboratory conditions that mitigate the influence of BBIs. Using simplified synthetic bacterial communities combined with microfluidic imaging platforms and transposon mutagenesis screening approaches, we are now able to begin unravelling the molecular mechanisms at play during the early stages of root colonization. This review explores the current state of knowledge regarding bacterial root colonization and identifies key tools for future exploration.

Proteus mirabilis Employs a Contact-Dependent Killing System against Competing Enterobacteriaceae

Many bacterial species employ systems for interference competition with other microorganisms. Some systems are effective without contact (e.g., through secretion of toxins), while other systems (e.g., type VI secretion system [T6SS]) require direct contact between cells. Here, we provide the initial characterization of a novel contact-dependent competition system for Proteus mirabilis. In neonatal mice, a commensal P. mirabilis strain apparently eliminated commensal Escherichia coli. We replicated the phenotype in vitro and showed that P. mirabilis efficiently reduced the viability of several Enterobacteriaceae species but not Gram-positive species or yeast cells. Importantly, P. mirabilis strains isolated from humans also killed E. coli. A reduction of viability occurred from early stationary phase to 24 h of culture and was observed in shaking liquid media as well as on solid media. Killing required contact but was independent of T6SS, which is the only contact-dependent killing system described for P. mirabilis. Expression of the killing system was regulated by osmolarity and components secreted into the supernatant. Stationary-phase P. mirabilis culture supernatant itself did not kill but was sufficient to induce killing in an exponentially growing coculture. In contrast, killing was largely prevented in media with low osmolarity. In summary, we provide the initial characterization of a potentially novel interbacterial competition system used by P. mirabilis.

IMPORTANCE The study of bacterial competition systems has received significant attention in recent years. These systems are important in a multitude of polymicrobial environments and collectively shape the composition of complex ecosystems like the mammalian gut. They are also being explored as narrow-spectrum alternatives to specifically eliminate problematic pathogenic species. However, only a small fraction of the estimated number of interbacterial competition systems has been identified. We discovered a competition system that is novel for Proteus mirabilis. Inspired by an observation in infant mice, we confirmed in vitro that P. mirabilis was able to efficiently kill several Enterobacteriaceae species. This killing system might represent a new function of a known competition system or even a novel system, as the observed characteristics do not fit with described contact-dependent competition systems. Further characterization of this system might help understand how P. mirabilis competes with other Enterobacteriaceae in various niches.

Genetic Modification of Sodalis Species by DNA Transduction

Bacteriophages (phages) are ubiquitous in nature. These viruses play a number of central roles in microbial ecology and evolution by, for instance, promoting horizontal gene transfer (HGT) among bacterial species. The ability of phages to mediate HGT through transduction has been widely exploited as an experimental tool for the genetic study of bacteria. As such, bacteriophage P1 represents a prototypical generalized transducing phage with a broad host range that has been extensively employed in the genetic manipulation of Escherichia coli and a number of other model bacterial species. Here we demonstrate that P1 is capable of infecting, lysogenizing, and promoting transduction in members of the bacterial genus Sodalis, including the maternally inherited insect endosymbiont Sodalis glossinidius. While establishing new tools for the genetic study of these bacterial species, our results suggest that P1 may be used to deliver DNA to many Gram-negative endosymbionts in their insect host, thereby circumventing a culturing requirement to genetically manipulate these organisms.

IMPORTANCE A large number of economically important insects maintain intimate associations with maternally inherited endosymbiotic bacteria. Due to the inherent nature of these associations, insect endosymbionts cannot be usually isolated in pure culture or genetically manipulated. Here we use a broad-host-range bacteriophage to deliver exogenous DNA to an insect endosymbiont and a closely related free-living species. Our results suggest that broad-host-range bacteriophages can be used to genetically alter insect endosymbionts in their insect host and, as a result, bypass a culturing requirement to genetically alter these bacteria.

Leaf-FISH: In Situ Hybridization Method for Visualizing Bacterial Taxa on Plant Surfaces

High-resolution, spatial characterization of microbial communities is critical for the accurate understanding of microbe-microbe and microbe-plant interactions in leaf surfaces (phyllosphere). However, leaves are specially challenging surfaces for imaging methods due to their high autofluorescence. In this chapter we describe the Leaf-FISH method. Leaf-FISH is a fluorescence in situ hybridization (FISH) method specially adapted to the requirements of plant tissues. Leaf-FISH uses a combination of leaf pretreatments coupled with spectral imaging confocal microscopy and image post-processing to visualize bacterial taxa on a structural-informed context recreated from the residual background autofluorescence of the tissues. Leaf-FISH is suitable for simultaneous identification of multiple bacterial taxa using multiple taxon-specific fluorescently labeled oligonucleotide probes (combinatorial labeling).

CRAGE-Duet Facilitates Modular Assembly of Biological Systems for Studying Plant-Microbe Interactions

Developing sustainable agricultural practices will require increasing our understanding of plant-microbe interactions. To study these interactions, new genetic tools for manipulating nonmodel microbes will be needed. To help meet this need, we recently reported development of chassis-independent recombinase-assisted genome engineering (CRAGE). CRAGE relies on cassette exchange between two pairs of mutually exclusive lox sites and allows direct, single-step chromosomal integration of large, complex gene constructs into diverse bacterial species. We then extended CRAGE by introducing a third mutually exclusive lox site, creating CRAGE-Duet, which allows modular integration of two constructs. CRAGE-Duet offers advantages over CRAGE, especially when a cumbersome recloning step is required to build single-integration constructs. To demonstrate the utility of CRAGE-Duet, we created a set of strains from the plant-growth-promoting rhizobacterium Pseudomonas simiae WCS417r that expressed various fluorescence marker genes. We visualized these strains simultaneously under a confocal microscope, demonstrating the usefulness of CRAGE-Duet for creating biological systems to study plant-microbe interactions.

Deep learning predicts microbial interactions from self-organized spatiotemporal patterns

Microbial communities organize into spatial patterns that are largely governed by interspecies interactions. This phenomenon is an important metric for understanding community functional dynamics, yet the use of spatial patterns for predicting microbial interactions is currently lacking. Here we propose supervised deep learning as a new tool for network inference. An agent-based model was used to simulate the spatiotemporal evolution of two interacting organisms under diverse growth and interaction scenarios, the data of which was subsequently used to train deep neural networks. For small-size domains (100 µm × 100 µm) over which interaction coefficients are assumed to be invariant, we obtained fairly accurate predictions, as indicated by an average R2 value of 0.84. In application to relatively larger domains (450 µm × 450 µm) where interaction coefficients are varying in space, deep learning models correctly predicted spatial distributions of interaction coefficients without any additional training. Lastly, we evaluated our model against real biological data obtained using Pseudomonas fluorescens and Escherichia coli co-cultures treated with polymeric chitin or N-acetylglucosamine, the hydrolysis product of chitin. While P. fluorescens can utilize both substrates for growth, E. coli lacked the ability to degrade chitin. Consistent with our expectations, our model predicted context-dependent interactions across two substrates, i.e., degrader-cheater relationship on chitin polymers and competition on monomers. The combined use of the agent-based model and machine learning algorithm successfully demonstrates how to infer microbial interactions from spatially distributed data, presenting itself as a useful tool for the analysis of more complex microbial community interactions.

Rpa1 mediates an immune response to avrRpm1Psa and confers resistance against Pseudomonas syringae pv. actinidiae

The type three effector AvrRpm1Pma from Pseudomonas syringae pv. maculicola (Pma) triggers an RPM1-mediated immune response linked to phosphorylation of RIN4 (RPM1-interacting protein 4) in Arabidopsis. However, the effector-resistance (R) gene interaction is not well established with different AvrRpm1 effectors from other pathovars. We investigated the AvrRpm1-triggered immune responses in Nicotiana species and isolated Rpa1 (Resistance to Pseudomonas syringae pv. actinidiae 1) via a reverse genetic screen in Nicotiana tabacum. Transient expression and gene silencing were performed in combination with co-immunoprecipitation and growth assays to investigate the specificity of interactions that lead to inhibition of pathogen growth. Two closely related AvrRpm1 effectors derived from Pseudomonas syringae pv. actinidiae biovar 3 (AvrRpm1Psa ) and Pseudomonas syringae pv. syringae strain B728a (AvrRpm1Psy ) trigger immune responses mediated by RPA1, a nucleotide-binding leucine-rich repeat protein with an N-terminal coiled-coil domain. In a display of contrasting specificities, RPA1 does not respond to AvrRpm1Pma , and correspondingly AvrRpm1Psa and AvrRpm1Psy do not trigger the RPM1-mediated response, demonstrating that separate R genes mediate specific immune responses to different AvrRpm1 effectors. AvrRpm1Psa co-immunoprecipitates with RPA1, and both proteins co-immunoprecipitate with RIN4. In contrast with RPM1, however, RPA1 was not activated by the phosphomimic RIN4T166D and silencing of RIN4 did not affect the RPA1 activity. Delivery of AvrRpm1Psa by Pseudomonas syringae pv. tomato (Pto) in combination with transient expression of Rpa1 resulted in inhibition of the pathogen growth in N. benthamiana. Psa growth was also inhibited by RPA1 in N. tabacum.

Litterbox-A gnotobiotic Zeolite-Clay System to Investigate Arabidopsis-Microbe Interactions

Plants are colonised by millions of microorganisms representing thousands of species withvarying effects on plant growth and health. The microbial communities found on plants arecompositionally consistent and their overall positive effect on the plant is well known. However,the effects of individual microbiota members on plant hosts and vice versa, as well as the underlyingmechanisms, remain largely unknown. Here, we describe "Litterbox", a highly controlled system toinvestigate plant-microbe interactions. Plants were grown gnotobiotically, otherwise sterile, onzeolite-clay, a soil replacement that retains enough moisture to avoid subsequent watering.Litterbox-grown plants resemble greenhouse-grown plants more closely than agar-grown plantsand exhibit lower leaf epiphyte densities (106 cfu/g), reflecting natural conditions. Apolydimethylsiloxane (PDMS) sheet was used to cover the zeolite, significantly lowering thebacterial load in the zeolite and rhizosphere. This reduced the likelihood of potential systemicresponses in leaves induced by microbial rhizosphere colonisation. We present results of exampleexperiments studying the transcriptional responses of leaves to defined microbiota members andthe spatial distribution of bacteria on leaves. We anticipate that this versatile and affordable plantgrowth system will promote microbiota research and help in elucidating plant-microbe interactionsand their underlying mechanisms.

Replicating Arabidopsis Model Leaf Surfaces for Phyllosphere Microbiology

Artificial surfaces are commonly used in place of leaves in phyllosphere microbiology to study microbial behaviour on plant leaf surfaces. These surfaces enable a reductionist approach to be undertaken, to enable individual environmental factors influencing microorganisms to be studied. Commonly used artificial surfaces include nutrient agar, isolated leaf cuticles, and reconstituted leaf waxes. Recently, replica surfaces mimicking the complex topography of leaf surfaces for phyllosphere microbiology studies are appearing in literature. Replica leaf surfaces have been produced in agar, epoxy, polystyrene, and polydimethylsiloxane (PDMS). However, none of these protocols are suitable for replicating fragile leaves such as of the model plant Arabidopsis thaliana. This is of importance, as A. thaliana is a model system for molecular plant genetics, molecular plant biology, and microbial ecology. To overcome this limitation, we introduce a versatile replication protocol for replicating fragile leaf surfaces into PDMS. Here we demonstrate the capacity of our replication process using optical microscopy, atomic force microscopy (AFM), and contact angle measurements to compare living and PDMS replica A. thaliana leaf surfaces. To highlight the use of our replica leaf surfaces for phyllosphere microbiology, we visualise bacteria on the replica leaf surfaces in comparison to living leaf surfaces.

Delivering "Chromatic Bacteria" Fluorescent Protein Tags to Proteobacteria Using Conjugation

Recently, we published a large and versatile set of plasmids, the chromatic bacteria toolbox, to deliver eight different fluorescent protein genes and four combinations of antibiotic resistance genes to Gram-negative bacteria. Fluorescent tags are important tools for single-cell microbiology, synthetic community studies, biofilm, and host-microbe interaction studies. Using conjugation helper strain E. coli S17-1 as a donor, we show how plasmid conjugation can be used to deliver broad host range plasmids, Tn5 transposons delivery plasmids, and Tn7 transposon delivery plasmids into species belonging to the Proteobacteria. To that end, donor and recipient bacteria are grown under standard growth conditions before they are mixed and incubated under non-selective conditions. Then, transconjugants or exconjugant recipients are selected on selective media. Mutant colonies are screened using a combination of tools to ensure that the desired plasmids or transposons are present and that the colonies are not containing any surviving donors. Through conjugation, a wide range of Gram-negative bacteria can be modified without prior, often time-consuming, establishment of competent cell and electroporation procedures that need to be adjusted for every individual strain. The here presented protocol is not exclusive for the delivery of Chromatic bacteria plasmids and transposons, but can also be used to deliver other mobilizable plasmids to bacterial recipients.

Effects of sub-lethal concentrations of copper ammonium acetate, pyrethrins and atrazine on the response of Escherichia coli to antibiotics

Background: Antibiotic resistance in human and animal pathogens is mainly the outcome of human use of antibiotics. However, bacteria are also exposed to thousands of other antimicrobial agents. Increasingly those exposures are being investigated as co-selective agents behind the rapid rise and spread of resistance in bacterial pathogens of people and our domesticated animals. Methods: We measured the sub-lethal effects on antibiotic tolerance of the human pathogen/commensal Escherichia coli caused by exposure to three common biocide formulations based on either copper, pyrethrins, or atrazine as active ingredients. The influence of the efflux pump AcrAB-TolC was investigated using deletion strains, and the persistence of observed effects was determined. Results: Some effects were seen for all biocides, but the largest effects were observed with copper in combination with the antibiotic tetracycline. The effect was caused by both the induction of the adaptive efflux system and by chelation of the antibiotic by copper. Finally, persistence of the adaptive response was measured and found to persist for about two generations. Conclusions: Through a combination of microbe-chemical and chemical-chemical interactions, humanity may be creating micro-environments in which resistance evolution is accelerated.