Biology subjects

Kosina, S. M.

Publications and source records attributed to Kosina, S. M..

At least 19 recordsLinked to original sources

bioRxiv2026

Distinct Strategies for Engineering Bioenergy Traits in Sorghum Drive Divergent Functional Shifts in the Rhizosphere Microbiome

Engineering bioenergy crops for enhanced biomass digestibility and high-value co-products is a promising approach to sustainable biofuel production. However, the impact of these engineered crops on the belowground microbiome remains poorly understood. In this study, we characterized the composition and functional responses of the belowground microbiome associated with transgenic sorghum lines: one with reduced cell wall crosslinking (AT10) and another with elevated protocatechuic acid (PCA) production (Qsub). The lines were grown under field conditions with four irrigation levels, and samples were collected twice during the growing season. We found that the two transgenic types drove a subtle but significant divergence in bacterial communities, both compositionally and functionally. Community-wide functional profiling showed that AT10 rhizospheres were consistently depleted in genes associated with mobile genetic elements, while Qsub rhizospheres were enriched in TonB-dependent transport and vanillate monooxygenase, an enzyme that funnels lignin-derived monomers toward PCA degradation, alongside reduced pectin- and cellulose-degradation genes. Genome-resolved analysis linked these community-level shifts to specific taxa: in Qsub, the enriched MAGs were taxonomically diverse, ranging from genome-reduced Patescibacteria with an episymbiotic lifestyle to taxa enriched in lignin-associated auxiliary activity enzymes. In AT10, the depleted Azospirillaceae MAGs carried unusually high mobile genetic element content, consistent with the community-wide pattern. Collectively, these findings offer new insights into how genetic modifications aimed at improving bioenergy traits shapes the composition and function of the rhizosphere microbiome, with potential downstream consequences for soil carbon cycling.

plant biology↗

bioRxiv2026

Signaling metabolites spatially organize a multispecies mutualism in the soil microbiome

A plant-independent avenue for N2-fixation takes place in desert topsoils through a "C-for-N" mutualism between heterodiazotrophs and the cyanobacterium Microcoleus vaginatus. These partners come together within a diverse soil microbiome under conditions of N-limitation for the phototroph and C limitation for the heterotrophs. We hypothesized that extracellular chemical signaling might enable partner selection and collocation, though infomolecules shaping inter-microbial architecture were unknown. We show that the complex chemical composition of M. vaginatus exometabolome depends on its N-limitation status, thus potentially offering information to mutualists. In chemotactic assays, the exometabolome effectively repelled most native soil bacteria, particularly intensely when under N-limitation. Bacterial assemblages circumventing the repulsion were enriched in species that are rare in the soil microbiome, and that functionally resemble mutualistic cyanospheres (showing high N2-fixation potential, secretion of urea, and copiotrophy), setting the stage for a working symbiosis. Further, we could reproduce the enrichment of copiotrophs and nitrogen-fixers using mixtures of N-acetylglutamic acid, N-acetylmethionine, indole-3-acetic acid, and 5'-methylthioadenosine, all preferentially released by M. vaginatus under N-limitation. These signaling molecules did not result in an enrichment of urea producers, however. The results demonstrate that trans-species communication through specific infochemicals, together with already known quorum-sensing-like intraspecific communication in M. vaginatus, act as a tool to organize microbiomes spatially and to attain mutualistic partner specificity in an open, crowded background.

microbiology↗

bioRxiv2026

Bioengineered algal lipids enriched in structured medium- and long-chain triacylglycerols, linoleate, and sn-2 palmitate for human milk fat substitutes

Triacylglycerols (TAGs) in human milkfat (HMF) provide over 50% of the calories for infant nutrition. Their unique architecture, featuring palmitic acid predominantly esterified at the sn-2 position, facilitates absorption as 2-palmitoyl monoacylglycerol after hydrolysis of the sn-1 and sn-3 fatty acids by gut lipases. Conventional vegetable oil-based infant formulas mimic the HMF fatty acid profile but lack its distinct regioisomeric structure, abundant medium- and long-chain triglycerides (MLCTs), and oleic-to-linoleic acid ratios that vary with maternal diet and geography. We have engineered the oleaginous green alga Auxenochlorella for biosynthesis of TAGs enriched in MLCTs, sn-2 palmitate, and linoleate via heterologous expression of acyl-acyl-carrier-protein (ACP) thioesterases, palmitate-specific lysophosphatidic acid acyltransferases, and lysophosphatidylcholine acyltransferase. These structured algal lipids replicate both the major fatty acid proportions and regioisomeric composition of authentic HMF, providing single-source bioengineered alternatives to plant-derived HMF substitutes for infant formula.

synthetic biology↗

bioRxiv2026

What microbes want: exploring microbial substrate preferences with the Web of Microbes Agent

Understanding and predicting bacterial substrate preferences has broad utility from microbial interactions to selecting prebiotics. Isolate exometabolite profiling directly measures which compounds a given microbe utilizes from an array of metabolites in the environment. However, modeling, mining, and integrating these data are challenging. Here, we introduce a Bayesian Personalized Ranking (BPR) model applied to substrate preferences which we find learns to rank compounds by a given microbes preference. It was found to outperform the other ranking models (AUC = 0.93), proved robust to ablation, showed strong within-genus isolate pairs correlation (Spearman rank = 0.78) and predictive ability for new data. BPR was then used to create the Web of Microbes (WoM) Agent by integrating it with the Phydon growth model and Large Language Model (LLM) for autonomous orchestration tool calling and analysis. The WoM Agent accurately predicted substrate consumption by existing strain grown on a novel medium and correctly identified bacteria enriched in soil metabolite spike-in experiments. Additionally, the WoM Agent can use autonomous reasoning including to predict substrates that will selectively promote the growth of one clade of bacteria over another including helping interpret results and suggest new hypotheses and experiments. We anticipate broad applications in microbial cultivation, microbiome engineering, and environmental microbiology, with the agents capabilities further extensible through the integration of additional tools and use of rapidly improving LLMs.

systems biology↗

bioRxiv2025

Dopamine biosynthesis in plants

Dopamine, an essential human neurotransmitter, also plays important roles in plant-microbe interactions and abiotic stress tolerance. While dopamine biosynthesis is well-characterized in mammals, it remains largely unclear in plants. Through metabolite-based genome-wide association studies, we identified two putative polyphenol oxidase genes for dopamine biosynthesis in Brachypodium distachyon, located in the same chromosomal region as two tyrosine decarboxylase genes. Biochemical and knockout mutant analyses demonstrated that dopamine biosynthesis proceeds primarily via tyramine as an intermediate and contributes to plant tissue browning. Homology searches and functional assays indicate that this dopamine biosynthetic pathway is conserved across diverse plant species. This discovery provides valuable insights into plant dopamine biosynthesis with potential applications in reducing food browning, improving stress resilience, and bioengineering valuable compounds.

plant biology↗

bioRxiv2025

TOR inhibition drives accumulation of amino acids through transcriptional activation in algae

Cellular homeostasis is maintained by the balance between energy production and breakdown and is fundamental to all forms of life. The conserved, ancient target of rapamycin (TOR) kinase is a central metabolic regulator in eukaryotes that integrates carbon and nitrogen to maintain homeostasis and promote growth and development through protein synthesis. While TOR regulatory mechanisms of amino acid accumulation are well known in yeast and mammals, they remain unknown in photosynthetic organisms. Here, we developed the unicellular green alga Chromochloris zofingiensis as a simpler model system for understanding TOR function. Multiomics experiments showed that TOR inhibition leads to an increase in amino acid levels independent of hexokinase-mediated glucose signaling. We observed upregulation of selective amino acid biosynthesis pathways at the transcript and protein levels as potential mechanisms driving the increase in amino acids. Transcriptomics and proteomics experiments identified a basic helix-loop-helix (bHLH) transcription factor with rapid upregulation during TOR inhibition. DAP-seq analysis demonstrated that bHLH can bind directly to the promoters of amino acid biosynthesis genes, potentially regulating their transcription in response to TOR inhibition. We found high conservation of the bHLH-binding motif in the genomes of other green algae and plants, suggesting a conserved regulatory mechanism for amino acid biosynthesis across Viridiplantae. Phosphoproteomics experiments also revealed novel conserved targets that are not currently recognized as part of the TOR pathway. Altogether, our findings elucidate the transcriptional regulation of amino acid metabolism and explain how TOR regulates nitrogen metabolism to support growth and development in photosynthetic organisms. Significance StatementCarbon and nitrogen metabolism play key roles in enhancing plant yield and reducing fertilizer use. Thus, improving nitrogen utilization can significantly boost crop productivity and algal biotechnology. From yeast to plants to mammals, the protein target of rapamycin (TOR) kinase is an essential metabolic regulator. Here, we developed the unicellular green alga Chromochloris zofingiensis as a simpler system to study conserved mechanisms in TOR signaling. Using a multiomics approach, we showed transcriptional regulation of amino acid accumulation upon TOR inhibition and identified a transcription factor with evolutionarily conserved DNA binding sites in nitrogen metabolism genes. We also discovered novel conserved targets of TOR. Our study demonstrates the role of TOR in regulating nitrogen metabolism to support growth and development in photosynthetic organisms.

plant biology↗

bioRxiv2025

Contrasting effects of glutamate and branched-chain amino acid metabolism on acid tolerance in a Castellaniella isolate from acidic groundwater

Groundwater acidification co-occurring with nitrate pollution is a common, global environmental health hazard. Denitrifying bacteria have been leveraged for the in-situ removal of nitrate in groundwater. However, co-existing stressors--like low pH--reduce the efficacy of biological removal processes. Castellaniella sp. str. MT123 is a complete denitrifier that was isolated from acidic, nitrate-contaminated groundwater. The strain grows robustly by nitrate respiration at pH < 6.0 completely reducing nitrate to dinitrogen gas. Genomic analyses of MT123 revealed few previously characterized acid tolerance genes. Thus, we utilized a combination of proteomics, metabolomics, and competitive mutant fitness to characterize the genetic mechanisms of MT123 acclimation to growth under mildly acidic conditions. We found that glutamate accumulation is critical in the acid acclimation of MT123, likely through consumption of intracellular protons via glutamate decarboxylation to GABA. This is despite the fact that MT123 lacks the canonical glutamate decarboxylase-glutamate/GABA antiporter system implicated in acid tolerance in other bacteria. Additionally, branched chain amino acid (BCAA) accumulation was detrimental to cell growth at lower pHs, possibly through indirect mechanisms impacting the cellular glutamate pool. Genetic analysis previously linked MT123 to a population of Castellaniella that bloomed--concurrent to nitrate removal--during a biostimulation effort to reduce groundwater nitrate concentrations at MT123s location of origin. Thus, our analyses provide novel insight into mechanisms of acclimation to acidic conditions in a strain with significant potential for nitrate bioremediation. IMPORTANCENitrate pollution in groundwater is a serious threat to both environmental and human health. This nitrate pollution can come from a variety of sources including fertilizers, sewage, and industrial discharge. Certain bacteria, known as "denitrifiers", can convert this nitrate into harmless nitrogen gas, a process known as "denitrification". Denitrifiers can be used to clean up nitrate-contaminated groundwater. However, their ability to do this can be disrupted by changing environmental conditions. For example, groundwater that is polluted with nitrate is often acidic. Acidic conditions make it challenging for denitrifiers to survive, which results in less conversion of nitrate to nitrogen gas. In this study, we investigated how one denitrifying bacterium--originating from acidic, nitrate-contaminated groundwater--can cope with acidic conditions

microbiology↗

bioRxiv2025

Engineered lignin composition in Brachypodium distachyon modulates the root-associated microbiome

Lignin is a key component of the plant cell wall and a barrier to microbial interaction and biomass digestibility. While lignin biosynthesis has been engineered in grasses to reduce recalcitrance for agroindustrial applications, the consequences for root-associated microbial communities remain poorly understood. Here, we show in the model grass species Brachypodium distachyon that genetic modification of lignin biosynthetic genes, particularly caffeic acid O-methyltransferase (COMT), alters root lignin syringyl/guaiacyl (S/G) ratios, root exudate composition, and significantly reshapes the rhizosphere microbiome. Using a synthetic microbial community (SYNCOM) in controlled fabricated ecosystem (EcoFAB) environments, we observed a distinct reduction in Burkholderia colonization and enrichment of Rhodococcus in COMT mutant lines. LC-MS/MS profiling of root exudates revealed increased p-coumaric acid, caffeic acid and hydroxycinnamic acid amides in these lines, potentially linked to both metabolic remodeling and plant stress responses. These findings demonstrate that altering lignin composition can have profound, genotype-specific impacts on rhizosphere microbiome assembly, with implications for plant-microbe interactions, nutrient cycling, and biomass conversion strategies in bioenergy crops.

plant biology↗

bioRxiv2025

Bacterial fitness for plant colonization is influenced by plant growth substrate

O_LIBacteria colonize plants and contribute to their health. Despite advances in our understanding of bacterial plant colonization, the extent to which growth substrate influences the molecular mechanisms enabling bacteria to efficiently colonize plants remains poorly understood. C_LIO_LITo evaluate if genes important for plant colonization are influenced by substrate, we used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Paraburkholderia graminis OAS925, an efficient rhizosphere colonizer, and Brachypodium distachyon plants grown in six different substrates. C_LIO_LIOf the 382 rhizosphere colonization genes that we identified in strain OAS925, 348 genes (91.1%) are dependent on the growth substrate evaluated, and 34 genes (8.9%) are shared across all the substrates. To further characterize the plant colonization fitness genes, we compared our data to growth in 110 distinct in vitro conditions. To validate our results, we used individual mutants of selected genes and tested them in different growth substrates. We also show the influence of substrate on colonization by P. phytofirmans PsJN, Variovorax sp. OAS795 and Rhizobium sp. OAE497. C_LIO_LIOur data confirms that bacterial fitness for plant colonization is strongly influenced by plant growth substrate type, and highlights the importance of taking this parameter into consideration when engineering bacterial strains for improved host colonization. C_LI

microbiology↗

bioRxiv2024

Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

microbiology↗

bioRxiv2024

Insights into the role of dopamine in rhizosphere microbiome assembly

Dopamine plays a critical role in animal physiology and interactions with gut microbes. In plants, dopamine is known to function in plant defense and abiotic stress tolerance; however, its role in mediating plant-microbiome interactions remains unexplored. In this study, we observed that dopamine is one of the most abundant exometabolites with natural variation in root exudates across diverse Brachypodium distachyon lines, suggesting a potential role in rhizosphere microbial assembly. To further investigate this, we colonized ten natural B. distachyon lines with a 16-member bacterial synthetic community (SynCom), collected paired metabolomic and 16S rRNA sequencing data, and performed an association analysis. Our results revealed that dopamine levels in root exudates were significantly associated with the abundance of six SynCom members in a hydroponic system. In vitro growth studies demonstrated that dopamine had a significant effect on the growth of the same six bacterial isolates. Additionally, treating soil directly with dopamine enriched Actinobacteria, consistent with both the SynCom-dopamine correlations and the isolate growth results. Collectively, our study underscores the selective influence of dopamine on rhizosphere microbial communities, with implications for precision microbiome management.

plant biology↗

bioRxiv2024

Insights into the role of root exudates in bacteriophage infection dynamics

Bacteriophages impact soil bacteria through lysis, altering the availability of organic carbon and plant nutrients. However, the magnitude of nutrient uptake by plants from lysed bacteria remains unknown, partly because this process is challenging to investigate in the field. In this study, we extend ecosystem fabrication (EcoFAB 2.0) approaches to study plant-bacteria-phage interactions by comparing the impact of phage-lysed and uninfected 15N-labeled bacterial necromass on plant nitrogen acquisition and rhizosphere exometabolites composition. We show that grass Brachypodium distachyon derives some nitrogen from amino acids in uninfected Pseudomonas putida necromass but not from virocell necromass. Additionally, the bacterial necromass elicits the formation of rhizosphere exometabolites, some of which (guanosine), alongside tested aromatic acids (p-coumaric and benzoic acid), show distinct effects on bacteriophage-induced lysis when tested in vitro. The study highlights the dynamic feedback between bacterial necromass and plants and suggests that root exudate metabolites can impact bacteriophage infection dynamics.

plant biology↗

bioRxiv2023

Early viral infection of cyanobacteria drives bacterial chemotaxis in the oceans

Interactions among marine microbes primarily occur through exudation and sensing of dissolved chemical compounds, which ultimately control ecosystem-scale processes such as biomass production, nutrient cycling, carbon fixation, and remineralization. Prior to lysis, viruses alter host metabolism, stimulating the release of dissolved chemical cues from intact plankton. However, the nature and degree of interactions between prelysis, virus-infected cells and neighbouring microbes remain unquantified. Here, we determine the impact of viral infection on dissolved metabolite pools from the marine cyanobacterium Synechococcus and the subsequent chemotactic response of heterotrophic bacteria using time-resolved metabolomics and microfluidics. Metabolites released from intact, virus-infected Synechococcus elicited vigorous chemoattractive responses from heterotrophic bacteria (Vibrio alginolyticus and Pseudoalteromonas haloplanktis), with the strongest responses occurring in the early infection stages and following cell lysis. We provide the first experimental observations of sustained chemotaxis towards live, infected Synechococcus, which is contrasted by no discernible chemotaxis toward uninfected Synechococcus. Finally, metabolite compounds and concentrations driving chemotactic responses were identified using a novel high-throughput microfluidic device. Our findings establish that prior to cell lysis, virus-infected picophytoplankton release compounds that significantly attract motile heterotrophic bacteria, illustrating a viable mechanism for resource transfer to chemotactic bacteria with implications for our understanding of carbon and nutrient flux across trophic levels.

biophysics↗

bioRxiv2023

Reproducible growth of Brachypodium distachyon in fabricated ecosystems (EcoFAB 2.0) reveals that nitrogen form and starvation modulate root exudation

Understanding plant-microbe interactions requires examination of root exudation under nutrient stress using standardized and reproducible experimental systems. We grew Brachypodium distachyon hydroponically in novel fabricated ecosystem devices (EcoFAB 2.0) under three inorganic nitrogen forms (NO3-, NH4+, NH4NO3), followed by nitrogen starvation. Analyses of exudates with LC-MS/MS, biomass, medium pH, and nitrogen uptake showed EcoFAB 2.0s low intra-treatment data variability. Furthermore, the three inorganic nitrogen forms caused differential exudation, generalized by abundant amino acids/peptides and alkaloids. Comparatively, N-deficiency decreased N-containing compounds but increased shikimates/phenylpropanoids. Subsequent bioassays with two shikimates/phenylpropanoids (shikimic and p-coumaric acids) on the rhizobacterium Pseudomonas putida or Brachypodium seedlings revealed that shikimic acid promoted bacterial and root growth, while p-coumaric acid stunted seedlings. Our results suggest: (i) Brachypodium alters exudation in response to nitrogen status, which can affect rhizobacterial growth; and (ii) EcoFAB 2.0 is a valuable standardized plant research tool. TeaserEcoFAB 2.0, a novel fabricated ecosystem device, has low data variability in studies of plant traits.

plant biology↗

bioRxiv2022

Ultraviolet radiation and dehydration stress induce overlapping transcriptional and metabolic responses in Syntrichia mosses

O_LIProtection from excess solar radiation and access to sufficient water are important problems for terrestrial plants to solve. Desiccation tolerance (DT), defined as the ability to equilibrate to dry air and resume normal metabolic activity after rehydration, allows organisms to survive dry periods by limiting metabolic activity to periods of moisture availability. We compared separate and combined effects of chronic ultraviolet radiation (UVR) treatments (UV-A and UV-A/B) and a dehydration treatment (as a surrogate for desiccation) in the mosses Syntrichia ruralis and S. caninervis to uncover the nature of correlation between DT and UVR tolerance (UVRT). C_LIO_LIUsing a fully factorial experiment with combined transcriptomics and metabolomics, we tested for cross-talk (overlap in signaling pathways in response to different stressors but separate mechanisms of protection) in the genetic underpinnings of DT and UVRT and cross-tolerance (overlap in the mechanism of protection) these two stressors. C_LIO_LIShared transcriptomic response to the two stressors with no significant interaction between them suggested cross-talk between UVRT and DT for S. caninervis. Phenolic metabolites and transcripts were involved in the response to UVR and dehydration in both species. C_LIO_LISome candidate UVRT genes and metabolites were induced by UVR in S. ruralis, but not S. caninervis, supporting the hypothesis that S. ruralis has a more plastic, acclimatable UVR response than S. caninervis, and that these differences are predictable by their unique interaction with these stressors as poikilohydric organisms. C_LI

plant biology↗

bioRxiv2022

Extensive plant use of exometabolites

Root exudation has been extensively studied due to its importance in soil carbon cycling and in supporting growth of soil microbes. However, the extent and dynamics of plant uptake of exogenous metabolites is poorly understood. To gain new insights into these processes we used 13C-tracing to characterize plant uptake of exometabolites across a panel of diverse plant species (Arabidopsis thaliana, Brachypodium distachyon, Lotus japonicus, Panicum virgatum, and Kalanchoe fedtschenkoi) grown in sterile hydroponic cultures. The uptake of exometabolites accounted for 23% of the overall B. distachyon carbon budget, and we identified 33 metabolites that were taken up by plants. Counterintuitively, many metabolites had higher uptake rates during the day vs. night. Thirteen of the metabolites from root exudates were found to promote root growth in A. thaliana, including hydroxybenzoate, threonate, N-acetyl-glucosamine, and uracil. Together these results indicate that the root uptake of organics can account for a significant portion of the plant carbon budget and that exogenous small molecules used by plants alter root growth with implications for plant nutrition, organic farming, soil nutrient cycling, and rhizosphere community dynamics.

plant biology↗

bioRxiv2022

Dynamic Phaeodactylum tricornutum Exometabolites Shape Surrounding Bacterial Communities

The roles of exometabolites in mediating algal-bacterial interactions and regulating microbial community composition are not well understood. Here, we identified specific exometabolites from the model diatom Phaeodactylum tricornutum affecting abundance of specific bacterial taxa in isolation and in a community setting. We examined the response of a P. tricornutum-adapted enrichment community and found that both algal exudates and algal presence drove similar changes in community composition compared to controls. Using LC-MS/MS, we identified 50 metabolites produced by axenic P. tricornutum and found that different exometabolites accumulated during different algal growth phases. Profiling growth of 12 bacterial isolates representative of the enrichment community uncovered two algal exometabolites (out of 12 tested) which supported growth of a subset of isolates as a primary carbon source. We compared enrichment community response with and without the addition of two contrasting metabolites: 4-hydroxybenzoic acid, which supported isolate growth, and lumichrome, which did not. Exogenous metabolite additions did promote increased abundances of taxa that were able to utilize the metabolite in the isolate study, but also revealed the importance of factors relating to algal presence in regulating community composition. Collectively, this work demonstrates the influence of specific algal exometabolites in driving microbial community composition.

microbiology↗

bioRxiv2021

Biofilm Interaction Mapping and Analysis (BIMA): A tool for deconstructing interspecific interactions in co-culture biofilms

Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition and invasion) between colony forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and thirteen other species of pseudomonas isolated from non-contaminated soil. The metabolites and genes associated with both active co-culture growth and inhibitory growth were investigated using mass spectrometry based metabolomics and mutant fitness profiling of a DNA-barcoded mutant library. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and metabolomics. IMPORTANCEThe Biofilm Interaction Mapping and Analysis (BIMA) methodology provides a way to rapidly screen for positive and negative interspecific interactions, followed by an analysis of the genes and metabolites that may be involved. Knowledge of these may offer opportunities for engineered strains with improved function in biotechnology systems. P. stutzeri, an organism with wide-spread utilization in consortia based biotechnologies, was used to demonstrate the utility of this approach. Where little is known about the factors influencing biofilm based interactions, elucidation of the genes and metabolites involved allows for better control of the system for improved function or yield.

microbiology↗