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DOE OSTI2023

KBase Narrative - MRA Genome Announcement Bradyrhizobium NP1

We report the complete genome sequence of Bradyrhizobium strain NP1, which was isolated from forest soil that had been subject to chronic warming. The diverse genus Bradyrhizobium is predicted to contain approximately 800 species (1) and includes non-symbiotic species that dominate forest soil (2). Bradyrhizobium NP1 was isolated from a Long-Term Ecological Research site in the Harvard Forest (HRF), in Petersham, MA (42.54, -72.18).

Morrow, Maureen↗

DOE OSTI2023

Genomes_SET2_178 - Shared

The dataset consists of 178 bacterial genomes in total. Of these, 145 genomes were drawn from published literature linked to Biolog Gen III growth data, while 33 genomes came from soil isolates collected at the Cedar Creek Ecosystem Science Research Reserve (CCESR) in Minnesota. The isolates were sequenced on an Illumina HiSeq platform (~50× coverage), assembled with Megahit, and annotated using RAST at PATRIC, with strict quality filtering (<90% completeness or >5% contamination).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Luteolibacter sp. strain Populi

Luteolibacter sp. strain Populi is bacterium from the phylum Verrucomicrobiota, isolated from the rhizosphere of a black cottonwood tree, Populus trichocarpa, from the Cascade mountains in Washington. Its 6.6 Mb chromosome was completely sequenced using Oxford Nanopore long-reads and is predicted to encode 5301 proteins and 60 RNAs. The bacteria was isolated from the rhizosphere of a mature Populus trichocarpa from the Tieton riverwatershed of Washington state, USA (Lat: 46°42’9” N, Lon: 120°25 39’36” W). A rhizosphere sample (fine roots and adhering soil) was used to obtain a microbial fraction by centrifugation on Histodenz (12) and stained with 5µM Syto59 (Thermo Fisher Scientific Inc). A Cytopeia Influx cell sorter (BD, Franklin Lakes, NJ) was used to sort and array single cells (100 per plate) based on forward-side scatter and fluorescence intensity on asparagine-glucose nutrient agar (ATCC medium 184). The Luteolibacter sp. Populi genome sequence has been deposited in GenBank under the accession number CP161812. A draft genome annotated with Prokka and DRAM is available in this Narrative as Luteolibacter_sp_Prokka.240711.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Genome collection processing for “Conserved upper thermal limits and small safety margins in soil copiotrophic bacteria”

We extracted the genomic DNA of 400 randomly selected isolates using a Quick-DNA Microprep Kit (Zymo Research D3020) according to the manufacturer’s protocol. We then submitted the extracted gDNA samples for short-read Illumina sequencing (200 Mbp) at SeqCoast Genomics (Portsmouth, NH, USA). After preprocessing the sequences using Trimmommatic (Bolger et al. 2014), we assembled the genomes using SPADES (Bankevich et al. 2012) and checked the quality of each assembly using QUAST (Gurevich et al. 2013). We processed the genome assemblies using a KBase (v1.4.0) pipeline (Allen et al. 2017; Arkin et al. 2018). Briefly, we used DRAM (v0.1.2) with default settings to annotate the genome assemblies. We then evaluated genome quality and possible contamination levels using CheckM (v1.0.18) (Parks et al. 2015) and retained genomes with completeness above 98% and contamination below 5% (n = 354), following the authors' guidelines. We then obtained taxonomic assignments for all remaining isolates using the Genome Taxonomy Database tool GTDB-Tk (v2.3.2, database version r214) (Chaumeil et al. 2019). We constructed a phylogenetic tree using the tool SpeciesTree (v2.2.0). We then trimmed the tree (using Trim SpeciesTree to GenomeSet- v1.4.0), retaining only tips within our collection with measured thermal performance.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Leisingera sp. ANG59 & Pseudoalteromonas sp. JC28 Genomes Overview

The Hawaiian bobtail squid, Euprymna scolopes, has a symbiotic bacterial consortium in the accessory nidamental gland (ANG), a female reproductive organ that protects eggs against fouling microorganisms. To test the antibacterial activity of ANG community members, 19 bacterial isolates were screened for their ability to inhibit Gram-negative and Gram-positive bacteria, of which two strains were inhibitory. These two antibacterial isolates, Leisingera sp. ANG59 and Pseudoalteromonas sp. JC28, were subjected to further genomic characterization. Genomic analysis of Leisingera sp. ANG59 revealed a biosynthetic gene cluster encoding the antimicrobial compound indigoidine. The genome of Pseudoalteromonas sp. JC28 had a 14-gene cluster with >95% amino acid identity to a known bromoalterochromide (BAC) cluster. Chemical analysis confirmed production of known BACs, BAC-A/A′ (compounds 1a/1b), as well as two new derivatives, BAC-D/D′ (compounds 2a/2b). Extensive nuclear magnetic resonance (NMR) analyses allowed complete structural elucidation of compounds 2a/2b, and the absolute stereochemistry was unambiguously determined using an optimized Marfey’s method. The BACs were then investigated for in vitro antibacterial, antifungal, and nitric oxide (NO) inhibitory activity. Compounds 1a/1b were active against the marine bacteria Bacillus algicola and Vibrio fischeri, while compounds 2a/2b were active only against B. algicola. Compounds 1a/1b inhibited NO production via lipopolysaccharide (LPS)-induced inflammation in RAW264.7 macrophage cells and also inhibited the pathogenic fungus Fusarium keratoplasticum, which, coupled with their antibacterial activity, suggests that these polyketide-nonribosomal peptides may be used for squid egg defense against potential pathogens and/or fouling microorganisms. These results indicate that BACs may provide Pseudoalteromonas sp. JC28 an ecological niche, facilitating competition against nonsymbiotic microorganisms in the host’s environment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in MOPS Medium

This narrative was used for the 4-member community modeling using MOPS medium for the bacteria isolated from Populus deltoides (PD). 10 bacterial strains isolated from PD were co-cultured as a synthetic microbial community in MOPS minimal medium. After 15 passages there were 4 members survived in MOPS medium. The genome of each community member was sequenced and uploaded into KBase for genome annotation and metabolic modeling. To simulate the metabolic interactions among the finally surviving community members, the individual metabolic models of each strain were merged into a compartmentalized community model, and then the community model was gapfilled using MOPS medium. The FBA modeling was performed and the metabolites exchange among community members was proposed. The publication by Jia Wang, Dana L. Carper, Leah H. Burdick, Him Shrestha, Manasa Appidi, Paul E. Abraham, Collin M. Timm, Robert L. Hettich, Dale A. Pelletier, Mitchel J. Doktycz can be found here: https://doi.org/10.1016/j.csbj.2021.03.034

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium

This narrative was used for the 3-member community modeling using R2A medium for the bacteria isolated from Populus deltoides (PD). 10 bacteiral strains isolated from PD were co-cultured as a synthetic microbial community in R2A complex medium. After 15 passages, there were 3 members survived in R2A medium. The genome of each community member was sequenced and uploaded into KBase for genome annotation and metabolic modeling. To simulate the metabolic interactions among the finally surviving community members, the individual metabolic models of each strain were merged into a compartmentalized community model, and then the community model was gapfilled using R2A medium. The FBA modeling was performed and the metabolites exchange among community members was proposed. The publication by Jia Wang, Dana L. Carper, Leah H. Burdick, Him Shrestha, Manasa Appidi, Paul E. Abraham, Collin M. Timm, Robert L. Hettich, Dale A. Pelletier, Mitchel J. Doktycz can be found here: https://doi.org/10.1016/j.csbj.2021.03.034

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Lignin molecular weights of Populus trichocarpa residues after CELF pretreatment

Here we present a dataset of molecular weights of lignin from a woody energy crop (Populus trichocarpa) residues after a series of co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment. The natural poplar variant GW-9947 from the Center for Bioenergy Innovation (CBI) was used. The poplar was knife milled and passed through a 1 mm sieve and CELF pretreatment was performed in a Parr autoclave reactor with 7.5 wt % solids loading, 0.5 wt% H2SO4 as catalyst at 150°C with various time. Tetrahydrofuran was added in a 1:1 mass ratio with water as the pretreatment solvent. Lignin was isolated from the pretreated samples after ball-milling in a porcelain jar with ceramic balls via Retsch PM 200 at 580 rpm for 2.5 h followed by enzymatic hydrolysis in acetate buffer (pH 4.8, 50 °C) for 48 h. The solid residue was isolated by centrifugation and hydrolyzed again with freshly added buffer and enzymes for another 48 h. After filtration, the solid residue was extracted twice with 96% (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover lignin. The lignin samples were then derivatized in an acetic anhydride/pyridine (1:1, v/v) mixture and stirred at room temperature for 24 h. Ethanol was added to the reaction mixture, left for 30 min and then removed with a rotary evaporator. The addition and removal of ethanol was repeated at least 3 times until all traces of acetic acid were removed. Acetylated lignin samples were then dissolved in tetrahydrofuran (THF) at a concentration of 1.0 mg/mL. The molecular weight of acetylated lignin was measured by a gel permeation chromatography (GPC) on a PSS-Polymer Standards Service (Warwick, RI, USA) GPC SECurity 1200 system featuring Agilent HPLC 1200 components equipped with four Waters Styragel columns (HR1, HR2, HR4 and HR6) and an UV detector (270 nm). Tetrahydrofuran was used as the mobile phase and flow rate was 0.3 mL/min. The Polymer Standards Service WinGPC Unity software (Build 6807) was used for data processing for all the samples. The data provides information about the effects of CELF pretreatment time at 150 ºC on lignin molecular weights.

09 BIOMASS FUELS↗

DOE OSTI2025

Fungal elemental profiling unleashed through rapid laser-induced breakdown spectroscopy (LIBS)

Elemental profiling of fungal species as a phenotyping tool is an understudied topic and is typically performed to examine plant tissue or non-biological materials. Traditional analytical techniques such as inductively coupled plasma–optical emission spectroscopy (ICP-OES) and inductively coupled plasma–mass spectrometry (ICP-MS) have been used to identify elemental profiles of fungi; however, these techniques can be cumbersome due to the difficulty of preparing samples. Additionally, the instruments used for these techniques can be expensive to procure and operate. Laser-induced breakdown spectroscopy (LIBS) is an alternative elemental analytical technique—one that is sensitive across the periodic table, easy to use on various sample types, and is cost-effective in both procurement and operation. LIBS has not been used on axenic filamentous fungal isolates grown in substrate media. In this work, as a proof of concept, we used LIBS on two genetically distinct fungal species grown on a nutrient-rich and nutrient-poor substrate media to determine whether robust elemental profiles can be detected and whether differences between the fungal isolates can be identified. This data set contains the raw LIBS spectral data for the summarized results described inRush, et. al. 2024

elemental profiling↗

DOE OSTI2022

Increased Attack Rates and Decreased Incubation Periods in Raccoons with Chronic Wasting Disease Passaged through Meadow Voles

Chronic wasting disease (CWD) is a naturally-occurring neurodegenerative disease of cervids. Raccoons (Procyon lotor) and meadow voles (Microtus pennsylvanicus) have previously been shown to be susceptible to the CWD agent. To investigate the potential for transmission of the agent of CWD from white-tailed deer to voles and subsequently to raccoons, we intracranially inoculated raccoons with brain homogenate from a CWD-affected white-tailed deer (CWD Wtd ) or derivatives of this isolate after it had been passaged through voles 1 or 5 times. We found that passage of the CWDWtd isolate through voles led to a change in the biologic behavior of the CWD agent, including increased attack rates and decreased incubation periods in raccoons. A better understanding of the dynamics of cross-species transmission of CWD prions can provide insights into how these infectious proteins evolve in new hosts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Improved Mobilome Delineation in Fragmented Genomes

The mobilome of a microbe, i.e., its set of mobile elements, has major effects on its ecology, and is important to delineate properly in each genome. This becomes more challenging for incomplete genomes, and even more so for metagenome-assembled genomes (MAGs), where misbinning of scaffolds and other losses can occur. Genomic islands (GIs), which integrate into the host chromosome, are a major component of the mobilome. Our GI-detection software TIGER, unique in its precise mapping of GI termini, was applied to 74,561 genomes from 2,473 microbial species, each species containing at least one MAG and one isolate genome. A species-normalized deficit of ∼1.6 GIs/genome was measured for MAGs relative to isolates. To test whether this undercount was due to the higher fragmentation of MAG genomes, TIGER was updated to enable detection of split GIs whose termini are on separate scaffolds or that wrap around the origin of a circular replicon. This doubled GI yields, and the new split GIs matched the quality of single-scaffold GIs, except that highly fragmented GIs may lack central portions. Cross-scaffold search is an important upgrade to GI detection as fragmented genomes increasingly dominate public databases. TIGER2 better captures MAG microdiversity, recovering niche-defining GIs and supporting microbiome research aims such as virus-host linking and ecological assessment.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Integration of proteomics and metabolomics into the Design, Build, Test, Learn cycle to improve 3-hydroxypropionic acid production in Aspergillus pseudoterreus

Biological engineering of microorganisms to produce value-added chemicals is a promising route to sustainable manufacturing. However, overproduction of metabolic intermediates at high titer, rate, and yield from inexpensive substrates is challenging in non-model systems where limited information is available regarding metabolic flux and its control in production conditions. Integrated multi-omic analyses of engineered strains offers an in-depth look at metabolites and proteins directly involved in growth and production of target and non-target bioproducts. Here we applied multi-omic analyses to overproduction of the polymer precursor 3-hydroxypropionic acid (3HP) in the filamentous fungus Aspergillus pseudoterreus. A synthetic pathway consisting of aspartate decarboxylase, beta-alanine pyruvate transaminase, and 3HP dehydrogenase was designed and built for A. pseudoterreus. Strains with single- and multi-copy integration events were isolated and multi-omics analysis consisting of intracellular and extracellular metabolomics and targeted and global proteomics was used to interrogate the strains in shake-flask and bioreactor conditions. Production of a variety of co-products (organic acids and glycerol) and oxidative degradation of 3HP were identified as metabolic pathways competing with 3HP production. Intracellular accumulation of nitrogen as 2,4-diaminobutanoate was identified as an off-target nitrogen sink that may also limit flux through the engineered 3HP pathway. Elimination of the high-expression oxidative 3HP degradation pathway by deletion of a putative malonate semialdehyde dehydrogenase improved the yield of 3HP by 3.4× after 10 days in shake-flask culture. This is the first report of 3HP production in a filamentous fungus amenable to industrial scale biomanufacturing of organic acids at high titer and low pH.

Pomraning, Kyle R.↗

DOE OSTI2022

Astronauts Plasma-Derived Exosomes Induced Aberrant EZH2-Mediated H3K27me3 Epigenetic Regulation of the Vitamin D Receptor

There are unique stressors in the spaceflight environment. Exposure to such stressors may be associated with adverse effects on astronauts' health, including increased cancer and cardiovascular disease risks. Small extracellular vesicles (sEVs, i.e., exosomes) play a vital role in intercellular communication and regulate various biological processes contributing to their role in disease pathogenesis. To assess whether spaceflight alters sEVs transcriptome profile, sEVs were isolated from the blood plasma of 3 astronauts at two different time points: 10 days before launch (L-10) and 3 days after return (R+3) from the Shuttle mission. AC16 cells (human cardiomyocyte cell line) were treated with L-10 and R+3 astronauts-derived exosomes for 24 h. Total RNA was isolated and analyzed for gene expression profiling using Affymetrix microarrays. Enrichment analysis was performed using Enrichr. Furthermore, transcription factor (TF) enrichment analysis using the ENCODE/ChEA Consensus TF database identified gene sets related to the polycomb repressive complex 2 (PRC2) and Vitamin D receptor (VDR) in AC16 cells treated with R+3 compared to cells treated with L-10 astronauts-derived exosomes. Further analysis of the histone modifications using datasets from the Roadmap Epigenomics Project confirmed enrichment in gene sets related to the H3K27me3 repressive mark. Interestingly, analysis of previously published H3K27me3–chromatin immunoprecipitation sequencing (ChIP-Seq) ENCODE datasets showed enrichment of H3K27me3 in the VDR promoter. Collectively, our results suggest that astronaut-derived sEVs may epigenetically repress the expression of the VDR in human adult cardiomyocytes by promoting the activation of the PRC2 complex and H3K27me3 levels.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Efficient Synthesis of Pinoresinol, an Important Lignin Dimeric Model Compound

Pinoresinol is a high-value monolignol-derived lignan used in plant defense and with human health-supporting effects. The synthetic yield and isolation efficiency of racemic pinoresinol from coniferyl alcohol by conventional radical coupling methods is sub-optimal. In this work, a facile and efficient synthetic approach was developed to synthesize pinoresinol with much higher yield. By using 5-bromoconiferyl alcohol, which was synthesized in high yield from 5-bromovanillin, to make 5,5′-bromopinoresinol via a peroxidase-mediated radical coupling reaction takes advantage of the smaller variety of radical coupling products from the 5-substituted monolignol, producing simpler product mixtures from which 5,5′-bromopinoresinol may be readily crystalized with good yield (total yield of 44.1% by NMR; isolated crystalline yield of 24.6%). Hydro-debromination of the crystalline 5,5′-bromopinoresinol to pinoresinol was essentially quantitative. Gram quantities of pinoresinol were conveniently synthesized by using this approach. This simple alternative pathway to make pinoresinol will impact pinoresinol-related research including structural characterization and modification of lignins, as well as clinical applications of pinoresinol and its derivatives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Structure and Fc-Effector Function of Rhesusized Variants of Human Anti-HIV-1 IgG1s

Passive transfer of monoclonal antibodies (mAbs) of human origin into Non-Human Primates (NHPs), especially those which function predominantly by a Fc-effector mechanism, requires an a priori preparation step, in which the human mAb is reengineered to an equivalent NHP IgG subclass. This can be achieved by changing both the Fc and Fab sequence while simultaneously maintaining the epitope specificity of the parent antibody. This Ab reengineering process, referred to as rhesusization, can be challenging because the simple grafting of the complementarity determining regions (CDRs) into an NHP IgG subclass may impact the functionality of the mAb. Here we describe the successful rhesusization of a set of human mAbs targeting HIV-1 envelope (Env) epitopes involved in potent Fc-effector function against the virus. This set includes a mAb targeting a linear gp120 V1V2 epitope isolated from a RV144 vaccinee, a gp120 conformational epitope within the Cluster A region isolated from a RV305 vaccinated individual, and a linear gp41 epitope within the immunodominant Cys-loop region commonly targeted by most HIV-1 infected individuals. Structural analyses confirm that the rhesusized variants bind their respective Env antigens with almost identical specificity preserving epitope footprints and most antigen-Fab atomic contacts with constant regions folded as in control RM IgG1s. In addition, functional analyses confirm preservation of the Fc effector function of the rhesusized mAbs including the ability to mediate Antibody Dependent Cell-mediated Cytotoxicity (ADCC) and antibody dependent cellular phagocytosis by monocytes (ADCP) and neutrophils (ADNP) with potencies comparable to native macaque antibodies of similar specificity. While the antibodies chosen here are relevant for the examination of the correlates of protection in HIV-1 vaccine trials, the methods used are generally applicable to antibodies for other purposes.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Range wide genetic differentiation in the bull kelp Nereocystis luetkeana with a seascape genetic focus on the Salish Sea

Introduction: In temperate regions, one of the most critical determinants of present range-wide genetic diversity was the Pleistocene climate oscillations, the most recent one created by the last glacial maximum (LGM). This study aimed to describe N. luetkeana genetic structure across its entire range (Alaska to California) and test different models of population connectivity within the Salish Sea. This region was colonized after the LGM and has been under increased disturbance in recent decades. Methods: We utilized microsatellite markers to study N. luetkeana genetic diversity at 53 sites across its range. Using higher sampling density in the Salish Sea, we employed a seascape genetics approach and tested isolation by hydrodynamic transport and environment models. Results: At the species distribution scale, we found four main groups of genetic co-ancestry, Alaska; Washington with Vancouver Island’s outer coast and Juan de Fuca Strait; Washington’s inner Salish Sea; and Oregon with California. The highest allelic richness (AR) levels were found in California, near the trailing range edge, although AR was also high in Alaska. The inner Salish Sea region had the poorest diversity across the species distribution. Nevertheless, a pattern of isolation by hydrodynamic transport and environment was supported in this region. Discussion: The levels of allelic, private allele richness and genetic differentiation suggest that during the LGM, bull kelp had both northern and southern glacial refugia in the Prince of Wales Island-Haida Gwaii region and Central California, respectively. Genetic diversity in Northern California sites seems resilient to recent disturbances, whereas the low levels of genetic diversity in the inner Salish Sea are concerning.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Microbial Phosphorus Mobilization Strategies Across a Natural Nutrient Limitation Gradient and Evidence for Linkage With Iron Solubilization Traits

Microorganisms have evolved several mechanisms to mobilize and mineralize occluded and insoluble phosphorus (P), thereby promoting plant growth in terrestrial ecosystems. However, the linkages between microbial P-solubilization traits and the preponderance of insoluble P in natural ecosystems are not well known. We tested the P solubilization traits of hundreds of culturable bacteria representative of the rhizosphere from a natural gradient where P concentration and bioavailability decline as soil becomes progressively more weathered. Aluminum, iron phosphate and organic P (phytate) were expected to dominate in more weathered soils. A defined cultivation medium with these chemical forms of P was used for isolation. A combination of soil chemical, spectroscopic analyses and 16S rRNA gene sequencing were used to understand the in situ ability for solubilization of these predominant forms of P. Locations with more occluded and organic P harbored the greatest abundance of P-mobilizing microorganisms, especially Burkholderiaceae ( Caballeronia and Paraburkholderia spp.). Nearly all bacteria utilized aluminum phosphate, however fewer could subsist on iron phosphate (FePO 4 ) or phytate. Microorganisms isolated from phytic acid were also most effective at solubilizing FePO 4 , suggesting that phytate solubilization may be linked to the ability to solubilize Fe. Significantly, we observed Fe to be co-located with P in organic patches in soil. Siderophore addition in lab experiments reinstated phytase mediated P-solubilization from Fe-phytate complexes. Taken together, these results indicate that metal-organic-P complex formation may limit enzymatic P solubilization from phytate in soil. Additionally, the linked traits of phytase and siderophore production were mostly restricted to specific clades within the Burkholderiaceae . We propose that Fe complexation of organic P (e.g., phytate) represents a major constraint on P turnover and availability in acidic soils, as only a limited subset of bacteria appear to possess the traits required to access this persistent pool of soil P.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas 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 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics.

59 BASIC BIOLOGICAL SCIENCES↗