Beyond anaerobic respiration-new physiological roles for DmsABC and other S-/N-oxide reductases in Escherichia coli

Sulfoxide reductases in pathogenic bacteria have recently received increasing attention for their association with virulence and survival within the host. Here, we have re-investigated the physiological role of the molybdenum-containing DmsABC dimethyl sulfoxide (DMSO) reductase from Escherichia coli, which has a proposed role in anaerobic respiration with DMSO. Our investigation into potential physiological substrates revealed that DmsABC efficiently reduces pyrimidine N-oxide, nicotinamide N-oxide, and methionine sulfoxide, and exposure to host cell-produced stressors such as hypochlorite or hydrogen peroxide specifically increased expression of the E. coli dmsA gene. E. coli strains lacking dmsA showed increased lag times in the presence of hypochlorite, and these strains also showed up to a 90% reduction in adherence to human bladder cells. Interestingly, in the presence of hypochlorite, expression of multiple alternative S-/N-oxide reductases present in E. coli was elevated by 2- to 4-fold in a ∆dmsA strain compared to the wild-type strain, suggesting functional redundancy. The phenotypes of the E. coli ∆dmsA strains were strikingly similar to ∆dmsA strains of the respiratory pathogen Haemophilus influenzae, which confirms the role of both enzymes in supporting host-pathogen interactions. We propose that this function is conserved in enzymes closely related to E. coli DmsABC. Our study also uncovered that the expression of many E. coli Mo enzymes was induced by oxidative stressors, including metals such as copper, and further work should be directed at determining the connection of these enzymes to host-pathogen interactions.IMPORTANCEBacterial urinary tract infections are debilitating and frequently recurring in human populations worldwide, and Escherichia coli strains are a major cause of these infections. In this study, we have uncovered a new mechanism by which E. coli can avoid being killed by the human immune system. The bacteria use a set of seven related enzymes that can reverse damage to essential cell components such as amino acids, vitamins, and DNA building blocks. Antibacterial compounds produced by the human immune system specifically induced the production of these enzymes, confirming that they play a role in helping E. coli survive during infection and making these enzymes potential future drug targets.

Evaluation of vectors for gene expression in Pseudovibrio marine bacteria

α-Proteobacteria belonging to the Pseudovibrio genus have been isolated from different marine organisms including marine sponges, corals, and algae. This genus was first described in 2004 and has since garnered attention due to the potential ecological relevance and biotechnological application of its metabolites. For instance, we recently reported specialized metabolites that we named pseudovibriamides from Pseudovibrio brasiliensis Ab134. The pseudovibriamide encoding ppp gene cluster is found in two-thirds of Pseudovibrio genomes. Pseudovibriamides coordinate motility and biofilm formation, behaviors that are known to be important for host colonization. Although we previously established reverse genetics methods to delete genes via homologous recombination, no self-replicative vectors have been reported for Pseudovibrio. We show that plasmid vectors containing two different broad-host-range replicons, RSF1010 and pBBR1, can be used in P. brasiliensis. The efficiency of vector transfer by electroporation averaged ~3 × 103 CFU/µg plasmid DNA, whereas the conjugation frequency from Escherichia coli ranged from 10-3 to 10-6. We then tested the vectors for fluorescent protein expression and consequent labeling, which allowed us to observe their effects on swarming motility and to compare plasmid stability. This study expands the genetic toolbox available for Pseudovibrio, which is expected to enable future ecological and biotechnological studies.IMPORTANCEThe genus Pseudovibrio of α-Proteobacteria has consistently been isolated from marine sponges and other marine organisms such as corals and algae. Pseudovibrio bacteria are a source of antibiotics and other secondary metabolites with the potential to be developed into pharmaceuticals. Moreover, the secondary metabolites they produce are important for their physiology and for interactions with other organisms. Here we expand the genetic toolbox available for Pseudovibrio bacteria by establishing self-replicative vectors that can be used for the expression of, for example, fluorescent proteins. The availability of genetic tools is important to enable us to explore the emerging ecological and biotechnological potentials of Pseudovibrio bacteria.

Evolution of a Plasmid Regulatory Circuit Ameliorates Plasmid Fitness Cost

Plasmids promote adaptation of bacteria by facilitating horizontal transfer of diverse genes, notably those conferring antibiotic resistance. Some plasmids, like those of the incompatibility group IncP-1, are known to replicate and persist in a broad range of bacteria. We investigated a poorly understood exception, the IncP-1β plasmid pBP136 from a clinical Bordetella pertussis isolate, which quickly became extinct in laboratory Escherichia coli populations. Through experimental evolution, we found that the inactivation of a previously uncharacterized plasmid gene, upf31, drastically improved plasmid persistence in E. coli. The gene inactivation caused alterations in the plasmid regulatory system, including decreased transcription of the global plasmid regulators (korA, korB, and korC) and numerous genes in their regulons. This is consistent with our findings that Upf31 represses its own transcription. It also caused secondary transcriptional changes in many chromosomal genes. In silico analyses predicted that Upf31 interacts with the plasmid regulator KorB at its C-terminal dimerization domain (CTD). We showed experimentally that adding the CTD of upf31/pBP136 to the naturally truncated upf31 allele of the stable IncP-1β archetype R751 results in plasmid destabilization in E. coli. Moreover, mutagenesis showed that upf31 alleles encoded on nearly half of the sequenced IncP-1β plasmids also possess this destabilization phenotype. While Upf31 might be beneficial in many hosts, we show that in E. coli some alleles have harmful effects that can be rapidly alleviated with a single mutation. Thus, broad-host-range plasmid adaptation to new hosts can involve fine-tuning their transcriptional circuitry through evolutionary changes in a single gene.

Plasmid Backbone Impacts Conjugation Rate, Transconjugant Fitness, and Community Assembly of Genetically Bioaugmented Soil Microbes for PAH Bioremediation

Many polycyclic aromatic hydrocarbons (PAHs) in the environment resulting from crude oil spills and the incomplete combustion of organic matter are highly toxic, mutagenic, or carcinogenic to microorganisms and humans. Bioremediation of PAHs using microorganisms that encode biodegradative genes is a promising approach for environmental PAH cleanup. However, the viability of exogenous microorganisms is often limited due to competition with the native microbial community. Instead of relying on the survival of one or a few species of bacteria, genetic bioaugmentation harnesses conjugative plasmids that spread functional genes to native microbes. In this study, two plasmid backbones that differ in copy number regulation, replication, and mobilization genes were engineered to contain a PAH dioxygenase gene (bphC) and conjugated to soil bacteria including Bacillus subtilis, Pseudomonas putida, and Acinetobacter sp., as well as a synthetic community assembled from these bacteria. Fitness effects of the plasmids in transconjugants significantly impacted the rates of conjugative transfer and biotransformation rates of a model PAH (2,3-dihydroxybiphenyl). A synergistic effect was observed in which synthetic communities bioaugmented with bphC had significantly higher PAH degradation rates than bacteria grown in monocultures. Finally, conjugation rates were significantly associated with the relative abundances of bacteria in synthetic communities, underscoring how fitness impacts of plasmids can shape the microbial community structure and function.

Prediction of aflatoxin contamination outbreaks in Texas corn using mechanistic and machine learning models

Aflatoxins are carcinogenic and mutagenic mycotoxins that contaminate food and feed. The objective of our research is to predict aflatoxin outbreaks in Texas-grown maize using dynamic geospatial data from remote sensing satellites, soil properties data, and meteorological data by an ensemble of models. We developed three model pipelines: two included mechanistic models that use weekly aflatoxin risk indexes (ARIs) as inputs, and one included a weather-centric model; all three models incorporated soil properties as inputs. For the mechanistic-dependent models, ARIs were weighted based on a maize phenological model that used satellite-acquired normalized difference vegetation index (NDVI) data to predict maize planting dates for each growing season on a county basis. For aflatoxin outbreak predictions, we trained, tested and validated gradient boosting and neural network models using inputs of ARIs or weather, soil properties, and county geodynamic latitude and longitude references. Our findings indicated that between the two ARI-mechanistic models evaluated (AFLA-MAIZE or Ratkowsky), the best performing was the Ratkowsky-ARI neural network (nnet) model, with an accuracy of 73%, sensitivity of 71% and specificity of 74%. Texas has significant geographical variability in ARI and ARI-hotspot responses due to the diversity of agroecological zones (hot-dry, hot-humid, mixed-dry and mixed-humid) that result in a wide variation of maize growth and development. Our Ratkowsky-ARI nnet model identified a positive correlation between aflatoxin outbreaks and prevalence of ARI hot-spots in the hot-humid areas of Texas. In these areas, temperature, precipitation and relative humidity in March and October were positively correlated with high aflatoxin contamination events. We found a positive correlation between aflatoxin outbreaks and soil pH in hot-dry and hot-humid regions and minimum saturated hydraulic conductivity in mixed-dry regions. Conversely, there was a negative relationship between aflatoxin outbreaks and maximum soil organic matter (hot-dry region), and calcium carbonate (hot-dry, and mixed-dry). It is likely soil fungal communities are more diverse, and plants are healthier in soils with high organic matter content, thereby reducing the risk of aflatoxin outbreaks. Our results demonstrate that intricate relationships between soil hydrological parameters, fungal communities and plant health should be carefully considered by Texas corn growers for aflatoxin mitigation strategies.

Expanding Yarrowia lipolytica's metabolic potential for detoxification of cyanogenic glycosides in edible plants

Cyanides are highly toxic chemicals in several edible plants that threaten food safety and human health. A phenotypically distinct Yarrowia lipolytica strain that efficiently detoxifies multiple cyanogenic glycosides from edible plants was constructed using a family 1 glycosyl-hydrolase (GH1). The strain displayed higher growth rates and metabolic activities when exposed to high concentrations of cyanides than the wild-type. It overexpressed genes that promoted the binding of molecular oxygen to the cytochrome iv complex. The engineered strain repressed fatty acid production to optimize energy production and activated the cyanide-resistant respiratory (AOX) pathway to circumvent HCN toxicity and maintain cellular homeostasis. It upregulated ribosome biogenesis, the sec-dependent protein export pathway, and the sulfur relay system to facilitate the production and transmembrane efflux of the secreted GH1 hydrolase. It efficiently degraded linamarin, amygdalin, prunasin, and dhurrin in food plants including cassava, germinated sorghum and Apricot seeds. The strain produced high phospholipids to support new membrane production and could be a cost-effective source of single-cell phospholipids. The findings demonstrate that the strain is a robust, sustainable, and potentially efficient strain that could be used for industrial bioconversion of plant materials containing glycosylated toxicants into safe foods and animal feeds.

Global prevalence and transmission of the mcr-9 in Salmonella: A genomic study with insights from Salmonella enterica serovar Thompson isolated from poultry food in China

The plasmid-mediated mcr-9 gene has been widely detected in Salmonella across multiple countries and regions, raising significant concerns for food safety and public health. To investigate the transmission dynamics of mcr-9 in Salmonella, we conducted a comprehensive genomic epidemiological study and explored the potential mechanisms of mcr-9 transmission in poultry-derived S. Thompson in China. This study analyzed 126 mcr-9-positive Salmonella isolates from food in China and genomic data of 1,487 publicly available mcr-9-positive Salmonella collected over the past 40 years from 32 countries and various sources. Two variants, mcr-9.1 and mcr-9.2, were detected, with mcr-9.1 being the most prevalent subtype globally. S. Typhimurium/I 4,[5],12:i:- (23.1 %, 372/1,613) was the dominant lineage of the total collection, followed by S. Saintpaul (15.9 %, 256/1,613), S. Heidelberg (11.4 %, 184/1,613), and S. Thompson (8.6 %, 139/1,613). S. Typhimurium/I 4,[5],12:i:- was widely distributed in North America and Europe, primarily prevalent in humans and swine, whereas S. Thompson was predominantly found in China, mainly prevalent in poultry-related foods and humans. Conjugation experiments were performed on 116 S. Thompson strains from 126 Salmonella isolates. The results showed that 85.3 % (99/116) of the mcr-9-positive plasmids were transferable. The IncHI2-IncHI2A plasmids from three representative donors demonstrated the ability to transfer at varying frequencies to seven Salmonella recipients of different serotypes including Typhimurium, Thompson, Enteritidis, Indiana, Rissen, London, and Derby. Chicken juice matrix significantly increased the proportion of mcr-9-positive S. Thompson conjugants. The inability of mcr-9-positive IncHI2-IncHI2A plasmids to transfer via conjugation may be due to the integration of the plasmid into the chromosome. In addition, the deletion of IS1B-cfdB-fucO-frmR-uvrA-fghA-gloA-frmA-uvrB-flhD-smc-copG-IS26 gene region was observed in the non-conjugative mcr-9-positive plasmids. These findings underscore the importance of ongoing surveillance of mcr-9-positive multidrug-resistant S. Thompson for food safety in China.

A framework for assessing microbial degradation of organophosphate ester plasticizers in seawater

The assessment of persistence of organic pollutants in seawater is limited by the lack of user-friendly, quick protocols for assessing one of their main sinks, degradation by marine bacteria. Here we present an experimental workflow to identify organic pollutants degradation, taking organophosphate esters flame retardants and plasticizers (OPEs-FR-PL), as a model family of synthetic chemicals released into the marine environment that are particularly widespread due to their persistence and semi-volatile nature. The proposed novel workflow combines culture-dependent techniques, solvent demulsification-dispersive liquid-liquid microextraction, with quantitative liquid chromatography coupled with mass spectrometry analyses in order to identify marine bacterial isolates with the potential to degrade OPEs-FR-PL in the marine environment. This methodology evaluates growth rates, degradation capacities of different OPEs-FR-PL, and the ability of bacteria to utilize these pollutants as a sole source of carbon, phosphorus and energy. The proposed framework is more cost-effective than previous approaches as it is less time-consuming, reduces the use of solvents making it environmentally friendly, and can be used as a high throughput screening methodology. Although optimized here for OPEs-FR-PL degradation, this methodology can be adapted to a wide variety of contaminants of emerging concern. Using this developed workflow, we could detect that coastal Antarctic seawater harbors several bacterial taxa with the potential to degrade OPEs-FR-PL.

Life history strategies complement niche partitioning to support the coexistence of closely related Gilliamella species in the bee gut

The maintenance of bacterial diversity at both species and strain levels is crucial for the sustainability of honey bee gut microbiota and host health. Periodic or random fluctuation in diet typically alters the metabolic niches available to gut microbes, thereby continuously reshaping bacterial diversity and interspecific interactions. It remains unclear how closely related bacteria adapt to these fluctuations and maintain coexistence within the bee gut. Here, we demonstrate that the five predominant Gilliamella species associated with Apis cerana, a widely distributed Asiatic honey bee, have diverged in carbohydrate metabolism to adapt to distinct nutrient niches driven by dietary fluctuation. Specifically, the glycan-specialists gain improved growth on a pollen-rich diet, but are overall inferior in competition to non-glycan-specialist on either a simple sugar or sugar-pollen diet, when co-inoculated in the bee host and transmitted across generations. Strikingly, despite of their disadvantage in a high-sugar condition, the glycan-specialists are found prevalent in natural A. cerana guts. We further reveal that these bacteria have adopted a life history strategy characterized by high biomass yield on a low-concentration sugar diet, allowing them to thrive under poor nutritional conditions, such as when the bee hosts undergo periodical starvation. Transcriptome analyses indicate that the divergence in life history strategies is attributed to gene expression programming rather than genetic variation. This study highlights the importance of integrative metabolic strategies in carbohydrate utilization, which facilitate the coexistence of closely related Gilliamella species in a changing bee gut environment.

Exploring the diversity of native Lachancea thermotolerans strains isolated by sugary extracts from manna ash to modulate the flavour of sour beers

The craft beer industry is becoming increasingly interested in the production of innovative beers. A novel approach, designated as "primary souring," employs diverse yeast species, including Lachancea thermotolerans, to produce sour beers. Furthermore, there is a growing interest in utilising unconventional yeasts to produce beers with distinctive flavours. For the first time, yeast strains of L. thermotolerans, isolated from sugar extracts of manna ash, were evaluated for their ability to produce and improve the sensory properties of sour beers. In particular, five strains exhibited notable resistance to ethanol, sugar and hops, as well as comparable lactic acid production (ranging from 0.33 to 0.45 g/L). Experimental beers produced using MNF105 (T1) were perceived as the most "fruity". This is the first study to examine the impact of this novel indigenous strain, derived from unconventional matrixes such as manna, on the organoleptic quality of craft sour beers. Consequently, elevated levels of ethyl decanoate, ethyl hexanoate, ethyl octanoate and ethyl nonanoate were found in T1 beer, exceeding the perception threshold. The ability of this strain to perform light bio-acidification is a valuable feature for the development of new brewing techniques, particularly for the creation of sour beers with balanced acidity and innovative flavours. The yeast L. thermotolerans MNF105, which is related to manna, has excellent technological properties and is a promising starter for beer production with the ability to light bio-acidify and modulate flavour.

The transcriptional response to low temperature is weakly conserved across the Enterobacteriaceae

Bacteria respond to changes in their external environment, such as temperature, by changing the transcription of their genes. We know little about how these regulatory patterns evolve. We used RNA-seq to study the transcriptional response to a shift from 37°C to 15°C in wild-type Escherichia coli, Salmonella enterica, Citrobacter rodentium, Enterobacter cloacae, Klebsiella pneumoniae, and Serratia marcescens, as well as ∆rpoS strains of E. coli and S. enterica. We found that these species change the transcription of between 626 and 1057 genes in response to the temperature shift, but there were only 16 differentially expressed genes in common among the six species. Species-specific transcriptional patterns of shared genes were a prominent cause of this lack of conservation. Gene ontology enrichment of regulated genes suggested many species-specific phenotypic responses to temperature changes, but enriched terms associated with iron metabolism, central metabolism, and biofilm formation were implicated in at least half of the species. The alternative sigma factor RpoS regulated about 200 genes between 37°C and 15°C in both E. coli and S. enterica, with only 83 genes in common between the two species. Overall, there was limited conservation of the response to low temperature generally, or the RpoS-regulated part of the response specifically. This study suggests that species-specific patterns of transcription of shared genes, rather than horizontal acquisition of unique genes, are the major reason for the lack of conservation of the transcriptomic response to low temperature.

IMPORTANCE

We studied how different species of bacteria from the same Family (Enterobacteriaceae) change the expression of their genes in response to a decrease in temperature. Using de novo-generated parallel RNA-seq data sets, we found that the six species in this study change the level of expression of many of their genes in response to a shift from human body temperature (37°C) to a temperature that might be found out of doors (15°C). Surprisingly, there were very few genes that change expression in all six species. This was due in part to differences in gene content, and in part due to shared genes with distinct expression profiles between the species. This study is important to the field because it illustrates that closely related species can share many genes but not use those genes in the same way in response to the same environmental change.

Evolution and maintenance of a large multidrug-resistant plasmid in a Salmonella enterica Typhimurium host under differing antibiotic selection pressures

The dissemination of antibiotic resistance genes (ARGs) through plasmids is a major mechanism for the development of bacterial antimicrobial resistance. The adaptation and evolution mechanisms of multidrug-resistant (MDR) plasmids with their hosts are not fully understood. Herein, we conducted experimental evolution of a 244 kb MDR plasmid (pJXP9) under various conditions including no antibiotics and mono- or combinational drug treatments of colistin (CS), cefotaxime (CTX), and ciprofloxacin (CIP). Our results showed that long-term with or without positive selections for pJXP9, spanning approximately 600 generations, led to modifications of the plasmid-encoded MDR and conjugative transfer regions. These modifications could mitigate the fitness cost of plasmid carriage and enhance plasmid maintenance. The extent of plasmid modifications and the evolution of plasmid-encoded antibiotic resistance depended on treatment type, particularly the drug class and duration of exposure. Interestingly, prolonged exposure to mono- and combinational drugs of CS and CIP resulted in a substantial loss of the plasmid-encoded MDR region and antibiotic resistance, comparable to the selection condition without antibiotic. By contrast, combinational treatment with CTX contributed to the maintenance of the MDR region over a long period of time. Furthermore, drug selection was able to maintain and even amplify the corresponding plasmid-encoded ARGs, with co-selection of ARGs in the adjacent regions. In addition, parallel mutations in chromosomal arcA were also found to be associated with pJXP9 plasmid carriage among endpoint-evolved clones from diverse treatments. Meanwhile, arcA deletion improved the persistence of pJXP9 plasmid without drugs. Overall, our findings indicated that plasmid-borne MDR region deletion and chromosomal arcA inactivation mutation jointly contributed to co-adaptation and co-evolution between MDR IncHI2 plasmid and Salmonella Typhimurium under different drug selection pressure.IMPORTANCEThe plasmid-mediated dissemination of antibiotic resistance genes has become a significant concern for human health, even though the carriage of multidrug-resistant (MDR) plasmids is frequently associated with fitness costs for the bacterial host. However, the mechanisms by which MDR plasmids and bacterial pairs evolve plasmid-mediated antibiotic resistance in the presence of antibiotic selections are not fully understood. Herein, we conducted an experimental evolution of a large multidrug-resistant plasmid in a Salmonella enterica Typhimurium host under single and combinatorial drug selection pressures. Our results show the adaptive evolution of plasmid-encoded antibiotic resistance through alterations of the MDR region in the plasmid, in particular substantial loss of the MDR region, in response to different positive selections, especially mono- and combinational drugs of colistin and ciprofloxacin. In addition, strong parallel mutations in chromosomal arcA were associated with pJXP9 carriage in Salmonella Typhimurium from diverse treatments. Our results thus highlight promoting the loss of the plasmid's MDR region could offer an alternative approach for combating plasmid-encoded antibiotic resistance.

Fermentation dynamics of bile salt hydrolase production in Heyndrickxia coagulans ATCC 7050 and Lactiplantibacillus plantarum ATCC 10012: Addressing ninhydrin assay limitations with a novel HPTLC-MS method

Bile salt hydrolase (BSH), a pivotal enzyme in cholesterol management, holds significant promise in both human and animal subjects. This study investigated the effect of fermentation dynamics in Heyndrickxia coagulans ATCC 7050 and Lactiplantibacillus plantarum ATCC 10012 to enhance BSH production. Cultivation of cultures in MRS and M17 media revealed that MRS medium enhanced BSH production by 235.98 % in H. coagulans ATCC 7050 and 147.37 % in L. plantarum ATCC 10012, compared to M 17 medium. Additionally, varying oxygen concentration levels indicated that H. coagulans ATCC 7050 exhibited its minimum doubling time of 79.8 ± 0.64 min in anaerobic conditions, whereas L.plantarum ATCC 10012 demonstrated its minimum doubling time of 85.5 ± 1.2 min under microaerophilic conditions. However, their highest BSH activity was observed during the stationary phase under anaerobic conditions, yielding 17.14 ± 0.78 U/mL by H. coagulans ATCC 7050 and 19.04 ± 0.81 U/mL by L.plantarum ATCC 10012. Furthermore, it was observed that both organisms did not retain BSH within their cells. BSH activity was assessed using ninhydrin assay that detected free taurine liberated from sodium taurocholate. However, ninhydrin can yield false-positive results owing to its interaction with other free amino acids. To subjugate this limitation, the study introduced a novel and sensitive HPTLC-MS method capable of accurately detecting taurine. By comprehending fermentation dynamics and selecting appropriate conditions, BSH production increased 2.1-fold in both organisms. These findings illuminate critical insights, offering a pathway for novel strategies to enhance the BSH-producing capabilities of these LAB strains.

Adjuvants restore colistin sensitivity in mouse models of highly colistin-resistant isolates, limiting bacterial proliferation and dissemination

Antimicrobial resistance (AMR) has led to a marked reduction in the effectiveness of many antibiotics, representing a substantial and escalating concern for global health. Particularly alarming is resistance in Gram-negative bacteria due to the scarcity of therapeutic options for treating infections caused by these pathogens. This challenge is further compounded by the rising incidence of resistance to colistin, an antibiotic traditionally considered a last resort for the treatment of multi-drug resistant (MDR) Gram-negative bacterial infections. In this study, we demonstrate that adjuvants restore colistin sensitivity in vivo. We previously reported that the salicylanilide kinase inhibitor IMD-0354, which was originally developed to inhibit the human kinase IKKβ in the NFκB pathway, is a potent colistin adjuvant. Subsequent analog synthesis using an amide isostere approach led to the creation of a series of novel benzimidazole compounds with enhanced colistin adjuvant activity. Herein, we demonstrate that both IMD-0354 and a lead benzimidazole effectively restore colistin susceptibility in mouse models of highly colistin-resistant Klebsiella pneumoniae and Acinetobacter baumannii-induced peritonitis. These novel adjuvants show low toxicity in vivo, significantly reduce bacterial load, and prevent dissemination that could otherwise result in systemic infection.

Rapid Emergence of Resistance to Broad-Spectrum Direct Antimicrobial Activity of Avibactam

Avibactam (AVI) is a diazabicyclooctane (DBO) β-lactamase inhibitor used clinically in combination with ceftazidime. At concentrations higher than those typically achieved in vivo, it also has broad-spectrum direct antibacterial activity against Enterobacterales strains, including metallo-β-lactamase-producing isolates, mediated by inhibition of penicillin-binding protein 2 (PBP2). This activity is mechanistically similar to that of more potent novel DBOs (zidebactam, nacubactam) in late clinical development. We found that resistance to AVI emerged readily, with a mutation frequency of 2×10-6 to 8×10-5. Whole genome sequencing of resistant isolates revealed a heterogeneous mutational target that permitted bacterial survival and replication despite PBP2 inhibition, in line with prior studies of PBP2-targeting drugs. While such mutations are believed to act by upregulating the bacterial stringent response, we found a similarly high mutation frequency in bacteria deficient in components of the stringent response, although we observed a different set of mutations in these strains. Although avibactam-resistant strains had increased lag time, suggesting a fitness cost that might render them less problematic in clinical infections, there was no statistically significant difference in growth rates between susceptible and resistant strains. The finding of rapid emergence of resistance to avibactam as the result of a large mutational target has important implications for novel DBOs with potent direct antibacterial activity, which are being developed with the goal of expanding cell wall-active treatment options for multidrug-resistant gram-negative infections but may be vulnerable to treatment-emergent resistance.

Neisseria meningitidis activates pyroptotic pathways in a mouse model of meningitis: role of a two-partner secretion system

There is evidence that in infected cells in vitro the meningococcal HrpA/HrpB two-partner secretion system (TPS) mediates the exit of bacteria from the internalization vacuole and the docking of bacteria to the dynein motor resulting in the induction of pyroptosis. In this study we set out to study the role of the HrpA/HrpB TPS in establishing meningitis and activating pyroptotic pathways in an animal model of meningitis using a reference serogroup C meningococcal strain, 93/4286, and an isogenic hrpB knockout mutant, 93/4286ΩhrpB. Survival experiments confirmed the role of HrpA/HrpB TPS in the invasive meningococcal disease. In fact, the ability of the hrpB mutant to replicate in brain and spread systemically was impaired in mice infected with hrpB mutant. Furthermore, western blot analysis of brain samples during the infection demonstrated that: i. N. meningitidis activated canonical and non-canonical inflammasome pyroptosis pathways in the mouse brain; ii. the activation of caspase-11, caspase-1, and gasdermin-D was markedly reduced in the hrpB mutant; iii. the increase in the amount of IL-1β and IL-18, which are an important end point of pyroptosis, occurs in the brains of mice infected with the wild-type strain 93/4286 and is strongly reduced in those infected with 93/4286ΩhrpB. In particular, the activation of caspase 11, which is triggered by cytosolic lipopolysaccharide, indicates that during meningococcal infection pyroptosis is induced by intracellular infection after the exit of the bacteria from the internalizing vacuole, a process that is hindered in the hrpB mutant. Overall, these results confirm, in an animal model, that the HrpA/HrpB TPS plays a role in the induction of pyroptosis and suggest a pivotal involvement of pyroptosis in invasive meningococcal disease, paving the way for the use of pyroptosis inhibitors in the adjuvant therapy of the disease.

Novel Teixobactin Analogues Show Promising In Vitro Activity on Biofilm Formation by Staphylococcus aureus and Enterococcus faecalis

The treatment of infections caused by biofilm-forming organisms is challenging. The newly discovered antibiotic teixobactin shows activity against a wide range of biofilm-forming bacteria. However, the laborious and low-yield chemical synthesis of teixobactin complicates its further development for clinical application. The use of more easily synthesized teixobactin analogues may offer promise in this regard. In this article, three newly developed analogues were tested for efficacy against Staphylococcus aureus and Enterococcus faecalis. Minimum inhibitory and -bactericidal concentrations were investigated. MIC values for S. aureus and E. faecalis ranged from 0.5-2 and 2-4 μg/mL, respectively. Moreover, the ability of the analogues to prevent biofilm formation and to inactivate bacterial cells in already established S. aureus biofilm on medical grade materials (PVC and PTFE) used in the production of infusion tubing and catheters were also tested. The analogues showed an ability to prevent biofilm formation and inactivate bacterial cells in established biofilms at concentrations as low as 1-2 μg/mL. Confocal laser scanning microscopy showed that the most promising analogue (TB3) inactivated S. aureus cells in a preformed biofilm and gave a reduction in biovolume. The relative ease of synthesis of the analogues and their in vitro efficacy, makes them promising candidates for pharmaceutical development.

Multigenerational inheritance drives symbiotic interactions of the bacterium Bacillus subtilis with its plant host

Bacillus subtilis is a beneficial bacterium that supports plant growth and protects plants from bacterial, fungal, and viral infections. Using a simplified system of B. subtilis and Arabidopsis thaliana interactions, we studied the fitness and transcriptome of bacteria detached from the root over generations of growth in LB medium. We found that bacteria previously associated with the root or exposed to its secretions had greater stress tolerance and were more competitive in root colonization than bacteria not previously exposed to the root. Furthermore, our transcriptome results provide evidence that plant secretions induce a microbial stress response and fundamentally alter signaling by the cyclic nucleotide c-di-AMP, a signature maintained by their descendants. The changes in cellular physiology due to exposure to plant exudates were multigenerational, as they allowed not only the bacterial cells that colonized a new plant but also their descendants to have an advance over naive competitors of the same species, while the overall plasticity of gene expression and rapid adaptation were maintained. These changes were hereditary but not permanent. Our work demonstrates a bacterial memory manifested by multigenerational reversible adaptation to plant hosts in the form of activation of the stressosome, which confers an advantage to symbiotic bacteria during competition.

Direct and indirect cumulative effects of temperature, nutrients, and light on phytoplankton growth

Temperature and resource availability are pivotal factors influencing phytoplankton community structures. Numerous prior studies demonstrated their significant influence on phytoplankton stoichiometry, cell size, and growth rates. The growth rate, serving as a reflection of an organism's success within its environment, is linked to stoichiometry and cell size. Consequently, alterations in abiotic conditions affecting cell size or stoichiometry also exert indirect effects on growth. However, such results have their limitations, as most studies used a limited number of factors and factor levels which gives us limited insights into how phytoplankton respond to environmental conditions, directly and indirectly. Here, we tested for the generality of patterns found in other studies, using a combined multiple-factor gradient design and two single species with different size characteristics. We used a structural equation model (SEM) that allowed us to investigate the direct cumulative effects of temperature and resource availability (i.e., light, N and P) on phytoplankton growth, as well as their indirect effects on growth through changes in cell size and cell stoichiometry. Our results mostly support the results reported in previous research thus some effects can be identified as dominant effects. We identified rising temperature as the dominant driver for cell size reduction and increase in growth, and nutrient availability (i.e., N and P) as dominant factor for changes in cellular stoichiometry. However, indirect effects of temperature and resources (i.e., light and nutrients) on species' growth rates through cell size and cell stoichiometry differed across the two species suggesting different strategies to acclimate to its environment.

Diatom abundance in the polar oceans is predicted by genome size

A principal goal in ecology is to identify the determinants of species abundances in nature. Body size has emerged as a fundamental and repeatable predictor of abundance, with smaller organisms occurring in greater numbers than larger ones. A biogeographic component, known as Bergmann's rule, describes the preponderance, across taxonomic groups, of larger-bodied organisms in colder areas. Although undeniably important, the extent to which body size is the key trait underlying these patterns is unclear. We explored these questions in diatoms, unicellular algae of global importance for their roles in carbon fixation and energy flow through marine food webs. Using a phylogenomic dataset from a single lineage with worldwide distribution, we found that body size (cell volume) was strongly correlated with genome size, which varied by 50-fold across species and was driven by differences in the amount of repetitive DNA. However, directional models identified temperature and genome size, not cell size, as having the greatest influence on maximum population growth rate. A global metabarcoding dataset further identified genome size as a strong predictor of species abundance in the ocean, but only in colder regions at high and low latitudes where diatoms with large genomes dominated, a pattern consistent with Bergmann's rule. Although species abundances are shaped by myriad interacting abiotic and biotic factors, genome size alone was a remarkably strong predictor of abundance. Taken together, these results highlight the cascading cellular and ecological consequences of macroevolutionary changes in an emergent trait, genome size, one of the most fundamental and irreducible properties of an organism.

Evidence for the Role of the Mitochondrial ABC Transporter MDL1 in the Uptake of Clozapine and Related Molecules into the Yeast Saccharomyces cerevisiae

Clozapine is an antipsychotic drug whose accumulation in white cells can sometimes prove toxic; understanding the transporters and alleles responsible is thus highly desirable. We used a strategy in which a yeast (Saccharomyces cerevisiae) CRISPR-Cas9 knock-out library was exposed to cytotoxic concentrations of clozapine to determine those transporters whose absence made it more resistant; we also recognised the structural similarity of the fluorescent dye safranin O (also known as safranin T) to clozapine, allowing it to be used as a surrogate marker. Strains lacking the mitochondrial ABC transporter MDL1 (encoded by YLR188W) showed substantial resistance to clozapine. MDL1 overexpression also conferred extra sensitivity to clozapine and admitted a massive increase in the cellular and mitochondrial uptake of safranin O, as determined using flow cytometry and microscopically. Yeast lacking mitochondria showed no such unusual accumulation. Mitochondrial MDL1 is thus the main means of accumulation of clozapine in S. cerevisiae. The closest human homologue of S. cerevisiae MDL1 is ABCB10.

gcplyr: an R package for microbial growth curve data analysis

BACKGROUND

Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the development of computational tools to handle and analyze these data to produce insights.

RESULTS

To address this need, here I present a newly-developed R package: gcplyr. gcplyr can flexibly import growth curve data in common tabular formats, and reshapes it under a tidy framework that is flexible and extendable, enabling users to design custom analyses or plot data with popular visualization packages. gcplyr can also incorporate metadata and generate or import experimental designs to merge with data. Finally, gcplyr carries out model-free (non-parametric) analyses. These analyses do not require mathematical assumptions about microbial growth dynamics, and gcplyr is able to extract a broad range of important traits, including growth rate, doubling time, lag time, maximum density and carrying capacity, diauxie, area under the curve, extinction time, and more.

CONCLUSIONS

gcplyr makes scripted analyses of growth curve data in R straightforward, streamlines common data wrangling and analysis steps, and easily integrates with common visualization and statistical analyses.

The 'Erlenmeter': a low-cost, open-source turbidimeter for no-sampling phenotyping of microorganism growth

This work presents a low-cost, open-source turbidimeter, the 'Erlenmeter', designed to monitor the growth of microorganisms in batch cultures. It is easy to build, based exclusively on inexpensive off-the-shelf electronic components and 3D-printed parts. The Erlenmeter allows measuring the optical density of cultures on standard Erlenmeyer flasks without the need to open the flasks to collect aliquots, ensuring speed, minimal use of consumables, and elimination of the risk of contamination. These features make it particularly well-suited not just for routine research assays but also for experimental teaching. Here we illustrate the use of the Erlenmeter turbidimeter to record the growth of the microalga Phaeodactylum tricornutum, of the bacterium Escherichia coli, and of the yeast Saccharomyces cerevisiae, model organisms that are widely used in research and teaching. The Erlenmeter allows a detailed characterization of the growth curves of all organisms, confirming its usefulness for studying microbial populations dynamics both for research purposes and in classroom settings.

Variation in the response to antibiotics and life-history across the major Pseudomonas aeruginosa clone type (mPact) panel

Pseudomonas aeruginosa is a ubiquitous, opportunistic human pathogen. Since it often expresses multidrug resistance, new treatment options are urgently required. Such new treatments are usually assessed with one of the canonical laboratory strains, PAO1 or PA14. However, these two strains are unlikely representative of the strains infecting patients, because they have adapted to laboratory conditions and do not capture the enormous genomic diversity of the species. Here, we characterized the major P. aeruginosa clone type (mPact) panel. This panel consists of 20 strains, which reflect the species' genomic diversity, cover all major clone types, and have both patient and environmental origins. We found significant strain variation in distinct responses toward antibiotics and general growth characteristics. Only few of the measured traits are related, suggesting independent trait optimization across strains. High resistance levels were only identified for clinical mPact isolates and could be linked to known antimicrobial resistance (AMR) genes. One strain, H01, produced highly unstable AMR combined with reduced growth under drug-free conditions, indicating an evolutionary cost to resistance. The expression of microcolonies was common among strains, especially for strain H15, which also showed reduced growth, possibly indicating another type of evolutionary trade-off. By linking isolation source, growth, and virulence to life history traits, we further identified specific adaptive strategies for individual mPact strains toward either host processes or degradation pathways. Overall, the mPact panel provides a reasonably sized set of distinct strains, enabling in-depth analysis of new treatment designs or evolutionary dynamics in consideration of the species' genomic diversity.

IMPORTANCE

New treatment strategies are urgently needed for high-risk pathogens such as the opportunistic and often multidrug-resistant pathogen Pseudomonas aeruginosa. Here, we characterize the major P. aeruginosa clone type (mPact) panel. It consists of 20 strains with different origins that cover the major clone types of the species as well as its genomic diversity. This mPact panel shows significant variation in (i) resistance against distinct antibiotics, including several last resort antibiotics; (ii) related traits associated with the response to antibiotics; and (iii) general growth characteristics. We further developed a novel approach that integrates information on resistance, growth, virulence, and life-history characteristics, allowing us to demonstrate the presence of distinct adaptive strategies of the strains that focus either on host interaction or resource processing. In conclusion, the mPact panel provides a manageable number of representative strains for this important pathogen for further in-depth analyses of treatment options and evolutionary dynamics.

Gradient boosted regression as a tool to reveal key drivers of temporal dynamics in a synthetic yeast community

Microbial communities are vital to our lives, yet their ecological functioning and dynamics remain poorly understood. This understanding is crucial for assessing threats to these systems and leveraging their biotechnological applications. Given that temporal dynamics are linked to community functioning, this study investigated the drivers of community succession in the wine yeast community. We experimentally generated population dynamics data and used it to create an interpretable model with a gradient boosted regression tree approach. The model was trained on temporal data of viable species populations in various combinations, including pairs, triplets, and quadruplets, and was evaluated for predictive accuracy and input feature importance. Key findings revealed that the inoculation dosage of non-Saccharomyces species significantly influences their performance in mixed cultures, while Saccharomyces cerevisiae consistently dominates regardless of initial abundance. Additionally, we observed multispecies interactions where the dynamics of Wickerhamomyces anomalus were influenced by Torulaspora delbrueckii in pairwise cultures, but this interaction was altered by the inclusion of S. cerevisiae. This study provides insights into yeast community succession and offers valuable machine learning-based analysis techniques applicable to other microbial communities, opening new avenues for harnessing microbial communities.

Synthetic genomes unveil the effects of synonymous recoding

Engineering the genetic code of an organism provides the basis for (i) making any organism safely resistant to natural viruses and (ii) preventing genetic information flow into and out of genetically modified organisms while (iii) allowing the biosynthesis of genetically encoded unnatural polymers1-4. Achieving these three goals requires the reassignment of multiple of the 64 codons nature uses to encode proteins. However, synonymous codon replacement-recoding-is frequently lethal, and how recoding impacts fitness remains poorly explored. Here, we explore these effects using whole-genome synthesis, multiplexed directed evolution, and genome-transcriptome-translatome-proteome co-profiling on multiple recoded genomes. Using this information, we assemble a synthetic Escherichia coli genome in seven sections using only 57 codons to encode proteins. By discovering the rules responsible for the lethality of synonymous recoding and developing a data-driven multi-omics-based genome construction workflow that troubleshoots synthetic genomes, we overcome the lethal effects of 62,007 synonymous codon swaps and 11,108 additional genomic edits. We show that synonymous recoding induces transcriptional noise including new antisense RNAs, leading to drastic transcriptome and proteome perturbation. As the elimination of select codons from an organism's genetic code results in the widespread appearance of cryptic promoters, we show that synonymous codon choice may naturally evolve to minimize transcriptional noise. Our work provides the first genome-scale description of how synonymous codon changes influence organismal fitness and paves the way for the construction of functional genomes that provide genetic firewalls from natural ecosystems and safely produce biopolymers, drugs, and enzymes with an expanded chemistry.

Influence of CO2 and Dust on the Survival of Non-Resistant and Multi-Resistant Airborne E. coli Strains

The airborne transmission of bacterial pathogens poses a significant challenge to public health, especially with the emergence of antibiotic-resistant strains. This study investigated environmental factors influencing the survival of airborne bacteria, focusing on the effects of different carbon dioxide (CO2) and dust concentrations. The experiments were conducted in an atmospheric simulation chamber using the non-resistant wild-type E. coli K12 (JM109) and a multi-resistant variant (JM109-pEC958). Different CO2 (100 ppm, 800 ppm, 3000 ppm) and dust concentrations (250 µg m-3, 500 µg m-3, 2000 µg m-3) were tested to encompass a wide range of CO2 and dust levels. The results revealed that JM109-pEC958 exhibited greater resilience to high CO2 and dust concentrations compared to its non-resistant counterpart. At 3000 ppm CO2, the survival rate of JM109 was significantly reduced, while the survival rate of JM109-pEC958 remained unaffected. At the dust concentration of 250 µg m-3, JM109 exhibited significantly reduced survival, whereas JM109-pEC958 did not. When the dust concentration was increased to 500 and 2000 µg m-3, even the JM109-pEC958 experienced substantially reduced survival rates, which were still significantly higher than those of its non-resistant counterpart at these concentrations. These findings suggest that multi-resistant E. coli strains possess mechanisms enabling them to endure extreme environmental conditions better than non-resistant strains, potentially involving regulatory genes or efflux pumps. The study underscores the importance of understanding bacterial adaptation strategies to develop effective mitigation approaches against antibiotic-resistant bacteria in atmospheric environments. Overall, this study provides valuable insights into the interplay between environmental stressors and bacterial survival, serving as a foundational step towards elucidating the adaptation mechanisms of multi-resistant bacteria and informing strategies for combating antibiotic resistance in the atmosphere.

Fructose-1-kinase has pleiotropic roles in Escherichia coli

In Escherichia coli, the master transcription regulator catabolite repressor activator (Cra) regulates >100 genes in central metabolism. Cra binding to DNA is allosterically regulated by binding to fructose-1-phosphate (F-1-P), but the only documented source of F-1-P is from the concurrent import and phosphorylation of exogenous fructose. Thus, many have proposed that fructose-1,6-bisphosphate (F-1,6-BP) is also a physiological regulatory ligand. However, the role of F-1,6-BP has been widely debated. Here, we report that the E. coli enzyme fructose-1-kinase (FruK) can carry out its "reverse" reaction under physiological substrate concentrations to generate F-1-P from F-1,6-BP. We further show that FruK directly binds Cra with nanomolar affinity and forms higher order, heterocomplexes. Growth assays with a ΔfruK strain and fruK complementation show that FruK has a broader role in metabolism than fructose catabolism. Since fruK itself is repressed by Cra, these newly-reported events add layers to the dynamic regulation of E. coli's central metabolism that occur in response to changing nutrients. These findings might have wide-spread relevance to other γ-proteobacteria, which conserve both Cra and FruK.

Centroid of the bacterial growth curves: a metric to assess phage efficiency

Phage replication can be studied using various approaches, including measuring the optical density (OD) of a bacterial culture in a liquid medium in the presence of phages. A few quantitative methods are available to measure and compare the efficiency of phages by using a single index based on the analysis of OD curves. However, these methods are not always applicable to non-canonical OD curves. Using the concept of center of area (centroid), we developed a metric called Centroid Index (CI), sensitive to the trend of the growth curves (OD distribution) including bacterial regrowth, which is not considered by the methods already available. We also provide a user-friendly software to facilitate the calculation of CI. This method offers an alternative and more precise way to determine phage efficiency by considering the OD variations over time, which may help in the selection of phages for biocontrol applications.

Evolution of a Plasmid Regulatory Circuit Ameliorates Plasmid Fitness Cost

Plasmids play a major role in rapid adaptation of bacteria by facilitating horizontal transfer of diverse genes, most notably those conferring antibiotic resistance. While most plasmids that replicate in a broad range of bacteria also persist well in diverse hosts, there are exceptions that are poorly understood. We investigated why a broad-host range plasmid, pBP136, originally found in clinical Bordetella pertussis isolates, quickly became extinct in laboratory Escherichia coli populations. Through experimental evolution we found that inactivation of a previously uncharacterized plasmid gene, upf31, drastically improved plasmid maintenance in E. coli. This gene inactivation resulted in decreased transcription of the global plasmid regulators (korA, korB, and korC) and numerous genes in their regulons. It also caused transcriptional changes in many chromosomal genes primarily related to metabolism. In silico analyses suggested that the change in plasmid transcriptome may be initiated by Upf31 interacting with the plasmid regulator KorB. Expression of upf31 in trans negatively affected persistence of pBP136Δupf31 as well as the closely related archetypal IncP-1β plasmid R751, which is stable in E. coli and natively encodes a truncated upf31 allele. Our results demonstrate that while the upf31 allele in pBP136 might advantageously modulate gene expression in its original host, B. pertussis, it has harmful effects in E. coli. Thus, evolution of a single plasmid gene can change the range of hosts in which that plasmid persists, due to effects on the regulation of plasmid gene transcription.

Cultivating efficiency: high-throughput growth analysis of anaerobic bacteria in compact microplate readers

Anaerobic microbes play crucial roles in environmental processes, industry, and human health. Traditional methods for monitoring the growth of anaerobes, including plate counts or subsampling broth cultures for optical density measurements, are time and resource-intensive. The advent of microplate readers revolutionized bacterial growth studies by enabling high-throughput and real-time monitoring of microbial growth kinetics. Yet, their use in anaerobic microbiology has remained limited. Here, we present a workflow for using small-footprint microplate readers and the Growthcurver R package to analyze the kinetic growth metrics of anaerobic bacteria. We benchmarked the small-footprint Cerillo Stratus microplate reader against a BioTek Synergy HTX microplate reader in aerobic conditions using Escherichia coli DSM 28618 cultures. The growth rates and carrying capacities obtained from the two readers were statistically indistinguishable. However, the area under the logistic curve was significantly higher in cultures monitored by the Stratus reader. We used the Stratus to quantify the growth responses of anaerobically grown E. coli and Clostridium bolteae DSM 29485 to different doses of the toxin sodium arsenite. The growth of E. coli and C. bolteae was sensitive to arsenite doses of 1.3 µM and 0.4 µM, respectively. Complete inhibition of growth was achieved at 38 µM arsenite for C. bolteae and 338 µM in E. coli. These results show that the Stratus performs similarly to a leading brand of microplate reader and can be reliably used in anaerobic conditions. We discuss the advantages of the small format microplate readers and our experiences with the Stratus.

IMPORTANCE

We present a workflow that facilitates the production and analysis of growth curves for anaerobic microbes using small-footprint microplate readers and an R script. This workflow is a cost and space-effective solution to most high-throughput solutions for collecting growth data from anaerobic microbes. This technology can be used for applications where high throughput would advance discovery, including microbial isolation, bioprospecting, co-culturing, host-microbe interactions, and drug/toxin-microbial interactions.

Two distinct regulatory systems control pulcherrimin biosynthesis in Bacillus subtilis

Regulation of transcription is a fundamental process that allows bacteria to respond to external stimuli with appropriate timing and magnitude of response. In the soil bacterium Bacillus subtilis, transcriptional regulation is at the core of developmental processes needed for cell survival. Gene expression in cells transitioning from exponential phase to stationary phase is under the control of a group of transcription factors called transition state regulators (TSRs). TSRs influence numerous developmental processes including the decision between biofilm formation and motility, genetic competence, and sporulation, but the extent to which TSRs influence bacterial physiology remains to be fully elucidated. Here, we demonstrate two TSRs, ScoC and AbrB, along with the MarR-family transcription factor PchR negatively regulate production of the iron chelator pulcherrimin in B. subtilis. Genetic analysis of the relationship between the three transcription factors indicate that all are necessary to limit pulcherrimin production during exponential phase and influence the rate and total amount of pulcherrimin produced. Similarly, expression of the pulcherrimin biosynthesis gene yvmC was found to be under control of ScoC, AbrB, and PchR and correlated with the amount of pulcherrimin produced by each background. Lastly, our in vitro data indicate a weak direct role for ScoC in controlling pulcherrimin production along with AbrB and PchR. The layered regulation by two distinct regulatory systems underscores the important role for pulcherrimin in B. subtilis physiology.

The distinct cell physiology of Bradyrhizobium at the population and cellular level

The α-Proteobacteria belonging to Bradyrhizobium genus are microorganisms of extreme slow growth. Despite their extended use as inoculants in soybean production, their physiology remains poorly characterized. In this work, we produced quantitative data on four different isolates: B. diazoefficens USDA110, B. diazoefficiens USDA122, B. japonicum E109 and B. japonicum USDA6 which are representative of specific genomic profiles. Notably, we found conserved physiological traits conserved in all the studied isolates: (i) the lag and initial exponential growth phases display cell aggregation; (ii) the increase in specific nutrient concentration such as yeast extract and gluconate hinders growth; (iii) cell size does not correlate with culture age; and (iv) cell cycle presents polar growth. Meanwhile, fitness, cell size and in vitro growth widely vary across isolates correlating to ribosomal RNA operon number. In summary, this study provides novel empirical data that enriches the comprehension of the Bradyrhizobium (slow) growth dynamics and cell cycle.

Parallel evolution of alternate morphotypes of Chryseobacterium gleum during experimental evolution with Caenorhabditis elegans

Microbial evolution within polymicrobial communities is a complex process. Here, we report within-species diversification within multispecies microbial communities during experimental evolution with the nematode Caenorhabditis elegans. We describe morphological diversity in the target species Chryseobacterium gleum, which developed a novel colony morphotype in a small number of replicate communities. Alternate morphotypes coexisted with original morphotypes in communities, as well as in single-species experiments using evolved isolates. We found that the original and alternate morphotypes differed in motility and in spatial expansion in the presence of C. elegans. This study provides insight into the emergence and maintenance of intraspecies diversity in the context of microbial communities.

The DmsABC S-oxide reductase is an essential component of a novel, hypochlorite-inducible system of extracellular stress defense in Haemophilus influenzae

Defenses against oxidative damage to cell components are essential for survival of bacterial pathogens during infection, and here we have uncovered that the DmsABC S-/N-oxide reductase is essential for virulence and in-host survival of the human-adapted pathogen, Haemophilus influenzae. In several different infection models, H. influenzae ΔdmsA strains showed reduced immunogenicity as well as lower levels of survival in contact with host cells. Expression of DmsABC was induced in the presence of hypochlorite and paraquat, closely linking this enzyme to defense against host-produced antimicrobials. In addition to methionine sulfoxide, DmsABC converted nicotinamide- and pyrimidine-N-oxide, precursors of NAD and pyrimidine for which H. influenzae is an auxotroph, at physiologically relevant concentrations, suggesting that these compounds could be natural substrates for DmsABC. Our data show that DmsABC forms part of a novel, periplasmic system for defense against host-induced S- and N-oxide stress that also comprises the functionally related MtsZ S-oxide reductase and the MsrAB peptide methionine sulfoxide reductase. All three enzymes are induced following exposure of the bacteria to hypochlorite. MsrAB is required for physical resistance to HOCl and protein repair. In contrast, DmsABC was required for intracellular colonization of host cells and, together with MtsZ, contributed to resistance to N-Chlorotaurine. Our work expands and redefines the physiological role of DmsABC and highlights the importance of different types of S-oxide reductases for bacterial virulence.

Understanding the effects of sub-inhibitory antibiotic concentrations on the development of β-lactamase resistance based on quantile regression analysis

AIMS

Quantile regression is an alternate type of regression analysis that has been shown to have numerous advantages over standard linear regression. Unlike linear regression, which uses the mean to fit a linear model, quantile regression uses a data set's quantiles (or percentiles), which leads to a more comprehensive analysis of the data. However, while relatively common in other scientific fields such as economic and environmental modeling, it is infrequently used to understand biological and microbiological systems.

METHODS AND RESULTS

We analyzed a set of bacterial growth rates using quantile regression analysis to better understand the effects of antibiotics on bacterial fitness. Using a bacterial model system containing 16 variant genotypes of the TEM β-lactamase enzyme, we compared our quantile regression analysis to a previously published study that uses the Tukey's range test, or Tukey honestly significantly difference (HSD) test. We find that trends in the distribution of bacterial growth rate data, as viewed through the lens of quantile regression, can distinguish between novel genotypes and ones that have been clinically isolated from patients. Quantile regression also identified certain combinations of genotypes and antibiotics that resulted in bacterial populations growing faster as the antibiotic concentration increased-the opposite of what was expected. These analyses can provide new insights into the relationships between enzymatic efficacy and antibiotic concentration.

CONCLUSIONS

Quantile regression analysis enhances our understanding of the impacts of sublethal antibiotic concentrations on enzymatic (TEM β-lactamase) efficacy and bacterial fitness. We illustrate that quantile regression analysis can link patterns in growth rates with clinically relevant mutations and provides an understanding of how increasing sub-lethal antibiotic concentrations, like those found in our modern environment, can affect bacterial growth rates, and provide insight into the genetic basis for varied resistance.

Plasmid-mediated phenotypic noise leads to transient antibiotic resistance in bacteria

The rise of antibiotic resistance is a critical public health concern, requiring an understanding of mechanisms that enable bacteria to tolerate antimicrobial agents. Bacteria use diverse strategies, including the amplification of drug-resistance genes. In this paper, we showed that multicopy plasmids, often carrying antibiotic resistance genes in clinical bacteria, can rapidly amplify genes, leading to plasmid-mediated phenotypic noise and transient antibiotic resistance. By combining stochastic simulations of a computational model with high-throughput single-cell measurements of blaTEM-1 expression in Escherichia coli MG1655, we showed that plasmid copy number variability stably maintains populations composed of cells with both low and high plasmid copy numbers. This diversity in plasmid copy number enhances the probability of bacterial survival in the presence of antibiotics, while also rapidly reducing the burden of carrying multiple plasmids in drug-free environments. Our results further support the tenet that multicopy plasmids not only act as vehicles for the horizontal transfer of genetic information between cells but also as drivers of bacterial adaptation, enabling rapid modulation of gene copy numbers. Understanding the role of multicopy plasmids in antibiotic resistance is critical, and our study provides insights into how bacteria can transiently survive lethal concentrations of antibiotics.

Synthetic and natural rubber associated chemicals drive functional and structural changes as well as adaptations to antibiotics in in vitro marine microbiomes

The leaching of additives from plastics and elastomers (rubbers) has raised concerns due to their potential negative impacts on the environment and the development of antibiotic resistance. In this study, we investigated the effects of chemicals extracted from two types of rubber on microbiomes derived from a benthic sea urchin and two pelagic fish species. Additionally, we examined whether bacterial communities preconditioned with rubber-associated chemicals displayed adaptations to antibiotics. At the highest tested concentrations of chemicals, we observed reduced maximum growth rates and yields, prolonged lag phases, and increased alpha diversity. While the effects on alpha and beta diversity were not always conclusive, several bacterial genera were significantly influenced by chemicals from the two rubber sources. Subsequent exposure of sea urchin microbiomes preconditioned with rubber chemicals to the antibiotic ciprofloxacin resulted in decreased maximum growth rates. This indicates a more sensitive microbiome to ciprofloxacin when preconditioned with rubber chemicals. Although no significant interaction effects between rubber chemicals and ciprofloxacin exposure were observed in bacterial alpha and beta diversity, we observed log-fold changes in two bacterial genera in response to ciprofloxacin exposure. These findings highlight the structural and functional alterations in microbiomes originating from various marine species when exposed to rubber-associated chemicals and underscore the potential risks posed to marine life.

Remediation of aniline-contaminated aquifer by combining in-well Rhizobium borbori and circulated groundwater electrolysis

Aniline has become a common groundwater contaminant due to its wide use as a raw material in agriculture and pharmaceutical products. The current technologies for in situ remediation of aniline in groundwater are limited by the strains deficient in bacterial species, limited oxygen supply, excessive waste gas load and cost. Accordingly, we conducted a laboratory sand tank experiment to remediate groundwater contaminated with aniline by combining circulated groundwater electrolysis and in-well Rhizobium borbori, which was isolated from activated sludge. The results of the experiment indicated that the optimum concentration of aniline for Rhizobium borbori is about 5 mg/L, beyond which the maximum cell density and the highest specific growth rate decreases as the aniline concentration increases. The optimized duration for immobilizing the Rhizobium borbori into the bioreactor is 4-5 days. Though the Rhizobium borbori was strongly inhibited by the high-concentration of aniline, the immobilized bioreactor in the 350 mg/L aniline solution successfully formed biofilm. The aniline volatilization had limited influence on the observation of bioremediation performance, and the combination of circulated groundwater and in-well Rhizobium borbori supplied a steady dose of oxygen to the bioreactor efficiently degrading the entire region between the injection and extraction well. In addition, a numerical model for the sand tank remediation experiment was used to estimate the yield coefficient of oxygen to be 0.484 g/g, which indicates the presence of ammonia nitrogen as by-products; accordingly, a smaller wellbore size as well a higher circulation flow rate and intensity of current are recommended to improve the water quality. Despite the positive outcomes and potential of the newly developed technology to degrade subsurface aniline, parallel experiments should be conducted to estimate the environmental risk of the by-products and explore the controlling mechanisms of each component in this comprehensive system.

Polyphosphate kinase regulates LPS structure and polymyxin resistance during starvation in E. coli

Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1,000 residues in length. In Escherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. However, the molecular pathways impacted by PPK activity and polyP accumulation remain poorly characterized. In this work, we used label-free mass spectrometry to study the response of bacteria that cannot produce polyP (Δppk) during starvation to identify novel pathways regulated by PPK. In response to starvation, we found 92 proteins significantly differentially expressed between wild-type and Δppk mutant cells. Wild-type cells were enriched for proteins related to amino acid biosynthesis and transport, while Δppk mutants were enriched for proteins related to translation and ribosome biogenesis, suggesting that without PPK, cells remain inappropriately primed for growth even in the absence of the required building blocks. From our data set, we were particularly interested in Arn and EptA proteins, which were down-regulated in Δppk mutants compared to wild-type controls, because they play a role in lipid A modifications linked to polymyxin resistance. Using western blotting, we confirm differential expression of these and related proteins in K-12 strains and a uropathogenic isolate, and provide evidence that this mis-regulation in Δppk cells stems from a failure to induce the BasRS two-component system during starvation. We also show that Δppk mutants unable to up-regulate Arn and EptA expression lack the respective L-Ara4N and pEtN modifications on lipid A. In line with this observation, loss of ppk restores polymyxin sensitivity in resistant strains carrying a constitutively active basR allele. Overall, we show a new role for PPK in lipid A modification during starvation and provide a rationale for targeting PPK to sensitize bacteria towards polymyxin treatment. We further anticipate that our proteomics work will provide an important resource for researchers interested in the diverse pathways impacted by PPK.

Dashing Growth Curves: a web application for rapid and interactive analysis of microbial growth curves

BACKGROUND

Recording and analyzing microbial growth is a routine task in the life sciences. Microplate readers that record dozens to hundreds of growth curves simultaneously are increasingly used for this task raising the demand for their rapid and reliable analysis.

RESULTS

Here, we present Dashing Growth Curves, an interactive web application ( http://dashing-growth-curves.ethz.ch/ ) that enables researchers to quickly visualize and analyze growth curves without the requirement for coding knowledge and independent of operating system. Growth curves can be fitted with parametric and non-parametric models or manually. The application extracts maximum growth rates as well as other features such as lag time, length of exponential growth phase and maximum population size among others. Furthermore, Dashing Growth Curves automatically groups replicate samples and generates downloadable summary plots for of all growth parameters.

CONCLUSIONS

Dashing Growth Curves is an open-source web application that reduces the time required to analyze microbial growth curves from hours to minutes.

Biotoxicity attenuation and the underlying physicochemical mechanism of biochar aged under simulated natural environmental conditions

Biochar (BC), with the benefits of enhancing soil fertility, absorbing heavy metals, carbon sequestration, and mitigating the greenhouse effect, has been extensively used for soil remediation. However, the long-term changes in the biotoxicity of BC under complex environmental conditions, which are the key factors influencing the sustainable application of BC in soil, are still unclear. Herein, the biotoxicity of BC aged with various processes, including dry‒wet cycle (DW) aging, freeze‒thaw cycle (FT) aging, ultraviolet irradiation (UV) aging, and low molecular weight organic acid (OA) aging, was systematically investigated by Escherichia coli (E. coli) culture experiments. The toxicity attenuation rate (%·week-1) was proposed to more concisely and clearly compare the influence of different aging methods on BC toxicity. The results indicated that after 5 weeks of aging, the toxicity attenuation rate during the four aging modes followed the order OA aging > FT aging > UV aging > DW aging. BC was nontoxic after 1 week of OA aging, 4 weeks of FT aging, 7 weeks of UV aging, and 14 weeks of DW aging. Spectroscopic characterizations revealed that humic acids in the dissolved organic matter of BC were the main reason for the biotoxicity. In addition, the attenuation of environmentally persistent free radicals on BC during aging was also an important factor for reducing environmental toxicity. This work provides insight into the detoxification mechanism of the BC aging process under ordinary environmental conditions and guidance for the safe application of BC in soil.

Microbial Primer: Bacterial growth kinetics

tGrowth of microorganisms and interpretation of growth data are core skills required by microbiologists. While science moves forward, it is of paramount importance that essential skills are not lost. The bacterial growth curve and the information that can gleaned from it is of great value to all of microbiology, whether this be a simple growth experiment, comparison of mutant strains or the establishment of conditions for a large-scale multi-omics experiment. Increasingly, the basics of plotting and interpreting growth curves and growth data are being overlooked. This primer article serves as a refresher for microbiologists on the fundamentals of microbial growth kinetics.

BactEXTRACT: an R Shiny app to quickly extract, plot and analyse bacterial growth and gene expression data

To streamline the analysis and visualization of bacterial growth and gene expression data obtained by microtitre plate readers, we developed BactEXTRACT, an intuitive, easy-to-use R Shiny application. BactEXTRACT simplifies the transition from raw optical density, fluorescence and luminescence measurements to publication-ready plots. This package offers a user-friendly interface that reduces the complexity involved in growth curve and gene expression analysis and is generally applicable. BactEXTRACT is available at https://veeninglab.com/bactextract.

Domestication signatures in the non-conventional yeast Lachancea cidri

Evaluating domestication signatures beyond model organisms is essential for a thorough understanding of the genotype-phenotype relationship in wild and human-related environments. Structural variations (SVs) can significantly impact phenotypes playing an important role in the physiological adaptation of species to different niches, including during domestication. A detailed characterization of the fitness consequences of these genomic rearrangements, however, is still limited in non-model systems, largely due to the paucity of direct comparisons between domesticated and wild isolates. Here, we used a combination of sequencing strategies to explore major genomic rearrangements in a Lachancea cidri yeast strain isolated from cider (CBS2950) and compared them to those in eight wild isolates from primary forests. Genomic analysis revealed dozens of SVs, including a large reciprocal translocation (~16 kb and 500 kb) present in the cider strain, but absent from all wild strains. Interestingly, the number of SVs was higher relative to single-nucleotide polymorphisms in the cider strain, suggesting a significant role in the strain's phenotypic variation. The set of SVs identified directly impacts dozens of genes and likely underpins the greater fermentation performance in the L. cidri CBS2950. In addition, the large reciprocal translocation affects a proline permease (PUT4) regulatory region, resulting in higher PUT4 transcript levels, which agrees with higher ethanol tolerance, improved cell growth when using proline, and higher amino acid consumption during fermentation. These results suggest that SVs are responsible for the rapid physiological adaptation of yeast to a human-related environment and demonstrate the key contribution of SVs in adaptive fermentative traits in non-model species.IMPORTANCEThe exploration of domestication signatures associated with human-related environments has predominantly focused on studies conducted on model organisms, such as Saccharomyces cerevisiae, overlooking the potential for comparisons across other non-Saccharomyces species. In our research, employing a combination of long- and short-read data, we found domestication signatures in Lachancea cidri, a non-model species recently isolated from fermentative environments in cider in France. The significance of our study lies in the identification of large array of major genomic rearrangements in a cider strain compared to wild isolates, which underly several fermentative traits. These domestication signatures result from structural variants, which are likely responsible for the phenotypic differences between strains, providing a rapid path of adaptation to human-related environments.

High-Yield Lasso Peptide Production in a Burkholderia Bacterial Host by Plasmid Copy Number Engineering

The knotted configuration of lasso peptides confers thermal stability and proteolytic resistance, addressing two shortcomings of peptide-based drugs. However, low isolation yields hinder the discovery and development of lasso peptides. While testing Burkholderia sp. FERM BP-3421 as a bacterial host to produce the lasso peptide capistruin, an overproducer clone was previously identified. In this study, we show that an increase in the plasmid copy number partially contributed to the overproducer phenotype. Further, we modulated the plasmid copy number to recapitulate titers to an average of 160% relative to the overproducer, which is 1000-fold higher than previously reported with E. coli, reaching up to 240 mg/L. To probe the applicability of the developed tools for lasso peptide discovery, we targeted a new lasso peptide biosynthetic gene cluster from endosymbiont Mycetohabitans sp. B13, leading to the isolation of mycetolassin-15 and mycetolassin-18 in combined titers of 11 mg/L. These results validate Burkholderia sp. FERM BP-3421 as a production platform for lasso peptide discovery.

Klebsiella pneumoniae OmpR facilitates lung infection through transcriptional regulation of key virulence factors

IMPORTANCE

Bacteria use two-component regulatory systems (TCSs) to adapt to changes in their environment by changing their gene expression. In this study, we show that the EnvZ/OmpR TCS of the clinically relevant opportunistic pathogen Klebsiella pneumoniae plays an important role in successfully establishing lung infection and virulence. In addition, we elucidate the K. pneumoniae OmpR regulon within the host. This work suggests that K. pneumoniae OmpR might be a promising target for innovative anti-infectives.

Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics

Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.

Two Distinct Regulatory Systems Control Pulcherrimin Biosynthesis in Bacillus subtilis

Regulation of transcription is a fundamental process that allows bacteria to respond to external stimuli with appropriate timing and magnitude of response. In the soil bacterium Bacillus subtilis, transcriptional regulation is at the core of developmental processes needed for cell survival. Gene expression in cells transitioning from exponential phase to stationary phase is under the control of a group of transcription factors called transition state regulators (TSRs). TSRs influence numerous developmental processes including the decision between biofilm formation and motility, genetic competence, and sporulation, but the extent to which TSRs influence bacterial physiology remains to be fully elucidated. Here, we demonstrate two TSRs, ScoC and AbrB, along with the MerR-family transcription factor PchR negatively regulate production of the iron chelator pulcherrimin in B. subtilis. Genetic analysis of the relationship between the three transcription factors indicate that all are necessary to limit pulcherrimin production during exponential phase and influence the rate and total amount of pulcherrimin produced. Similarly, expression of the pulcherrimin biosynthesis gene yvmC was found to be under control of ScoC, AbrB, and PchR and correlated with the amount of pulcherrimin produced by each background. Lastly, our in vitro data indicate a weak direct role for ScoC in controlling pulcherrimin production along with AbrB and PchR. The layered regulation by two distinct regulatory systems underscores the important, and somewhat enigmatic, role for pulcherrimin in B. subtilis physiology.

Mammalian cell growth characterisation by a non-invasive plate reader assay

Automated and non-invasive mammalian cell analysis is currently lagging behind due to a lack of methods suitable for a variety of cell lines and applications. Here, we report the development of a high throughput non-invasive method for tracking mammalian cell growth and performance based on plate reader measurements. We show the method to be suitable for both suspension and adhesion cell lines, and we demonstrate it can be adopted when cells are grown under different environmental conditions. We establish that the method is suitable to inform on effective drug treatments to be used depending on the cell line considered, and that it can support characterisation of engineered mammalian cells over time. This work provides the scientific community with an innovative approach to mammalian cell screening, also contributing to the current efforts towards high throughput and automated mammalian cell engineering.