Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis

Functional and Mechanistic Insights into the Fatty-Acid CoA Ligase FadK in Escherichia coli

BACKGROUND

Escherichia coli (E. coli) is a common opportunistic bacterial pathogen in both human and animal populations. Fatty acids serve as the central carbon and energy source, a process mediated by fatty acid-coenzyme A (CoA) ligases encoded by fad genes such as FadK. However, the function and the mechanism of FadK remain unclear.

METHODS

The three-dimensional structure of FadK was modeled using AlphaFold2. After expression and purification, monomeric FadK was successfully isolated. The enzymatic activity was assayed, and real-time quantitative polymerase chain reaction (RT-qPCR) was performed to quantify FadK expression levels.

RESULTS

In enzymatic assays of fatty acid CoA ligase activity, caprylic acid was found to be the optimal substrate for FadK. We determined the optimal catalytic conditions for FadK, which include a pH of 7.4, ATP concentration of 0.6 mM, CoA concentration of 0.8 mM, and Mg2+ concentration of 0.8 mM at 37 °C. Notably, the activity of FadK showed a decrease with increasing concentrations of dodecyl-AMP, which was further confirmed by the RT-qPCR results.

CONCLUSIONS

Our findings will serve as a fundamental framework for the development of innovative therapeutics that target E. coli infections.

Development of novel and efficient Corynebacterium glutamicum gene expression systems for industrial enzyme production

An ideal microbial gene expression system for industrial enzyme production should possess a function complementary selection marker, a cost-effective inducer, and the ability for extracellular protein secretion. In this study，we employed CRISPR-Cpf1 gene editing technology to construct an engineered Corynebacterium glutamicum host strain, C. glutamicum Δalr∷araE ΔmurI, by deleting the alanine racemase-encoding gene alr and the glutamate racemase-encoding gene murI, and by integrating the Bacillus subtilis arabinose-related compounds permease-encoding gene araE into the chromosome. The two secretion-type expression vectors pAU30S (Sec-type) and pAU30T (Tat-type) that both employ alr as selection marker, the T7 transcription system to transcribe target genes, and the B. subtilis AraR-ORA1/ORA2 negative control system to control gene transcription, were constructed. The α-amylase AmyF from Geobacillus stearothermophilus was used as reporter protein to test the applicability of the L-arabinose-induced gene expression systems C. glutamicum/pAU30S and C. glutamicum Δalr∷araE ΔmurI/pAU30T. The results of transparent circle investigation, SDS-PAGE and amylase activity analysis demonstrated that the recombinant AmyF was efficiently expressed and completely secreted into the culture medium in its active form. The C. glutamicum Δalr∷araE ΔmurI/pAU30S and C. glutamicum Δalr∷araE ΔmurI/pAU30T systems represent highly efficient gene expression platforms suitable for the secretory production of industrial enzymes.

Structural and bioinformatics analyses identify deoxydinucleotide-specific nucleases and their association with genomic islands in gram-positive bacteria

Dinucleases of the DEDD superfamily, such as oligoribonuclease, Rexo2 and nanoRNase C, catalyze the essential final step of RNA degradation, the conversion of di- to mononucleotides. The active sites of these enzymes are optimized for substrates that are two nucleotides long, and do not discriminate between RNA and DNA. Here, we identified a novel DEDD subfamily, members of which function as dedicated deoxydinucleases (diDNases) that specifically hydrolyze single-stranded DNA dinucleotides in a sequence-independent manner. Crystal structures of enzyme-substrate complexes reveal that specificity for DNA stems from a combination of conserved structural elements that exclude diribonucleotides as substrates. Consistently, diDNases fail to complement the loss of enzymes that act on diribonucleotides, indicating that these two groups of enzymes support distinct cellular functions. The genes encoding diDNases are found predominantly in genomic islands of Actinomycetes and Clostridia, which, together with their association with phage-defense systems, suggest potential roles in bacterial immunity.

Insights into the functional mechanisms of three terpene synthases from Lavandula angustifolia (Lavender)

Lavender species are of significant economic value being cultivated extensively worldwide for their essential oils (EOs), which include terpenes that play crucial roles in the cosmetic, personal care, and pharmaceutical industries. The terpene synthases in lavender, such as Lavandula angustifolia linalool synthase (LaLINS), limonene synthase (LaLIMS), and bergamotene synthase (LaBERS), are key enzymes in terpene biosynthesis. However, the functional mechanisms underlying these enzymes remain poorly understood. Here, we used AlphaFold2 to predict the three-dimensional structures of LaLINS, LaLIMS, and LaBERS. The hydrodynamic radii of LaLINS, LaLIMS, and LaBERS were 5.7 ± 0.2, 6.2 ± 0.3, and 5.4 ± 0.2 nm, respectively. Mutations D320A or D324A led to a complete loss of activity in LaLINS compared to the wild-type (WT) enzyme; similarly, mutations D356A or D360A abolished activity in LaLIMS, and D291A or D295A eliminated activity in LaBERS. Furthermore, the genes LaLINS, LaLIMS, and LaBERS exhibited significantly higher expression levels in leaves compared to stems and flowers, with peak expression occurring at 8:00 a.m. Our findings contribute to a deeper understanding of terpene biosynthesis in lavender and offer insights for improving essential oil production through genetic engineering.

Expression of Rhodococcus erythropolis stress genes in planctonic culture supplemented with various hydrocabons

Studying Rhodococcus erythropolis stress response is of significant scientific interest, since this microorganism is widely used for bioremediation of oil-contaminated sites and is essential for environmental biotechnology. In addition, much less data was published on molecular mechanisms of stress resistance and adaptation to effects of pollutants for Gram-positive oil degraders compared to Gram-negative ones. This study provided an assessment of changes in the transcription level of the soxR, sodA, sodC, oxyR, katE, katG, recA, dinB, sigF, sigH genes in the presence of decane, hexadecane, cyclohexane, benzene, naphthalene, anthracene and diesel fuel. Judging by the changes in the expression of target genes, hydrocarbons as the main carbon source caused oxidative stress in R. erythropolis cells, which resulted in DNA damage. It was documented by enhanced transcription of genes encoding antioxidant enzymes (superoxide dismutase and catalase), SOS response, DNA polymerase IV, and sigma factors of RNA polymerase SigH and SigF. At this, it was likely that in the presence of hydrocarbons, transcription of catalase genes (katE and katG) was coordinated primarily by the sigF regulator.

The bacterial strains JAM1T and GP59 of the species Methylophaga nitratireducenticrescens differ in their expression profiles of denitrification genes in oxic and anoxic cultures

Background

Strain JAM1T and strain GP59 of the methylotrophic, bacterial species Methylophaga nitratireducenticrescens were isolated from a microbial community of the biofilm that developed in a fluidized-bed, methanol-fed, marine denitrification system. Despite of their common origin, both strains showed distinct physiological characters towards the dynamics of nitrate (NO 3 - ) reduction. Strain JAM1T can reduceNO 3 - to nitrite (NO 2 - ) but notNO 2 - to nitric oxide (NO) as it lacks a NO-formingNO 2 - reductase. Strain GP59 on the other hand can carry the complete reduction ofNO 3 - to N2. Strain GP59 cultured under anoxic conditions shows a 24-48h lag phase beforeNO 3 - reduction occurs. In strain JAM1T cultures,NO 3 - reduction begins immediately with accumulation ofNO 2 - . Furthermore,NO 3 - is reduced under oxic conditions in strain JAM1T cultures, which does not appear in strain GP59 cultures. These distinct characters suggest differences in the regulation pathways impacting the expression of denitrification genes, and ultimately growth.

Methods

Both strains were cultured under oxic conditions either with or withoutNO 3 - , or under anoxic conditions withNO 3 - . Transcript levels of selected denitrification genes (nar1 and nar2 encodingNO 3 - reductases, nirK encodingNO 2 - reductase, narK12f encodingNO 3 - /NO 2 - transporter) and regulatory genes (narXL and fnr) were determined by quantitative reverse transcription polymerase chain reaction. We also derived the transcriptomes of these cultures and determined their relative gene expression profiles.

Results

The transcript levels of nar1 were very low in strain GP59 cultured under oxic conditions withoutNO 3 - . These levels were 37 times higher in strain JAM1T cultured under the same conditions, suggesting that Nar1 was expressed at sufficient levels in strain JAM1T before the inoculation of the oxic and anoxic cultures to carryNO 3 - reduction with no lag phase. Transcriptomic analysis revealed that each strain had distinct relative gene expression profiles, and oxygen had high impact on these profiles. Among denitrification genes and regulatory genes, the nnrS3 gene encoding factor involved in NO-response function had its relative gene transcript levels 5 to 10 times higher in strain GP59 cultured under oxic conditions withNO 3 - than those in both strains cultured under oxic conditions withoutNO 3 - . Since NnrS senses NO, these results suggest that strain GP59 reducedNO 3 - to NO under oxic conditions, but because of the oxic environment, NO is oxidized back toNO 3 - by flavohemoproteins (NO dioxygenase; Hmp), explaining whyNO 3 - reduction is not observed in strain GP59 cultured under oxic conditions.

Conclusions

Understanding how these two strains manage the regulation of the denitrification pathway provided some clues on how they response to environmental changes in the original biofilm community, and, by extension, how this community adapts in providing efficient denitrifying activities.

Dietary zinc supplementation inhibits bacterial plasmid conjugation in vitro by regulating plasmid replication (rep) and transfer (tra) genes

Humans use dietary supplements for several intended effects, such as supplementing malnutrition. While these compounds have been developed for host end benefits, their ancillary impact on the gut microbiota remains unclear. The human gut has been proposed as a reservoir for the prevalent lateral transfer of antimicrobial resistance and virulence genes in bacteria through plasmid conjugation. Here, we studied the effect of dietary zinc supplements on the incidence of plasmid conjugation in vitro. Supplement effects were analyzed through standardized broth conjugation assays. The avian pathogenic Escherichia coli (APEC) strain APEC-O2-211 was a donor of the multidrug resistance plasmid pAPEC-O2-211A-ColV, and the human commensal isolate E. coli HS-4 was the plasmid-free recipient. Bacterial strains were standardized and mixed 1:1 and supplemented 1:10 with water, or zinc derived from either commercial zinc supplements or zinc gluconate reagent at varying concentrations. We observed a significant reduction in donors, recipients, and transconjugant populations in conjugations supplemented with zinc, with a dose-dependent relationship. Additionally, we observed a significant reduction (P < 0.05) in log conjugation efficiency in zinc-treated reactions. Upregulation of the mRNA for the plasmid replication initiation gene repA and the subset of transfer genes M, J, E, K, B, P, C, W, U, N, F, Q, D, I, and X was observed. Furthermore, we observed a downregulation of the conjugal propilin gene traA and the entry exclusion gene traS. This study demonstrates the effect of dietary zinc supplements on the conjugal transfer of a multidrug resistance plasmid between pathogenic and commensal bacteria during in vitro conditions.IMPORTANCEThis study identifies dietary zinc supplementation as a potential novel intervention for mitigating the emergence of multidrug resistance in bacteria, thus preventing antibiotic treatment failure and death in patients and animals. Further studies are required to determine the applicability of this approach in an in vivo model.

[Viable Bacteria Assay of Helicobacter pylori by RT-qPCR Measurement of cgt Gene Expression Levels: Establishment and Application of a New Method]

Objective

To establish a viable bacteria assay for Helicobacter pylori (H. pylori) by assessing the cgt gene expression, and to develop accordingly a rapid and novel testing method for clinical precision treatment.

Methods

Viable bacteria count was determined in bacterial cultures. The transcriptional expression level of cgt (hp0421), the conserved gene that encodes cholesterol-α-glucosyltransferase (CGT) in H. pylori, was measured by RT-PCR. The correlation between the number of colonies and cgt gene transcription expression was analyzed and the regression model was constructed. The linear range, sensitivity, and specificity of the new method were examined accordingly. The bactericidal action of clarithromycin was assessed using this method to verify the performance of the method in determining clinical bacterial drug resistance.

Results

The Ct values of cgt for H. pylori colony counts of 102, 104, 106, and 108 CFU/mL were 29.67±0.14, 23.37±0.36, 17.65±0.37, and 11.38±0.39, respectively. In the range of 101-108 CFU/mL, the regression equation for cgt gene expression and viable bacterial counts determined by RT-qPCR was y=-0.3501x+12.49, with the correlation coefficient being R 2=0.9992 and the sensitivity being 101 CFU/mL, showing no cross-reaction with 13 other bacteria. The lg values of live H. pylori bacteria treated with clarithromycin at 0, 5, 10, 20, and 40 μg/mL for 12 h were 2.57±0.02, 2.45±0.01, 2.19±0.02, 1.91±0.07, and 1.33±0.05, respectively. The corresponding cgt gene Ct values were 27.76±0.09, 28.37±0.24, 29.51±0.14, 30.11±0.12, and 31.66±0.11. By applying the cgt gene expression in the equation, the estimated counts of viable bacteria were found to be 2.73±0.03, 2.52±0.08, 2.11±0.05, 1.89±0.02, and 1.33±0.04, showing no significant difference in statistical analysis (P>0.05).

Conclusion

The method for assessing viable bacteria account by evaluating cgt gene expression in H. pylori was successfully established, significantly reducing the time required to determine viable bacteria count and providing a new method for clinical viable bacteria testing.

Comparative Genomic Analysis of Campylobacter rectus and Closely Related Species

Campylobacter rectus is a gram-negative, anaerobic bacterium strongly associated with periodontitis. It also causes various extraoral infections and is linked to adverse pregnancy outcomes in humans and murine models. C. rectus and related oral Campylobacters have been termed "emerging Campylobacter species" because infections by these organisms are likely underreported. Previously, no comparative methods have been used to analyze more than single C. rectus strains and until recently, very few C. rectus genomes have been publicly available. More sequenced genomes and comparative analyses are needed to study the genomic features and pathogenicity of this species. We sequenced eight new C. rectus strains and used comparative methods to identify regions of interest. An emphasis was put on the type III flagellar secretion system (T3SS), type IV secretion system (T4SS), and type VI secretion system (T6SS) because these protein complexes are important for pathogenesis in other Campylobacter species. RAST, BV-BRC, and other bioinformatics tools were used to assemble, annotate, and compare these regions in the genomes. The pan-genome of C. rectus consists of 2670 genes with core and accessory genomes of 1429 and 1241 genes, respectively. All isolates analyzed in this study have T3SS and T6SS hallmark proteins, while five of the isolates are missing a T4SS system. Twenty-one prophage clusters were identified across the panel of isolates, including four that appear intact. Overall, significant genomic islands were found, suggesting regions in the genomes that underwent horizontal gene transfer. Additionally, the high frequency of CRISPR arrays and other repetitive elements has led to genome rearrangements across the strains, including in areas adjacent to secretion system gene clusters. This study describes the substantial diversity present among C. rectus isolates and highlights tools/assays that have been developed to permit functional genomic studies. Additionally, we have expanded the studies on C. showae T4SS since we have two new C. showae genomes to report. We also demonstrate that unlike C. rectus , C showae does not demonstrate evidence of intact T6SS except for the strain CAM. The only strain of sequenced C. massilensis has neither T4SS or T6SS.

RNA-seq validation: software for selection of reference and variable candidate genes for RT-qPCR

BACKGROUND

Real-time quantitative PCR (RT-qPCR) is one of the most widely used gene expression analyses for validating RNA-seq data. This technique requires reference genes that are stable and highly expressed, at least across the different biological conditions present in the transcriptome. Reference and variable candidate gene selection is often neglected, leading to misinterpretation of the results.

RESULTS

We developed a software named "Gene Selector for Validation" (GSV), which identifies the best reference and variable candidate genes for validation within a quantitative transcriptome. This tool also filters the candidate genes concerning the RT-qPCR assay detection limit. GSV was compared with other software using synthetic datasets and performed better, removing stable low-expression genes from the reference candidate list and creating the variable-expression validation list. GSV software was used on a real case, an Aedes aegypti transcriptome. The top GSV reference candidate genes were selected for RT-qPCR analysis, confirming that eiF1A and eiF3j were the most stable genes tested. The tool also confirmed that traditional mosquito reference genes were less stable in the analyzed samples, highlighting the possibility of inappropriate choices. A meta-transcriptome dataset with more than ninety thousand genes was also processed successfully.

CONCLUSION

The GSV tool is a time and cost-effective tool that can be used to select reference and validation candidate genes from the biological conditions present in transcriptomic data.

Elucidating sleep disorders: a comprehensive bioinformatics analysis of functional gene sets and hub genes

Background

Sleep disorders (SD) are known to have a profound impact on human health and quality of life although their exact pathogenic mechanisms remain poorly understood.

Methods

The study first accessed SD datasets from the GEO and identified DEGs. These DEGs were then subjected to gene set enrichment analysis. Several advanced techniques, including the RF, SVM-RFE, PPI networks, and LASSO methodologies, were utilized to identify hub genes closely associated with SD. Additionally, the ssGSEA approach was employed to analyze immune cell infiltration and functional gene set scores in SD. DEGs were also scrutinized in relation to miRNA, and the DGIdb database was used to explore potential pharmacological treatments for SD. Furthermore, in an SD murine model, the expression levels of these hub genes were confirmed through RT-qPCR and Western Blot analyses.

Results

The findings of the study indicate that DEGs are significantly enriched in functions and pathways related to immune cell activity, stress response, and neural system regulation. The analysis of immunoinfiltration demonstrated a marked elevation in the levels of Activated CD4+ T cells and CD8+ T cells in the SD cohort, accompanied by a notable rise in Central memory CD4 T cells, Central memory CD8 T cells, and Natural killer T cells. Using machine learning algorithms, the study also identified hub genes closely associated with SD, including IPO9, RAP2A, DDX17, MBNL2, PIK3AP1, and ZNF385A. Based on these genes, an SD diagnostic model was constructed and its efficacy validated across multiple datasets. In the SD murine model, the mRNA and protein expressions of these 6 hub genes were found to be consistent with the results of the bioinformatics analysis.

Conclusion

In conclusion, this study identified 6 genes closely linked to SD, which may play pivotal roles in neural system development, the immune microenvironment, and inflammatory responses. Additionally, the key gene-based SD diagnostic model constructed in this study, validated on multiple datasets showed a high degree of reliability and accuracy, predicting its wide potential for clinical applications. However, limited by the range of data sources and sample size, this may affect the generalizability of the results.

Reference Genes for Expression Analyses by qRT-PCR in Enterobacter cancerogenus

The Enterobacter cancerogenus strain EcHa1 was isolated from the dead larvae of Helicoverpa armigera, and has the potential for biocontrol of some Lepidoptera insects. In order to screen insecticidal-related genes by qRT-PCR, stable endogenous reference genes used for normalizing qRT-PCR data were selected and evaluated from 13 housekeeping genes (HKGs). The expression levels of the HKGs were determined using qRT-PCR under different experimental conditions, including two culture temperatures and three bacterial OD values. Five stability analysis methods (Ct, BestKeeper, NormFinder, geNorm, and RefFinder) were used to comprehensively rank the candidate genes. The results showed that the optimal reference genes varied under different experimental conditions. The combination of gyrA and gyrB was recommended as the best reference gene combination at 28 °C, while gyrA and rpoB was the best combination at 37 °C. When the OD values were 0.5, 1.0 and 2.0, the recommended reference gene combinations were ftsZ and gyrA, rpoB and gyrB, and gyrA and pyk, respectively. The most suitable reference genes were gyrA and gyrB under all experimental conditions. Using gyrA and gyrB as the reference genes for qRT-PCR, EcHa1 was found to invade all tissues of the H. armigera larvae, and expressed a candidate pathogenic factor Hcp at high levels in gut, Malpighian tubules, and epidermis tissues. This study not only establishes an accurate and reliable normalization for qRT-PCR in entomopathogenic bacteria but also lays a solid foundation for further study of functional genes in E. cancerogenus.

The inactivation of tolC sensitizes Escherichia coli to perturbations in lipopolysaccharide transport

The Escherichia coli outer membrane channel TolC complexes with several inner membrane efflux pumps to export compounds across the cell envelope. All components of these complexes are essential for robust efflux activity, yet E. coli is more sensitive to antimicrobial compounds when tolC is inactivated compared to the inactivation of genes encoding the inner membrane drug efflux pumps. While investigating these susceptibility differences, we identified a distinct class of inhibitors targeting the core-lipopolysaccharide translocase, MsbA. We show that tolC null mutants are sensitized to structurally unrelated MsbA inhibitors and msbA knockdown, highlighting a synthetic-sick interaction. Phenotypic profiling revealed that tolC inactivation induced cell envelope softening and increased outer membrane permeability. Overall, this work identified a chemical probe of MsbA, revealed that tolC is associated with cell envelope mechanics and integrity, and highlighted that these findings should be considered when using tolC null mutants to study efflux deficiency.

Molecular weight control of poly-γ-glutamic acid reveals novel insights into extracellular polymeric substance synthesis in Bacillus licheniformis

BACKGROUND

The structural diversity of extracellular polymeric substances produced by microorganisms is attracting particular attention. Poly-gamma-glutamic acid (γ-PGA) is a widely studied extracellular polymeric substance from Bacillus species. The function of γ-PGA varies with its molecular weight (Mw).

RESULTS

Herein, different endogenous promoters in Bacillus licheniformis were selected to regulate the expression levels of pgdS, resulting in the formation of γ-PGA with Mw values ranging from 1.61 × 103 to 2.03 × 104 kDa. The yields of γ-PGA and exopolysaccharides (EPS) both increased in the pgdS engineered strain with the lowest Mw and viscosity, in which the EPS content was almost tenfold higher than that of the wild-type strain. Subsequently, the compositions of EPS from the pgdS engineered strain also changed. Metabolomics and RT-qPCR further revealed that improving the transportation efficiency of EPS and the regulation of carbon flow of monosaccharide synthesis could affect the EPS yield.

CONCLUSIONS

Here, we present a novel insight that increased pgdS expression led to the degradation of γ-PGA Mw and changes in EPS composition, thereby stimulating EPS and γ-PGA production. The results indicated a close relationship between γ-PGA and EPS in B. licheniformis and provided an effective strategy for the controlled synthesis of extracellular polymeric substances.

Selection and validation of reference genes suitable for gene expression analysis by Reverse Transcription Quantitative real-time PCR in Acinetobacter baumannii

Acinetobacter baumannii is a Gram-negative bacterium considered an emerging multi-drug-resistant pathogen. Furthermore, this bacterium can survive in extreme environmental conditions, which makes it a frequent cause of nosocomial infection outbreaks. Gene expression analyses by Reverse Transcription Quantitative real-time PCR (RT-qPCR) depend on a reference gene, also called an endogenous gene, which is used to normalize the generated data and thus ensure an accurate analysis with minimal errors. Currently, gene expression analyses in A. baumannii are compromised, as there are no reports in the literature describing the identification of validated reference genes for use in RT-qPCR analyses. For this reason, we selected twelve candidate reference genes of A. baumannii and assessed their expression profile under different experimental and culture conditions. The expression stability of the candidate genes was evaluated by using statistical algorithms such as BestKeeper, geNorm, NormFinder, Delta CT, and RefFinder, in order to identify the most suitable candidate reference genes for RT-qPCR analyses. The statistical analyses indicated rpoB, rpoD, and fabD genes as the most adequate to ensure accurate normalization of RT-qPCR data in A. baumannii. The accuracy of the proposed reference genes was validated by using them to normalize the expression of the ompA gene, encoding the outer membrane protein A, in A. baumannii sensible and resistant to the antibiotic polymyxin. The present work provides suitable reference genes for precise RT-qPCR data normalization on future gene expression studies with A. baumannii.

Niche differentiation within bacterial key-taxa in stratified surface waters of the Southern Pacific Gyre

One of the most hostile marine habitats on Earth is the surface of the South Pacific Gyre (SPG), characterized by high solar radiation, extreme nutrient depletion, and low productivity. During the SO-245 "UltraPac" cruise through the center of the ultra-oligotrophic SPG, the marine alphaproteobacterial group AEGEAN169 was detected by fluorescence in situ hybridization at relative abundances up to 6% of the total microbial community in the uppermost water layer, with two distinct populations (Candidatus Nemonibacter and Ca. Indicimonas). The high frequency of dividing cells combined with high transcript levels suggests that both clades may be highly metabolically active. Comparative metagenomic and metatranscriptomic analyses of AEGEAN169 revealed that they encoded subtle but distinct metabolic adaptions to this extreme environment in comparison to their competitors SAR11, SAR86, SAR116, and Prochlorococcus. Both AEGEAN169 clades had the highest percentage of transporters per predicted proteins (9.5% and 10.6%, respectively). In particular, the high expression of ABC transporters in combination with proteorhodopsins and the catabolic pathways detected suggest a potential scavenging lifestyle for both AEGEAN169 clades. Although both AEGEAN169 clades may share the genomic potential to utilize phosphonates as a phosphorus source, they differ in their metabolic pathways for carbon and nitrogen. Ca. Nemonibacter potentially use glycine-betaine, whereas Ca. Indicimonas may catabolize urea, creatine, and fucose. In conclusion, the different potential metabolic strategies of both clades suggest that both are well adapted to thrive resource-limited conditions and compete well with other dominant microbial clades in the uppermost layers of SPG surface waters.

Potential use of two Serratia strains for cadmium remediation based on microbiologically induced carbonate precipitation and their cadmium resistance

Cadmium (Cd) presence and bioavailability in soils is a serious concern for cocoa producers. Cocoa plants can bioaccumulate Cd that can reach humans through the food chain, thus posing a threat to human health, as Cd is a highly toxic metal. Currently, microbiologically induced carbonate precipitation (MICP) by the ureolytic path has been proposed as an effective technique for Cd remediation. In this work, the Cd remediation potential and Cd resistance of two ureolytic bacteria, Serratia sp. strains 4.1a and 5b, were evaluated. The growth of both Serratia strains was inhibited at 4 mM Cd(II) in the culture medium, which is far higher than the Cd content that can be found in the soils targeted for remediation. Regarding removal efficiency, for an initial concentration of 0.15 mM Cd(II) in liquid medium, the maximum removal percentages for Serratia sp. 4.1.a and 5b were 99.3% and 99.57%, respectively. Their precipitates produced during Cd removal were identified as calcite by X-ray diffraction. Energy dispersive X-ray spectroscopy analysis showed that a portion of Cd was immobilized in this matrix. Finally, the presence of a partial gene from the czc operon, involved in Cd resistance, was observed in Serratia sp. 5b. The expression of this gene was found to be unaffected by the presence of Cd(II), and upregulated in the presence of urea. This work is one of the few to report the use of bacterial strains of the Serratia genus for Cd remediation by MICP, and apparently the first one to report differential expression of a Cd resistance gene due to the presence of urea.

Effects of NaCl Treatment on Root Nodule Formation, Isoflavone Secretion in Soybean, and Nodulation Gene Expression in Rhizobia

We herein investigated the effects of salt (NaCl) stress on soybean nodulation by rhizobial strains. We specifically exami-ned: (1) the effects of NaCl on nodule maturity and positioning by inoculating three rhizobial strains (Bradyrhizobium diazoefficiens USDA110T, Bradyrhizobium elkanii USDA31, and Sinorhizobium fredii USDA191) onto soybean variety CNS, (2) the effects of the NaCl treatment on isoflavones (daidzein and genistein) secretion by CNS, (3) the effects of the NaCl treatment on gene expression induced by daidzein and genistein in rhizobia, and (4) the effects of the NaCl treatment on rhizobial growth. The results obtained were as follows: (1) the NaCl treatment delayed nodule development and reduced nodulation on the primary root following the USDA110T inoculation, minimal sensitivity regarding nodule formation in the USDA 31 inoculation, and significantly increased the mature nodule number and nodules on the primary root following the USDA 191 inoculation. (2) The NaCl treatment significantly reduced the secretion of daidzein from soybean roots, but did not significantly affect that of genistein. (3) NaCl treatment induced a significant decrease in genistein-induced nodC expression in USDA110T, but not in USDA31, and also caused a significant reduction in daidzein-induced nodC expression, but not genistein-induced expression, in USDA191. (4) NaCl treatment reduced survivability under acidic conditions, but increased survivability under saline-alkaline conditions for USDA191 than bradyrhizobia. These results indicate that saline conditions give S. fredii a competitive advantage over Bradyrhizobium during soybean infection.

Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota

The identification of processes activated by specific microbes during microbiota colonization of plant roots has been hampered by technical constraints in metatranscriptomics. These include lack of reference genomes, high representation of host or microbial rRNA sequences in datasets, or difficulty to experimentally validate gene functions. Here, we recolonized germ-free Arabidopsis thaliana with a synthetic, yet representative root microbiota comprising 106 genome-sequenced bacterial and fungal isolates. We used multi-kingdom rRNA depletion, deep RNA-sequencing and read mapping against reference microbial genomes to analyse the in planta metatranscriptome of abundant colonizers. We identified over 3,000 microbial genes that were differentially regulated at the soil-root interface. Translation and energy production processes were consistently activated in planta, and their induction correlated with bacterial strains' abundance in roots. Finally, we used targeted mutagenesis to show that several genes consistently induced by multiple bacteria are required for root colonization in one of the abundant bacterial strains (a genetically tractable Rhodanobacter). Our results indicate that microbiota members activate strain-specific processes but also common gene sets to colonize plant roots.

HYAL1 deficiency attenuates lipopolysaccharide-triggered renal injury and endothelial glycocalyx breakdown in septic AKI in mice

BACKGROUND

Renal dysfunction and disruption of renal endothelial glycocalyx are two important events during septic acute kidney injury (AKI). Here, the role and mechanism of hyaluronidase 1 (HYAL1) in regulating renal injury and renal endothelial glycocalyx breakdown in septic AKI were explored for the first time.

METHODS

BALB/c mice were injected with lipopolysaccharide (LPS, 10 mg/kg) to induce AKI. HYAL1 was blocked in vivo using lentivirus-mediated short hairpin RNA targeting HYAL1 (LV-sh-HYAL1). Biochemical assays were performed to measure the levels and concentrations of biochemical parameters associated with AKI as well as levels of inflammatory cytokines. Renal pathological lesions were determined by hematoxylin-eosin (HE) staining. Cell apoptosis in the kidney was detected using terminal-deoxynucleoitidyl transferase-mediated nick end labeling (TUNEL) assay. Immunofluorescence and immunohistochemical (IHC) staining assays were used to examine the levels of hyaluronic acid in the kidney. The protein levels of adenosine monophosphate-activated protein kinase (AMPK)/mammalian target of rapamycin (mTOR) signaling, endothelial glycocalyx, and autophagy-associated indicators were assessed by western blotting.

RESULTS

The knockdown of HYAL1 in LPS-subjected mice by LV-sh-HYAL1 significantly reduced renal inflammation, oxidative stress, apoptosis and kidney dysfunction in AKI, as well as alleviated renal endothelial glycocalyx disruption by preventing the release of hyaluronic acid to the bloodstream. Additionally, autophagy-related protein analysis indicated that knockdown of HYAL1 significantly enhanced autophagy in LPS mice. Furthermore, the beneficial actions of HYAL1 blockade were closely associated with the AMPK/mTOR signaling.

CONCLUSION

HYAL1 deficiency attenuates LPS-triggered renal injury and endothelial glycocalyx breakdown in septic AKI in mice.

Promoter Identification and Optimization for the Response of Lactobacillus plantarum WCFS1 to the Gram-Negative Pathogen-Associated Molecule N-3-Oxododecanoyl Homoserine Lactone

Quorum sensing (QS) in bacteria has been well studied as a cellular communication phenomenon for decades. In recent years, such systems have been repurposed for the use of biosensors in both cellular and cell-free contexts as well as for inducible protein expression in nontraditional chassis organisms. Such biosensors are particularly intriguing when considering the association between the pathogenesis of some bacteria and their signaling intermediates. Considering this relationship and considering the recent demonstration of the species Lactobacillus plantarum WCFS1 as both a synthetic biology chassis and an organism capable of detecting a pathogen-associated QS molecule, we wanted to develop this organism as a QS sentinel. We used an approach combining techniques from both systems and synthetic biology to identify a number of native QS-response genes and to alter associated promoter activity to tune the output of L. plantarum cultures exposed to N-3-oxododecanoyl homoserine lactone. The resulting engineered QS sentinel reinforces the potential of modified lactic acid bacteria (LAB) for use in human-health-promoting applications and also demonstrates a simple rational workflow to engineer sentinel organisms to respond to any environmental or chemical stimuli.

The coenzyme B12 precursor 5,6-dimethylbenzimidazole is a flavin antagonist in Salmonella

Salmonella enterica subsp. enterica sv. Typhimurium str. LT2 (hereafter S. Typhimurium) synthesizes adenosylcobalamin (AdoCbl, CoB12) de novo only under anoxic conditions, but it can assemble the lower ligand loop (a.k.a. the nucleotide loop) and can form the unique C-Co bond present in CoB12 in the presence or absence of molecular oxygen. During studies of nucleotide loop assembly in S. Typhimurium, we noticed that the growth of this bacterium could be arrested by the lower ligand nucleobase, namely 5,6-dimethylbenzimidazole (DMB). Here we report in vitro and in vivo evidence that shows that the structural similarity of DMB to the isoalloxazine moiety of flavin cofactors causes its deleterious effect on cell growth. We studied DMB inhibition of the housekeeping flavin dehydrogenase (Fre) and three flavoenzymes that initiate the catabolism of tricarballylate, succinate or D-alanine in S. Typhimurium. Notably, while growth with tricarballylate was inhibited by 5-methyl-benzimidazole (5-Me-Bza) and DMB, growth with succinate or glycerol was arrested by DMB but not by 5-Me-Bza. Neither unsubstituted benzimidazole nor adenine inhibited growth of S. Typhimurium at DMB inhibitory concentrations. Whole genome sequencing analysis of spontaneous mutant strains that grew in the presence of inhibitory concentrations of DMB identified mutations effecting the cycA (encodes D-Ala/D-Ser transporter) and dctA (encodes dicarboxylate transporter) genes and in the coding sequence of the tricarballylate transporter (TcuC), suggesting that increased uptake of substrates relieved DMB inhibition. We discuss two possible mechanisms of inhibition by DMB.

Dynamically Quantifying Intracellular Elemental Sulfur and Predicting Pertinent Gene Transcription by Raman Spectroscopy in Living Cells

The ability to monitor changes in metabolites and corresponding gene transcription within living cells is highly desirable. However, most current assays for quantification of metabolites or for gene transcription are destructive, precluding tracking the real-time dynamics of living cells. Here, we used the intracellular elemental sulfur in a Thiophaeococcus mangrovi cell as a proof-of-concept to link the quantity of metabolites and relevant gene transcription in living cells by a nondestructive Raman approach. Raman spectroscopy was utilized to quantify intracellular elemental sulfur noninvasively, and a computational mRR (mRNA and Raman) model was developed to infer the transcription of genes relevant to elemental sulfur. The results showed a significant linear correlation between the exponentially transformed Raman spectral intensity of intracellular elemental sulfur and the mRNA levels of genes encoding sulfur globule proteins in T. mangrovi. The mRR model was verified independently in two genera of Thiocapsa and Thiorhodococcus, and the mRNA levels predicted by mRR showed high consistency with actual gene expression detected by real-time polymerase chain reaction (PCR). This approach could enable noninvasive assessment of the quantity of metabolites and link the pertinent gene expression profiles in living cells, providing useful baseline data to spectroscopically map various omics in real time.

Insights into Regulating Mechanism of Mutagenesis Strains of Elizabethkingia meningoseptica sp. F2 by Omics Analysis

Vitamin K₂ plays an important role in electron transport, blood coagulation, and calcium homeostasis, and researchers have been trying to use microbes to produce it. Although our previous studies have shown that gradient radiation, breeding, and culture acclimation can improve vitamin K₂ production in Elizabethkingia meningoseptica, the mechanism is still unclear. This study is the first which performs genome sequencing of E. meningoseptica sp. F2 as a basis for subsequent experiments and further comparative analyses with other strains. Comparative metabolic pathway analysis of E. meningoseptica sp. F2, E. coli, Bacillus subtilis, and other vitamin K₂ product strains revealed that the mevalonate pathway of E. meningoseptica sp. F2 is different in bacteria at the system level. The expressions of menA, menD, menH, and menI in the menaquinone pathway and idi, hmgR, and ggpps in the mevalonate pathway were higher than those in the original strain. A total of 67 differentially expressed proteins involved in the oxidative phosphorylation metabolic pathway and citric acid cycle (TCA cycle) were identified. Our results reveal that combined gradient radiation breeding and culture acclimation can promote vitamin K₂ accumulation probably by regulating the vitamin K₂ pathway, oxidative phosphorylation metabolism pathway, and the citrate cycle (TCA cycle).

Quantitative evaluation of endogenous reference genes for ddPCR under salt stress using a moderate halophile

Droplet digital PCR (ddPCR) is being increasingly adopted for gene detection and quantification because of its higher sensitivity and specificity. According to previous observations and our laboratory data, it is essential to use endogenous reference genes (RGs) when investigating gene expression at the mRNA level under salt stress. This study aimed to select and validate suitable RGs for gene expression under salt stress using ddPCR. Six candidate RGs were selected based on the tandem mass tag (TMT)-labeled quantitative proteomics of Alkalicoccus halolimnae at four salinities. The expression stability of these candidate genes was evaluated using statistical algorithms (geNorm, NormFinder, BestKeeper and RefFinder). There was a small fluctuation in the cycle threshold (Ct) value and copy number of the pdp gene. Its expression stability was ranked in the vanguard of all algorithms and was the most suitable RG for quantification of expression by both qPCR and ddPCR of A. halolimnae under salt stress. Single RG pdp and RG combinations were used to normalize the expression of ectA, ectB, ectC and ectD under four salinities. The present study constitutes the first systematic analysis of endogenous RG selection for halophiles responding to salt stress. This work provides a valuable theory and an approach reference of internal control identification for ddPCR-based stress response models.

Copper ions inhibit Streptococcus mutans-Veillonella parvula dual biofilm by activating Streptococcus mutans reactive nitrogen species

BACKGROUND

To investigate the inhibition mechanism of copper ions on Streptococcus mutans-Veillonella parvula dual biofilm.

METHODS

S. mutans-V. parvula dual biofilm was constructed and copper ions were added at different concentrations. After the biofilm was collected, RNA-seq and qRT-PCR were then performed to get gene information.

RESULTS

The coculture of S. mutans and V. parvula formed a significantly better dual biofilm of larger biomass than S. mutans mono biofilm. And copper ions showed a more significant inhibitory effect on S. mutans-V. parvula dual biofilm than on S. mutans mono biofilm when copper ions concentration reached 100 µM, and copper ions showed a decreased inhibitory effect on S. gordonii-V. parvula dual biofilm and S. sanguis-V.parvula dual biofilm than on the two mono biofilms as the concentration of copper ions increased. And common trace elements such as iron, magnesium, and zinc showed no inhibitory effect difference on S. mutans-V. parvula dual biofilm. The RNA-seq results showed a significant difference in the expression of a new ABC transporter SMU_651c, SMU_652c, SMU_653c, and S. mutans copper chaperone copYAZ. SMU_651c, SMU_652c, and SMU_653c were predicted to function as nitrite/nitrate transporter-related proteins, which suggested the specific inhibition of copper ions on S. mutans-V. parvula dual biofilm may be caused by the activation of S. mutans reactive nitrogen species.

CONCLUSIONS

Streptococcus mutans and Veillonella parvula are symbiotic, forming a dual biofilm of larger biomass to better resist the external antibacterial substances, which may increase the virulence of S. mutans. While common trace elements such as iron, magnesium, and zinc showed no specific inhibitory effect on S. mutans-V. parvula dual biofilm, copper ion had a unique inhibitory effect on S. mutans-V. parvula dual biofilm which may be caused by activating S. mutans RNS when copper ions concentration reached 250 µM.

Cadmium effects on net N2O production by the deep-sea isolate Shewanella loihica PV-4

Deep-sea mining may lead to the release of high concentrations of metals into the surrounding seabed, which can disturb important ecosystem functions provided by microbial communities. Among these, the production of N2O and its reduction to N2 is of great relevance since N2O is an important greenhouse gas. Metal impacts on net N2O production by deep-sea bacteria are, however, currently unexplored. Here, we evaluated the effects of cadmium (Cd) on net N2O production by a deep-sea isolate, Shewanella loihica PV-4. We performed a series of Cd exposure incubations in oxic conditions and determined N2O fluxes during induced anoxic conditions, as well as the relative expression of the nitrite reductase gene (nirK), preceding N2O production, and N2O reductase gene (nosZ), responsible for N2O reduction. Net N2O production by S. loihica PV-4 exposed to Cd was strongly inhibited when compared to the control treatment (no metal). Both nirK and nosZ gene expression were inhibited in reactors with Cd, but nirK inhibition was stronger, supporting the lower net N2O production observed with Cd. The Cd inhibition of net N2O production observed in this study poses the question whether other deep-sea bacteria would undergo the same effects. Future studies should address this question as well as its applicability to complex communities and other physicochemical conditions, which remain to be evaluated.

Novel neurolisteriosis therapy using SPION as a drivable nanocarrier in gallic acid delivery to CNS

Neurolisteriosis is an infectious disease of the central nervous system (CNS) with a high mortality rate caused by Listeria monocytogenes. The CNS disorders suffer from inadequacy of drugs accessibility. An experimental in vivo model of neurolisteriosis was developed by oral administration of the bacteria in Wistar rats. It's speculated the capability of magnetite nanoparticles (MNPs) in ferrying gallic acid (GA), as a natural antimicrobial agent, through the blood-brain barrier (BBB) with the assistance of an external magnetic field (EMF). The capability of the formulated nanodrug in traversing through the BBB was approved by detecting blue spots in the Perls' Prussian staining of the brain tissue sections and by an increased iron content of the brain determined by the inductively coupled plasma spectroscopy. The GA release pattern and the nanodrug toxicity assay were promising. Anti-listeriosis effect of the formulated nanodrug was evaluated by molecular quantification of the relative abundance of survived bacteria in brain tissue samples. Besides, the relative expression of the listeriolysin O-encoding hly gene, the prominent virulence factor of L. monocytogenes, was determined using the rplD gene as a reference gene. The nanodrug-received rats showed a significantly less viable bacteria (13.2 ± 7.6%) and a 4.4-fold reduction in the relative expression of the hly gene in comparison to the sham group. Magnetite nanoparticles (MNPs) were synthesized by co-precipitation method, functionalized with GA, and finally coated with Tween 80. The physicochemical properties of the bare and surface modified materials were investigated using different techniques including X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopies, transmission electron microscopy (TEM), field-emission scanning electron microscopy (FESEM), dynamic light scattering (DLS) and Zeta Potential analyses, and vibrating sample magnetometry. In conclusion, MNPs displayed a considerable potential for drug delivery intentions to various target sites such as the CNS. Gallic acid exhibited a binary anti-listerial effect, the destruction of L. monocytogenes bacteria in addition to reducing the expression of the hly gene, which in turn causes reduced survivability of the bacteria in the CNS.

Accurate Absolute Quantification of Bacterial Populations in Mixed Cultures by qPCR

Quantitative PCR (qPCR) is a well-established technique that allows to accurately quantify nucleic acids or proteins, being widely used in several types of biological samples for bacterial load quantification. However, there are many recent studies that do not consider the potential pitfalls involved in key experimental qPCR stages, namely, those related to the extraction and purification of genomic DNA and to the thermal amplification process, that can lead to biased results in mixed cultures. Herein, we outline a proper protocol for bacterial quantification by qPCR, addressing how to overcome the main issues in that methodology.

Sequestration and efflux largely account for cadmium and copper resistance in the deep-sea Nitratiruptor sp. SB155-2 (phylum Campylobacterota)

In deep-sea hydrothermal vent environments, metal-enriched fluids and sediments abound, making these habitats ideal to study metal resistance in prokaryotes. In this investigation, we employed transcriptomics and shotgun proteomics with scanning transmission electron microscopy and energy-dispersive x-ray spectroscopy (STEM-EDX) to better understand mechanisms of tolerance for cadmium (Cd) and copper (Cu) at stress-inducing concentrations in Nitratiruptor sp. SB155-2 (phylum Campylobacterota). Transcriptomic profiles were remarkably different in the presence of these two metals, displaying 385 (19%) and 629 (31%) differentially transcribed genes (DTG) in the presence of Cd(II) and Cu(II), respectively, while only 7% of differentially transcribed (DT) genes were shared, with genes for non-specific metal transporters and genes involved in oxidative stress-response predominating. Transcriptomic and proteomic analyses confirmed that metal-specific DT pathways under Cu(II) stress, including those involving sulfur, cysteine, and methionine, are likely required for high-affinity efflux systems, while flagella formation and chemotaxis were over-represented under Cd(II) stress. Consistent with these differences, STEM-EDX analysis revealed that polyphosphate-like granules (pPLG), the formation of CdS particles, and the periplasmic space are crucial for Cd(II) sequestration. Overall, this study provides new insights regarding metal-specific adaptations of Campylobacterota to deep-sea hydrothermal vent environments.

Evaluation of candidate reference genes stability for gene expression analysis by reverse transcription qPCR in Clostridium perfringens

Identification of stable reference genes for normalization purposes is necessary for obtaining reliable and accurate results of reverse transcription quantitative polymerase chain reaction (RT-qPCR) analyses. To our knowledge, no reference gene(s) have been validated for this purpose in Clostridium perfringens. In this study, the expression profile of ten candidate reference genes from three strains of C. perfringens were assessed for stability under various experimental conditions using geNorm in qbase + . These stability rankings were then compared to stability assessments evaluated by BestKeeper, NormFinder, delta Ct, and RefFinder algorithms. When comparing all the analyses; gyrA, ftsZ, and recA were identified within the most stable genes under the different experimental conditions and were further tested as a set of reference genes for normalization of alpha toxin gene expression over a 22-h period. Depending on the condition, rpoA and rho might also be suitable to include as part of the reference set. Although commonly used for the purpose of normalizing RT-qPCR data, the 16S rRNA gene (rrs) was found to be an unsuitable gene to be used as a reference. This work provides a framework for the selection of a suitable stable reference gene set for data normalization of C. perfringens gene expression.

Rapid and simultaneous detection of multiple pathogens in the lower reproductive tract during pregnancy based on loop-mediated isothermal amplification-microfluidic chip

Background

Female reproductive tract infection (RTI) is the common source of varied diseases, especially as an important risk factor for pregnancy outcomes, therefore the rapid, accurate and simultaneous detection of multiple pathogens is in urgent need for assisting the diagnosis and treatment of RTI in pregnant women. Streptococcus agalactiae (S. agalactiae), Enterococcus faecalis (E. faecalis), Gardnerella vaginalis (G. vaginalis), Candida albicans (C. albicans) and Chlamydia trachomatis (C. trachomatis) are five main pathogens in lower genital tract with high risk, serious consequences and clinical demands. The combination of loop-mediated isothermal amplification (LAMP) and microfluidic technology was used to develop the LAMP-microfluidic chip for rapid, simple, sensitive and simultaneous detection of the five target pathogens above.

Results

Standard strains and clinical isolates were used for the establishment of the novel LAMP method in tube and LAMP-microfluidic chip, followed by the chip detection on 103 clinical samples and PCR verification partially. The sensitivities of LAMP of S. agalactiae, E. faecalis, G. vaginalis, and C. albicans in tube were 22.0, 76.0, 13.2, 1.11 CFU/μL, respectively, and C. trachomatis was 41.3 copies/μL; on LAMP-microfluidic chip they were 260, 154, 3.9 and 7.53 CFU/μL, respectively, and C. trachomatis was 120 copies/μL. The positive coincidence rates of clinical stains in tube and on chip experiments were 100%. Compared with the classic culture method performed in hospitals, the positive coincidence rate of the 103 clinical samples detected by LAMP-microfluidic chip were 100%. For the six inconsistent ones, including four G. vaginalis and two C. albicans positive samples tested by LAMP-microfluidic chip and verified by PCR were negative by culturing method in hospitals, indicating the lack of efficient detection by the classic culturing method.

Conclusion

Our study suggested that the LAMP-microfluidic chips could simultaneously, efficiently, and accurately detect multiple main pathogens, including S. agalactiae, E. faecalis, G. vaginalis, C. albicans and C. trachomatis, in clinical samples of female RTI to give a great clinical value. Accordingly, this novel method has the potential to provide a valuable reference for female RTI screening and early diagnosis during pregnancy.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02657-0.

Enabling Ethanologenesis in Moorella thermoacetica through Construction of a Replicating Shuttle Vector

Replicating plasmid shuttle vectors are key tools for efficient genetic and metabolic engineering applications, allowing the development of sustainable bioprocesses using non-model organisms with unique metabolic capabilities. To date, very limited genetic manipulation has been achieved in the thermophilic acetogen, Moorella thermoacetica, partly due to the lack of suitable shuttle vectors. However, M. thermoacetica has considerable potential as an industrial chassis organism, which can only be unlocked if reliable and effective genetic tools are in place. This study reports the construction of a replicating shuttle vector for M. thermoacetica through the identification and implementation of a compatible Gram-positive replicon to allow plasmid maintenance within the host. Although characterisation of plasmid behaviour proved difficult, the designed shuttle vector was subsequently applied for ethanologenesis, i.e., ethanol production in this organism. The non-native ethanologenesis in M. thermoacetica was achieved via plasmid-borne overexpression of the native aldh gene and heterologous expression of Clostridium autoethanogenum adhE1 gene. This result demonstrates the importance of the developed replicating plasmid vector for genetic and metabolic engineering efforts in industrially important M. thermoacetica.

Biogenic propane production by a marine Photobacterium strain isolated from the Western English Channel

Propane is a major component of liquefied petroleum gas, a major energy source for off-grid communities and industry. The replacement of fossil fuel-derived propane with more sustainably derived propane is of industrial interest. One potential production route is through microbial fermentation. Here we report, for the first time, the isolation of a marine bacterium from sediment capable of natural propane biosynthesis. Propane production, both in mixed microbial cultures generated from marine sediment and in bacterial monocultures was detected and quantified by gas chromatography–flame ionization detection. Using DNA sequencing of multiple reference genes, the bacterium was shown to belong to the genus Photobacterium. We postulate that propane biosynthesis is achieved through inorganic carbonate assimilation systems. The discovery of this strain may facilitate synthetic biology routes for industrial scale production of propane via microbial fermentation.

Activating Silent Glycolysis Bypasses in Escherichia coli

All living organisms share similar reactions within their central metabolism to provide precursors for all essential building blocks and reducing power. To identify whether alternative metabolic routes of glycolysis can operate in E. coli, we complementarily employed in silico design, rational engineering, and adaptive laboratory evolution. First, we used a genome-scale model and identified two potential pathways within the metabolic network of this organism replacing canonical Embden-Meyerhof-Parnas (EMP) glycolysis to convert phosphosugars into organic acids. One of these glycolytic routes proceeds via methylglyoxal and the other via serine biosynthesis and degradation. Then, we implemented both pathways in E. coli strains harboring defective EMP glycolysis. Surprisingly, the pathway via methylglyoxal seemed to immediately operate in a triosephosphate isomerase deletion strain cultivated on glycerol. By contrast, in a phosphoglycerate kinase deletion strain, the overexpression of methylglyoxal synthase was necessary to restore growth of the strain. Furthermore, we engineered the "serine shunt" which converts 3-phosphoglycerate via serine biosynthesis and degradation to pyruvate, bypassing an enolase deletion. Finally, to explore which of these alternatives would emerge by natural selection, we performed an adaptive laboratory evolution study using an enolase deletion strain. Our experiments suggest that the evolved mutants use the serine shunt. Our study reveals the flexible repurposing of metabolic pathways to create new metabolite links and rewire central metabolism.

New insights into the energy metabolism and taxonomy of Deferribacteres revealed by the characterization of a new isolate from a hypersaline microbial mat

Strain L21-Ace-BES^T , isolated from a lithifying cyanobacterial mat, could be assigned to a novel species and genus within the Deferribacteres. It is an important model organism for the study of anaerobic acetate degradation under hypersaline conditions. The metabolism of strain L21-Ace-BES^T was characterized by biochemical studies, comparative genome analyses, and the evaluation of gene expression patterns. The central metabolic pathway is the citric acid cycle, which is mainly controlled by the enzyme succinyl-CoA:acetate-CoA transferase. The potential use of a reversed oxidative citric acid cycle to fix CO₂ has been revealed through genome analysis. However, no autotrophic growth was detected in this strain, whereas sulfide and H₂ can be used mixotrophically. Preferred electron acceptors for the anaerobic oxidation of acetate are nitrate, fumarate and DMSO, while oxygen can be utilized only under microoxic conditions. Aerotolerant growth by fermentation was observed at higher oxygen concentrations. The redox cycling of sulfur/sulfide enables the generation of reducing power for the assimilation of acetate during growth and could prevent the over-reduction of cells in stationary phase. Extracellular electron transfer appears to be an essential component of the respiratory metabolism in this clade of Deferribacteres and may be involved in the reduction of nitrite to ammonium. This article is protected by copyright. All rights reserved.

Involvement of E. coli 6S RNA in Oxidative Stress Response

6S RNA, a small non-coding RNA present in almost all bacteria, inhibits transcription via direct binding to RNA polymerase holoenzymes. The mechanism of 6S RNA action was investigated to a large extent in E. coli, however, lack of 6S RNA (ΔssrS) was demonstrated to be unfavorable but not essential for cell survival under various growth conditions. In the present study, we revealed, for the first time, a lethal phenotype of the ΔssrS strain in the presence of high concentrations of H₂O₂. This phenotype was rescued by complementation of the ssrS gene on a plasmid. We performed comparative qRT-PCR analyses on an enlarged set of mRNAs of genes associated with the oxidative stress response, allowing us to identify four genes known to be involved in this pathway (soxS, ahpC, sodA and tpx) that had decreased mRNA levels in the ΔssrS strain. Finally, we performed comparative proteomic analyses of the wild-type and ΔssrS strains, confirming that ΔssrS bacteria have reduced levels of the proteins AhpC and Tpx involved in H₂O₂ reduction. Our findings substantiate the crucial role of the riboregulator 6S RNA for bacterial coping with extreme stresses.

Validation of housekeeping genes as internal controls for gene expression studies on biofilm formation in Bacillus velezensis

Bacillus velezensis is an important bacterium widely applied in agriculture and industry, and biofilms play critical roles in its environmental tolerance. The appropriate choice of reference genes is essential for key gene expression studies. Multiple internal control genes were selected and validated from the 21 housekeeping genes of B. velezensis by expression stability evaluation during biofilm formation and were used to study the expression of key genes involved in the process. The results showed that pyk, gyrA, recA, and gyrB were stably expressed, and the expression of pyk was the most stable during biofilm formation. A pair of two genes, pyk and gyrA, provided high-quality data when used as internal controls, and the combination of three genes, pyk, gyrA, and recA, was even better. The expression levels of pyk, gyrA, and recA approximated those of five key genes, abrB, epsD, kinC, sinR, and tasA, in biofilm formation, meeting the requirements of ideal internal control genes. The expression patterns of 5 key genes were studied with 16S, pyk, the pair of 2 genes, pyk and gyrA, and the combination of 3 genes, pyk, gyrA, and recA, as internal controls during the biofilm formation process. The results proved that pyk was a suitable internal control, as were the pair of 2 genes, pyk and gyrA, and the combination of 3 genes, pyk, gyrA, and recA. This study provided genes and gene combinations which were validated as suitable internal controls for gene expression studies, especially those on the mechanism of biofilm formation in B. velezensis or even other Bacillus spp. KEY POINTS: • Reference genes is necessary for gene expression study in biofilm formation of Bacillus velezensis • Pyk and 2 gene combinations were selected and validated from 21 common used genes • Expression of key genes in biofilm formation was normalized with the selected internal controls.

Unraveling Fe(II)-Oxidizing Mechanisms in a Facultative Fe(II) Oxidizer, Sideroxydans lithotrophicus Strain ES-1, via Culturing, Transcriptomics, and Reverse Transcription-Quantitative PCR

Sideroxydans lithotrophicus ES-1 grows autotrophically either by Fe(II) oxidation or by thiosulfate oxidation, in contrast to most other isolates of neutrophilic Fe(II)-oxidizing bacteria (FeOB). This provides a unique opportunity to explore the physiology of a facultative FeOB and constrain the genes specific to Fe(II) oxidation. We compared the growth of S. lithotrophicus ES-1 on Fe(II), thiosulfate, and both substrates together. While initial growth rates were similar, thiosulfate-grown cultures had higher yield with or without Fe(II) present, which may give ES-1 an advantage over obligate FeOB. To investigate the Fe(II) and S oxidation pathways, we conducted transcriptomics experiments, validated with reverse transcription-quantitative PCR (RT-qPCR). We explored the long-term gene expression response at different growth phases (over days to a week) and expression changes during a short-term switch from thiosulfate to Fe(II) (90 min). The dsr and sox sulfur oxidation genes were upregulated in thiosulfate cultures. The Fe(II) oxidase gene cyc2 was among the top expressed genes during both Fe(II) and thiosulfate oxidation, and addition of Fe(II) to thiosulfate-grown cells caused an increase in cyc2 expression. These results support the role of Cyc2 as the Fe(II) oxidase and suggest that ES-1 maintains readiness to oxidize Fe(II), even in the absence of Fe(II). We used gene expression profiles to further constrain the ES-1 Fe(II) oxidation pathway. Notably, among the most highly upregulated genes during Fe(II) oxidation were genes for alternative complex III, reverse electron transport, and carbon fixation. This implies a direct connection between Fe(II) oxidation and carbon fixation, suggesting that CO2 is an important electron sink for Fe(II) oxidation. IMPORTANCE Neutrophilic FeOB are increasingly observed in various environments, but knowledge of their ecophysiology and Fe(II) oxidation mechanisms is still relatively limited. Sideroxydans isolates are widely observed in aquifers, wetlands, and sediments, and genome analysis suggests metabolic flexibility contributes to their success. The type strain ES-1 is unusual among neutrophilic FeOB isolates, as it can grow on either Fe(II) or a non-Fe(II) substrate, thiosulfate. Almost all our knowledge of neutrophilic Fe(II) oxidation pathways comes from genome analyses, with some work on metatranscriptomes. This study used culture-based experiments to test the genes specific to Fe(II) oxidation in a facultative FeOB and refine our model of the Fe(II) oxidation pathway. We gained insight into how facultative FeOB like ES-1 connect Fe, S, and C biogeochemical cycling in the environment and suggest a multigene indicator would improve understanding of Fe(II) oxidation activity in environments with facultative FeOB.

Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea

Sulfate-coupled anaerobic oxidation of methane (AOM) is a major methane sink in marine sediments. Multiple lineages of anaerobic methanotrophic archaea (ANME) often coexist in sediments and catalyze this process syntrophically with sulfate-reducing bacteria (SRB), but the potential differences in ANME ecophysiology and mechanisms of syntrophy remain unresolved. A humic acid analog, anthraquinone 2,6-disulfonate (AQDS), could decouple archaeal methanotrophy from bacterial sulfate reduction and serve as the terminal electron acceptor for AOM (AQDS-coupled AOM). Here in sediment microcosm experiments, we examined variations in physiological response between two co-occurring ANME-2 families (ANME-2a and ANME-2c) and tested the hypothesis of sulfate respiration by ANME-2. Sulfate concentrations as low as 100 µM increased AQDS-coupled AOM nearly 2-fold matching the rates of sulfate-coupled AOM. However, the SRB partners remained inactive in microcosms with sulfate and AQDS and neither ANME-2 families respired sulfate, as shown by their cellular sulfur contents and anabolic activities measured using nanoscale secondary ion mass spectrometry. ANME-2a anabolic activity was significantly higher than ANME-2c, suggesting that ANME-2a was primarily responsible for the observed sulfate stimulation of AQDS-coupled AOM. Comparative transcriptomics showed significant upregulation of ANME-2a transcripts linked to multiple ABC transporters and downregulation of central carbon metabolism during AQDS-coupled AOM compared to sulfate-coupled AOM. Surprisingly, genes involved in sulfur anabolism were not differentially expressed during AQDS-coupled AOM with and without sulfate amendment. Collectively, this data indicates that ANME-2 archaea are incapable of respiring sulfate, but sulfate availability differentially stimulates the growth and AOM activity of different ANME lineages.

Identification of catabolic pathway for 1-deoxy-D-sorbitol in Bacillus licheniformis

1-Deoxy-D-sorbitol, the 1-deoxy analogue of D-sorbitol, has been detected in human urine as well as in natural herbs and spices. Although there are sporadic reports about 1-deoxy-D-sorbitol dehydrogenase, the complete catabolic pathway of 1-deoxy-D-sorbitol remains unsolved. Informed by the promiscuous activities of fructose-6-phosphate aldolase (FSA) which is involved in the sorbitol (glucitol) utilization (gut) operon and guided by the large scale bioinformatics analysis, we predicted and then experimentally verified the gut operon encoded by Bacillus licheniformis ATCC14580 is responsible for the catabolism of both D-sorbitol and 1-deoxy-D-sorbitol by in vitro activity assays of pathway enzymes, in vivo growth phenotypes, and transcriptomic studies. Moreover, the phylogenetic distribution analysis suggests that the D-sorbitol and 1-deoxy-D-sorbitol catabolic gene cluster is mostly conserved in members of Firmicutes phylum.

Transcriptomic studies of solventogenic clostridia, Clostridium acetobutylicum and Clostridium beijerinckii

Solventogenic clostridia are not a strictly defined group within the genus Clostridium but its representatives share some common features, i.e. they are anaerobic, non-pathogenic, non-toxinogenic and endospore forming bacteria. Their main metabolite is typically 1-butanol but depending on species and culture conditions, they can form other metabolites such as acetone, isopropanol, ethanol, butyric, lactic and acetic acids, and hydrogen. Although these organisms were previously used for the industrial production of solvents, they later fell into disuse, being replaced by more efficient chemical production. A return to a more biological production of solvents therefore requires a thorough understanding of clostridial metabolism. Transcriptome analysis, which reflects the involvement of individual genes in all cellular processes within a population, at any given (sampling) moment, is a valuable tool for gaining a deeper insight into clostridial life. In this review, we describe techniques to study transcription, summarize the evolution of these techniques and compare methods for data processing and visualization of solventogenic clostridia, particularly the species Clostridium acetobutylicum and Clostridium beijerinckii. Individual approaches for evaluating transcriptomic data are compared and their contributions to advancements in the field are assessed. Moreover, utilization of transcriptomic data for reconstruction of computational clostridial metabolic models is considered and particular models are described. Transcriptional changes in glucose transport, central carbon metabolism, the sporulation cycle, butanol and butyrate stress responses, the influence of lignocellulose-derived inhibitors on growth and solvent production, and other respective topics, are addressed and common trends are highlighted.

Terrestrial-type nitrogen-fixing symbiosis between seagrass and a marine bacterium

Symbiotic N2-fixing microorganisms have a crucial role in the assimilation of nitrogen by eukaryotes in nitrogen-limited environments1-3. Particularly among land plants, N2-fixing symbionts occur in a variety of distantly related plant lineages and often involve an intimate association between host and symbiont2,4. Descriptions of such intimate symbioses are lacking for seagrasses, which evolved around 100 million years ago from terrestrial flowering plants that migrated back to the sea5. Here we describe an N2-fixing symbiont, 'Candidatus Celerinatantimonas neptuna', that lives inside seagrass root tissue, where it provides ammonia and amino acids to its host in exchange for sugars. As such, this symbiosis is reminiscent of terrestrial N2-fixing plant symbioses. The symbiosis between Ca. C. neptuna and its host Posidonia oceanica enables highly productive seagrass meadows to thrive in the nitrogen-limited Mediterranean Sea. Relatives of Ca. C. neptuna occur worldwide in coastal ecosystems, in which they may form similar symbioses with other seagrasses and saltmarsh plants. Just like N2-fixing microorganisms might have aided the colonization of nitrogen-poor soils by early land plants6, the ancestors of Ca. C. neptuna and its relatives probably enabled flowering plants to invade nitrogen-poor marine habitats, where they formed extremely efficient blue carbon ecosystems7.

Impact of Phage CDHS-1 on the Transcription, Physiology and Pathogenicity of a Clostridioides difficile Ribotype 027 Strain, R20291

All known Clostridioides difficile phages encode integrases rendering them potentially able to lyse or lysogenise bacterial strains. Here, we observed the infection of the siphovirus, CDHS-1 on a ribotype 027 strain, R20291 and determined the phage and bacterial gene expression profiles, and impacts of phage infection on bacterial physiology and pathogenicity. Using RNA-seq and RT-qPCR we analysed transcriptomic changes during early, mid-log and late phases of phage replication at an MOI of 10. The phage has a 20 min latent period, takes 80 min to lyse cells and a burst size of ~37. All phage genes are highly expressed during at least one time point. The Cro/C1-transcriptional regulator, ssDNA binding protein and helicase are expressed early, the holin is expressed during the mid-log phase and structural proteins are expressed from mid-log to late phase. Most bacterial genes, particularly the metabolism and toxin production/regulatory genes, were downregulated from early phage replication. Phage-resistant strains and lysogens showed reduced virulence during Galleria mellonella colonization as ascertained by the larval survival and expression of growth (10), reproduction (2) and infection (2) marker genes. These data suggest that phage infection both reduces colonization and negatively impacts bacterial pathogenicity, providing encouraging data to support the development of this phage for therapy to treat C. difficile infection.

Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes

Lesions to DNA compromise chromosome integrity, posing a direct threat to cell survival. The bacterial SOS response is a widespread transcriptional regulatory mechanism to address DNA damage. This response is coordinated by the LexA transcriptional repressor, which controls genes involved in DNA repair, mutagenesis and cell-cycle control. To date, the SOS response has been characterized in most major bacterial groups, with the notable exception of the Bacteroidetes. No LexA homologs had been identified in this large, diverse and ecologically important phylum, suggesting that it lacked an inducible mechanism to address DNA damage. Here, we report the identification of a novel family of transcriptional repressors in the Bacteroidetes that orchestrate a canonical response to DNA damage in this phylum. These proteins belong to the S24 peptidase family, but are structurally different from LexA. Their N-terminal domain is most closely related to CI-type bacteriophage repressors, suggesting that they may have originated from phage lytic phase repressors. Given their role as SOS regulators, however, we propose to designate them as non-canonical LexA proteins. The identification of a new class of repressors orchestrating the SOS response illuminates long-standing questions regarding the origin and plasticity of this transcriptional network.

Soil organic matter is essential for colony growth in subterranean termites

Intrinsic dinitrogen (N₂) fixation by diazotrophic bacteria in termite hindguts has been considered an important pathway for nitrogen acquisition in termites. However, studies that supported this claim focused on measuring instant N₂ fixation rates and failed to address their relationship with termite colony growth and reproduction over time. We here argue that not all wood-feeding termites rely on symbiotic diazotrophic bacteria for colony growth. The present study looks at dietary nitrogen acquisition in a subterranean termite (Rhinotermitidae, Coptotermes). Young termite colonies reared with wood and nitrogen-rich organic soil developed faster, compared to those reared on wood and inorganic sand. More critically, further colony development was arrested if access to organic soil was removed. In addition, no difference of relative nitrogenase expression rates was found when comparing the hindguts of termites reared between the two conditions. We therefore propose that subterranean termite (Rhinotermitidae) colony growth is no longer restricted to metabolically expensive intrinsic N₂ fixation, as the relationship between diazotrophic bacteria and subterranean termites may primarily be trophic rather than symbiotic. Such reliance of Rhinotermitidae on soil microbial decomposition activity for optimal colony growth may also have had a critical mechanistic role in the initial emergence of Termitidae.

BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes

Microbial gene clusters encoding the biosynthesis of primary and secondary metabolites play key roles in shaping microbial ecosystems and driving microbiome-associated phenotypes. Although effective approaches exist to evaluate the metabolic potential of such bacteria through identification of these metabolic gene clusters in their genomes, no automated pipelines exist to profile the abundance and expression levels of such gene clusters in microbiome samples to generate hypotheses about their functional roles, and to find associations with phenotypes of interest. Here, we describe BiG-MAP, a bioinformatic tool to profile abundance and expression levels of gene clusters across metagenomic and metatranscriptomic data and evaluate their differential abundance and expression under different conditions. To illustrate its usefulness, we analyzed 96 metagenomic samples from healthy and caries-associated human oral microbiome samples and identified 252 gene clusters, including unreported ones, that were significantly more abundant in either phenotype. Among them, we found the muc operon, a gene cluster known to be associated with tooth decay. Additionally, we found a putative reuterin biosynthetic gene cluster from a Streptococcus strain to be enriched but not exclusively found in healthy samples; metabolomic data from the same samples showed masses with fragmentation patterns consistent with (poly)acrolein, which is known to spontaneously form from the products of the reuterin pathway and has been previously shown to inhibit pathogenic Streptococcus mutans strains. Thus, we show how BiG-MAP can be used to generate new hypotheses on potential drivers of microbiome-associated phenotypes and prioritize the experimental characterization of relevant gene clusters that may mediate them. IMPORTANCE Microbes play an increasingly recognized role in determining host-associated phenotypes by producing small molecules that interact with other microorganisms or host cells. The production of these molecules is often encoded in syntenic genomic regions, also known as gene clusters. With the increasing numbers of (multi)omics data sets that can help in understanding complex ecosystems at a much deeper level, there is a need to create tools that can automate the process of analyzing these gene clusters across omics data sets. This report presents a new software tool called BiG-MAP, which allows assessing gene cluster abundance and expression in microbiome samples using metagenomic and metatranscriptomic data. Here, we describe the tool and its functionalities, as well as its validation using a mock community. Finally, using an oral microbiome data set, we show how it can be used to generate hypotheses regarding the functional roles of gene clusters in mediating host phenotypes.

Can only one physiological trait determinate the adverse effect of green fluorescent protein (GFP) incorporation on Vibrio virulence?

Green fluorescent protein (GFP) has been used extensively for in situ animal studies that follow up bacterial infection under epifluorescence microscopy. It is assumed that GFP is acting as a "neutral" protein with no influence on the bacterial physiology. To verify this hypothesis, the virulence of Vibrio splendidus ME9, Vibrio anguillarum NB10, and their respective GFP-tagged strains ME9-GFP and NB10-GFP (transconjugants) was compared in vitro and tested in vivo towards blue mussel (Mytilus edulis) larvae. Results showed that the incorporation of GFP negatively impacted the growth and swimming motility of NB10 in vitro. Correspondingly, the mRNA levels of genes involved in bacterial swimming motility (flaA, flaE, and cheR) were significantly down-regulated in NB10-GFP. As for the strain ME9 on the other hand, GFP incorporation only had a negative effect on swimming motility. However, both the strains NB10-GFP and ME9-GFP showed almost the same virulence as their respective parental strain towards mussel larvae in vivo. Overall, the data presented here demonstrated that incorporation of GFP may cause modifications in cell physiology and highlight the importance of preliminary physiological tests to minimize the negative influence of GFP tagging when it is used to monitor the target localization. The study also supports the idea that the virulence of Vibrio species is determined by complex regulatory networks. Notwithstanding the change of a single physiological trait, especially growth or swimming motility, the GFP-tagged Vibrio strain can thus still be considered usable in studies mainly focusing on the virulence of the strain. KEY POINTS: • The effect of GFP incorporation on physiological trait of Vibrio strains. • The virulence in vibrios could be multifactorial. • The stable virulence of Vibrio strains after GFP incorporation.

Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS

Nitrate reduction coupled to Fe(II) oxidation (NRFO) has been recognized as an environmentally important microbial process in many freshwater ecosystems. However, well-characterized examples of autotrophic nitrate-reducing Fe(II)-oxidizing bacteria are rare, and their pathway of electron transfer as well as their interaction with flanking community members remain largely unknown. Here, we applied meta-omics (i.e., metagenomics, metatranscriptomics, and metaproteomics) to the nitrate-reducing Fe(II)-oxidizing enrichment culture KS growing under autotrophic or heterotrophic conditions and originating from freshwater sediment. We constructed four metagenome-assembled genomes with an estimated completeness of ≥95%, including the key players of NRFO in culture KS, identified as Gallionellaceae sp. and Rhodanobacter sp. The Gallionellaceae sp. and Rhodanobacter sp. transcripts and proteins likely involved in Fe(II) oxidation (e.g., mtoAB, cyc2, and mofA), denitrification (e.g., napGHI), and oxidative phosphorylation (e.g., respiratory chain complexes I to V) along with Gallionellaceae sp. transcripts and proteins for carbon fixation (e.g., rbcL) were detected. Overall, our results indicate that in culture KS, the Gallionellaceae sp. and Rhodanobacter sp. are interdependent: while Gallionellaceae sp. fixes CO2 and provides organic compounds for Rhodanobacter sp., Rhodanobacter sp. likely detoxifies NO through NO reduction and completes denitrification, which cannot be performed by Gallionellaceae sp. alone. Additionally, the transcripts and partial proteins of cbb3- and aa3-type cytochrome c suggest the possibility for a microaerophilic lifestyle of the Gallionellaceae sp., yet culture KS grows under anoxic conditions. Our findings demonstrate that autotrophic NRFO is performed through cooperation among denitrifying and Fe(II)-oxidizing bacteria, which might resemble microbial interactions in freshwater environments. IMPORTANCE Nitrate-reducing Fe(II)-oxidizing bacteria are widespread in the environment, contribute to nitrate removal, and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing Fe(II)-oxidizing bacteria is rarely investigated and not fully understood. The most prominent model system for this type of study is the enrichment culture KS. To gain insights into the metabolism of nitrate reduction coupled to Fe(II) oxidation in the absence of organic carbon and oxygen, we performed metagenomic, metatranscriptomic, and metaproteomic analyses of culture KS and identified Gallionellaceae sp. and Rhodanobacter sp. as interdependent key Fe(II) oxidizers in culture KS. Our work demonstrates that autotrophic nitrate reduction coupled to Fe(II) oxidation is not performed by an individual strain but is a cooperation of at least two members of the bacterial community in culture KS. These findings serve as a foundation for our understanding of nitrate-reducing Fe(II)-oxidizing bacteria in the environment.