Conformational plasticity of SpyCas9 induced by AcrIIA4 and AcrIIA2: Insights from molecular dynamics simulation

CRISPR-Cas9 systems constitute bacterial adaptive immune systems that protect against phage infections. Bacteriophages encode anti-CRISPR proteins (Acrs) that mitigate the bacterial immune response. However, the structural basis for their inhibitory actions from a molecular perspective remains elusive. In this study, through microsecond atomistic molecular dynamics simulations, we demonstrated the remarkable flexibility of Streptococcus pyogenes Cas9 (SpyCas9) and its conformational adaptability during interactions with AcrIIA4 and AcrIIA2. Specifically, we demonstrated that the binding of AcrIIA4 and AcrIIA2 to SpyCas9 induces a conformational rearrangement that causes spatial separation between the nuclease and cleavage sites, thus making the endonuclease inactive. This separation disrupts the transmission of signals between the protospacer adjacent motif recognition and nuclease domains, thereby impeding the efficient processing of double-stranded DNA. The simulation also reveals that AcrIIA4 and AcrIIA2 cause different structural variations of SpyCas9. Our research illuminates the precise mechanisms underlying the suppression of SpyCas9 by AcrIIA4 and AcrIIA2, thus presenting new possibilities for controlling genome editing with higher accuracy.

Regulatory role of the Cpx ESR in bacterial behaviours

The envelope demarcates the boundary between bacterial cell and its environment, providing a place for bacteria to transport nutrients and excrete metabolic waste, while buffering external environmental stress. Envelope stress responses (ESRs) are important tools for bacteria to sense and repair envelope damage. In this review, we discussed evidence that indicates the important role of the Cpx ESR in pathogen-host interactions, including environmental stress sensing and responses, modulation of bacterial virulence, antimicrobial resistance, and inter-kingdom signaling.

Structure-guided identification and characterization of potent inhibitors targeting PhoP and MtrA to combat mycobacteria

Mycobacteria are causative agents of tuberculosis (TB), which is a global health concern. Drug-resistant TB strains are rapidly emerging, thereby necessitating the urgent development of new drugs. Two-component signal transduction systems (TCSs) are signaling pathways involved in the regulation of various bacterial behaviors and responses to environmental stimuli. Applying specific inhibitors of TCSs can disrupt bacterial signaling, growth, and virulence, and can help combat drug-resistant TB. We conducted a comprehensive pharmacophore-based inhibitor screening and biochemical and biophysical examinations to identify, characterize, and validate potential inhibitors targeting the response regulators PhoP and MtrA of mycobacteria. The constructed pharmacophore model Phar-PR-n4 identified effective inhibitors of formation of the PhoP-DNA complex: ST132 (IC50 = 29 ± 1.6 µM) and ST166 (IC50 = 18 ± 1.3 µM). ST166 (KD = 18.4 ± 4.3 μM) and ST132 (KD = 14.5 ± 0.1 μM) strongly targeted PhoP in a slow-on, slow-off manner. The inhibitory potency and binding affinity of ST166 and ST132 for MtrAC were comparable to those of PhoP. Structural analyses and molecular dynamics simulations revealed that ST166 and ST132 mainly interact with the α8-helix and C-terminal β-hairpin of PhoP, with functionally essential residue hotspots for structure-based inhibitor optimization. Moreover, ST166 has in vitro antibacterial activity against Macrobacterium marinum. Thus, ST166, with its characteristic 1,2,5,6-tetrathiocane and terminal sulphonic groups, has excellent potential as a candidate for the development of novel antimicrobial agents to combat pathogenic mycobacteria.

Pseudomonas aeruginosa quorum sensing and biofilm attenuation by a di-hydroxy derivative of piperlongumine (PL-18)

Bacterial communication, Quorum Sensing (QS), is a target against virulence and prevention of antibiotic-resistant infections. 16 derivatives of Piperlongumine (PL), an amide alkaloid from Piper longum L., were screened for QS inhibition. PL-18 had the best QSI activity. PL-18 inhibited the lasR-lasI, rhlR-rhlI, and pqs QS systems of Pseudomonas aeruginosa. PL-18 inhibited pyocyanin and rhamnolipids that are QS-controlled virulence elements. Iron is an essential element for pathogenicity, biofilm formation and resilience in harsh environments, its uptake was inhibited by PL-18. Pl-18 significantly reduced the biofilm biovolume including in established biofilms. PL-18-coated silicon tubes significantly inhibited biofilm formation. The transcriptome study of treated P. aeruginosa showed that PL-18 indeed reduced the expression of QS and iron homeostasis related genes, and up regulated sulfur metabolism related genes. Altogether, PL-18 inhibits QS, virulence, iron uptake, and biofilm formation. Thus, PL-18 should be further developed against bacterial infection, antibiotic resistance, and biofilm formation.

Adaptive laboratory evolution for improved tolerance of vitamin K in Bacillus subtilis

Menaquinone-7 (MK-7), a subtype of vitamin K2 (VK2), assumes crucial roles in coagulation function, calcium homeostasis, and respiratory chain transmission. The production of MK-7 via microbial fermentation boasts mild technological conditions and high biocompatibility. Nevertheless, the redox activity of MK-7 imposes constraints on its excessive accumulation in microorganisms. To address this predicament, an adaptive laboratory evolution (ALE) protocol was implemented in Bacillus subtilis BS011, utilizing vitamin K3 (VK3) as a structural analog of MK-7. The resulting strain, BS012, exhibited heightened tolerance to high VK3 concentrations and demonstrated substantial enhancements in biofilm formation and total antioxidant capacity (T-AOC) when compared to BS011. Furthermore, MK-7 production in BS012 exceeded that of BS011 by 76% and 22% under static and shaking cultivation conditions, respectively. The molecular basis underlying the superior performance of BS012 was elucidated through genome and transcriptome analyses, encompassing observations of alterations in cell morphology, variations in central carbon and nitrogen metabolism, spore formation, and antioxidant systems. In summation, ALE technology can notably enhance the tolerance of B. subtilis to VK and increase MK-7 production, thus offering a theoretical framework for the microbial fermentation production of other VK2 subtypes. Additionally, the evolved strain BS012 can be developed for integration into probiotic formulations within the food industry to maintain intestinal flora homeostasis, mitigate osteoporosis risk, and reduce the incidence of cardiovascular disease. KEY POINTS: • Bacillus subtilis was evolved for improved vitamin K tolerance and menaquinone-7 (MK-7) production • Evolved strains formed wrinkled biofilms and elongated almost twofold in length • Evolved strains induced sporulation to improve tolerance when carbon was limited.

A c-di-GMP binding effector STM0435 modulates flagellar motility and pathogenicity in Salmonella

Flagella play a crucial role in the invasion process of Salmonella and function as a significant antigen that triggers host pyroptosis. Regulation of flagellar biogenesis is essential for both pathogenicity and immune escape of Salmonella. We identified the conserved and unknown function protein STM0435 as a new flagellar regulator. The ∆stm0435 strain exhibited higher pathogenicity in both cellular and animal infection experiments than the wild-type Salmonella. Proteomic and transcriptomic analyses demonstrated dramatic increases in almost all flagellar genes in the ∆stm0435 strain compared to wild-type Salmonella. In a surface plasmon resonance assay, purified STM0435 protein-bound c-di-GMP had an affinity of ~8.383 µM. The crystal structures of apo-STM0435 and STM0435&c-di-GMP complex were determined. Structural analysis revealed that R33, R137, and D138 of STM0435 were essential for c-di-GMP binding. A Salmonella with STM1987 (GGDEF protein) or STM4264 (EAL protein) overexpression exhibits completely different motility behaviours, indicating that the binding of c-di-GMP to STM0435 promotes its inhibitory effect on Salmonella flagellar biogenesis.

Ser/Thr protein kinase Stk1 phosphorylates the key transcriptional regulator AlgR to modulate virulence and resistance in Pseudomonas aeruginosa

Pseudomonas aeruginosa is one of the leading causes of nosocomial infections worldwide and has emerged as a serious public health threat, due in large part to its multiple virulence factors and remarkable resistance capabilities. Stk1, a eukaryotic-type Ser/Thr protein kinase, has been shown in our previous work to be involved in the regulation of several signalling pathways and biological processes. Here, we demonstrate that deletion of stk1 leads to alterations in several virulence- and resistance-related physiological functions, including reduced pyocyanin and pyoverdine production, attenuated twitching motility, and enhanced biofilm production, extracellular polysaccharide secretion, and antibiotic resistance. Moreover, we identified AlgR, an important transcriptional regulator, as a substrate for Stk1, with its phosphorylation at the Ser143 site catalysed by Stk1. Intriguingly, both the deletion of stk1 and the mutation of Ser143 of AlgR to Ala result in similar changes in the above-mentioned physiological functions. Furthermore, assays of algR expression in these strains suggest that changes in the phosphorylation state of AlgR, rather than its expression level, underlie changes in these physiological functions. These findings uncover Stk1-mediated phosphorylation of AlgR as an important mechanism for regulating virulence and resistance in P. aeruginosa.

Bacterial extracellular vesicle: A non-negligible component in biofilm life cycle and challenges in biofilm treatments

Bacterial biofilms, especially those formed by pathogens, have been increasingly impacting human health. Bacterial extracellular vesicle (bEV), a kind of spherical membranous structure released by bacteria, has not only been reported to be a component of the biofilm matrix but also plays a non-negligible role in the biofilm life cycle. Nevertheless, a comprehensive overview of the bEVs functions in biofilms remains elusive. In this review, we summarize the biogenesis and distinctive features characterizing bEVs, and consolidate the current literature on their functions and proposed mechanisms in the biofilm life cycle. Furthermore, we emphasize the formidable challenges associated with vesicle interference in biofilm treatments. The primary objective of this review is to raise awareness regarding the functions of bEVs in the biofilm life cycle and lay the groundwork for the development of novel therapeutic strategies to control or even eliminate bacterial biofilms.

New bacteriophage-derived lysins, LysJ and LysF, with the potential to control Bacillus anthracis

Bacillus anthracis is an etiological agent of anthrax, a severe zoonotic disease that can be transmitted to people and cause high mortalities. Bacteriophages and their lytic enzymes, endolysins, have potential therapeutic value in treating infections caused by this bacterium as alternatives or complements to antibiotic therapy. They can also be used to identify and detect B. anthracis. Endolysins of two B. anthracis Wbetavirus phages, J5a and F16Ba which were described by us recently, differ significantly from the best-known B. anthracis phage endolysin PlyG from Wbetavirus genus bacteriophage Gamma and a few other Wbetavirus genus phages. They are larger than PlyG (351 vs. 233 amino acid residues), contain a signal peptide at their N-termini, and, by prediction, have a different fold of cell binding domain suggesting different structural basis of cell epitope recognition. We purified in a soluble form the modified versions of these endolysins, designated by us LysJ and LysF, respectively, and depleted of signal peptides. Both modified endolysins could lyse the B. anthracis cell wall in zymogram assays. Their activity against the living cells of B. anthracis and other species of Bacillus genus was tested by spotting on the layers of bacteria in soft agar and by assessing the reduction of optical density of bacterial suspensions. Both methods proved the effectiveness of LysJ and LysF in killing the anthrax bacilli, although the results obtained by each method differed. Additionally, the lytic efficiency of both proteins was different, which apparently correlates with differences in their amino acid sequence. KEY POINTS: • LysJ and LysF are B. anthracis-targeting lysins differing from lysins studied so far • LysJ and LysF could be overproduced in E. coli in soluble and active forms • LysJ and LysF are active in killing cells of B. anthracis virulent strains.

Impact of metal ions on PMS/Cl- disinfection efficacy: Enhancing or impeding microbial inactivation?

Peroxymonosulfate (PMS) is an eco-friendly disinfectant gaining attention. This study examined the influence of metal ions (Co(II), Cu(II), Fe(II)) on PMS disinfection with chloride ions (Cl-) against waterborne microorganisms, encompassing both bacteria and fungal spores. The findings elucidated that metal ions augment the inactivation of bacteria in the PMS/Cl- system while concurrently impeding the inactivation of fungal spores. Specifically, the PMS/Co(II)/Cl- process increased E. coli inactivation rates by 2.25 and 2.75 times compared to PMS/Co(II) and PMS/Cl-, respectively. Conversely, PMS/Me(II)/Cl- generally exhibited a diminished inactivation capacity against the three fungal spores compared to PMS/Cl-, albeit surpassing the efficacy of PMS/Me(II). For instance, the inactivation levels of A. niger by PMS/Cl-, PMS/Cu(II)/Cl-, and PMS/Cu(II) are 4.47-log, 1.92-log, and 0.11-log, respectively. Notably, fungal spores demonstrated a substantially higher resistance to disinfectants compared to bacteria. Differences in microbial susceptibility were linked to cell wall structure, composition, antioxidant defenses, and reactive species generation, such as hydroxyl radicals (•OH), sulfate radicals (SO4•-), and reactive chlorine species (RCS). This study demonstrated the novel and unique phenomenon of metal ions' dual role in modulating the PMS/Cl- disinfection process, which has not been reported before and has important implications for the field of water treatment.

Autotrophic adaptive laboratory evolution of the acetogen Clostridium autoethanogenum delivers the gas-fermenting strain LAbrini with superior growth, products, and robustness

Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for bioreactor fermentations. In this work, we used three different and independent adaptive laboratory evolution (ALE) strategies to evolve the wild-type C. autoethanogenum to grow faster, without yeast extract and to be robust in operating continuous bioreactor cultures. Multiple evolved strains with improved phenotypes were isolated on minimal media with one strain, named "LAbrini", exhibiting superior performance regarding the maximum specific growth rate, product profile, and robustness in continuous cultures. Whole-genome sequencing of the evolved strains identified 25 mutations. Of particular interest are two genes that acquired seven different mutations across the three ALE strategies, potentially as a result of convergent evolution. Reverse genetic engineering of mutations in potentially sporulation-related genes CLAU_3129 (spo0A) and CLAU_1957 recovered all three superior features of our ALE strains through triggering significant proteomic rearrangements. This work provides a robust C. autoethanogenum strain "LAbrini" to accelerate phenotyping and genetic engineering and to better understand acetogen metabolism.

Methane oxidation driven by multiple electron acceptors in the water level fluctuation zone of the Three Gorges Reservoir area, China

Water level fluctuations in China's Three Gorges Reservoir (TGR) area are typical of many reservoirs and significantly impact water level fluctuation zones (WLFZ), including upstream rivers. Understanding methane oxidation in the TGR-WLFZ is crucial for evaluating the impact of large-scale reservoir construction on global climate change. In this study, we investigated methane oxidation rates in the TGR-WLFZ, focusing on periods of drying and flooding. The highest methane oxidation rates were observed during the drying period, ranging from 35.69 to 56.32 nmol/(g soil)/d, while the lowest rates were recorded during the flooding period, at 11.58 to 11.98 nmol/(g soil)/d, in lab-scale simulated columns. Using 13CH4 labeling experiments, we measured CH4 oxidation potentials for aerobic methane oxidation (AMO) using oxygen and anaerobic oxidation of methane (AOM) using nitrite, nitrate, sulfate, ferric iron, and manganese oxide as electron acceptors at varying concentrations. AMO was the dominant process across all experiments, with potentials ranging from 145.71 to 180.77 nmol 13CO2/(g soil)/d. For AOM, metal-dependent oxidation, particularly with Fe (III) and Mn(IV), was predominant (12.64-17.59 and 3.91-12.69 nmol 13CO2/(g soil)/d, respectively), followed by nitrite and nitrate-dependent pathways (1.49-9.10 nmol 13CO2/(g soil)/d). Sulfate-dependent AOM was limited (1.33-3.27 nmol 13CO2/(g soil)/d). Metagenomic analysis identified key microorganisms responsible for AMO, such as unclassified_f_Methylobacteriaeae and Methylobacterium sp., and for AOM are Ca. Methylomirabilis oxyfera, Ca. Methanoperedens nitroreducens and Ca. Methylomirabilis sp. Complete functional genes and enzymes for the methane oxidation and reverse methanogenesis pathways were obtained in each hydrological period, with the highest content during the drying period and the lowest during flooding. Our study shows that reservoirs, traditionally considered significant sources of methane, may also act as methane sinks. This finding raises new questions: How do different methane oxidation pathways respond to water level fluctuations in reservoirs, and are some pathways more resilient to changes in hydrological conditions?

A landscape limnology approach to assessing controls on soluble reactive phosphorus in sediment porewater and internal loading risk

Sediment nutrients can be mobilized to overlying water via internal loading, which can be important to aquatic productivity. Using data from 143 Canadian lakes, we show high (~2400-fold) variation of soluble reactive phosphorus (SRP) concentrations in surficial sediment porewater, with results suggesting internal phosphorus loading (IPL) is also likely to vary widely. Consistent with past work at smaller scales, we show that lake depth, pH, trophic status, and bulk sediment Al:P and Fe:P influence porewater SRP, and IPL. Median porewater SRP concentration in lakes with high Al:P (molar ratios >10) were 4.8-fold smaller than in lakes with lower Al:P. In lakes where bulk sedimentary Fe:P molar ratios were >10 porewater SRP was 3.9-fold lower than in lakes with lower Fe:P. High pH (>7.8), along with hyper-eutrophic lakes were associated with higher porewater SRP. Finally, shallow lakes (<4 m depth) had median porewater SRP concentration 6-fold higher than deep lakes (>9 m depth). Important regional differences emerged, linked to regional variation in pH, soils, lake depth and trophic status, and paralleling areas of poor water quality. For example, median porewater SRP in lakes from the Boreal Plains and Prairies ecozones (dominated by Chernozems/Mollisols) was 64-fold and 44-fold higher than in the Boreal Shield (dominated by Podzols/Spodosols) (respectively), although we note that IPL risk is likely important across many ecozones. Using national data, we found in-lake measurements (particularly pH, and salinity) showed strong capacity in predicting porewater SRP (explaining 60-72 % of the variance in the data). Importantly, watershed predictors showed good predictive power, explaining ~50 % of variance in porewater SRP using variables including soil types, and % agriculture. Porewater SRP can be predicted with reasonable accuracy using easily measured variables, as can estimates of internal phosphorus loading, suggesting that landscape limnology holds strong potential in helping to inform lake management by informing understanding of in-lake nutrient sources.

The sewer advances: How to select eco-friendly pipe materials for environmental protection

Sewer pipe materials exhibit diverse inner-surface features, which can affect the attachment of biofilm and influence microbial metabolic processes. To investigate the role of the type of pipe material on the composition and metabolic capabilities of the adhering microorganisms, three sets of urban sewers (High-Density Polyethylene Pipe (HDPE), Ductile Iron Pipe (DIP), and Concrete Pipe (CP)) were constructed. Measurements of biofilm thickness and environmental factors revealed that the thickest biofilm in CP pipes reached 2000 μm, with ORP values as low as -325 mV, indicating a more suitable anaerobic microbial habitat. High-throughput sequencing showed similar relative abundances of genera related to carbon and sulfur metabolism in the DIP and CP pipes, whereas HDPE exhibited only half the relative abundance compared to that found in the other pipes. To explore the impact of pipe materials on the mechanisms of microbial response, a metagenomic approach was used to investigate the biological transformation of carbon and sulfur in wastewater. The annotations of the crucial enzyme-encoding genes related to methyl coenzyme M and sulfite reductase in DIP and CP were 50 and 110, respectively, whereas HDPE exhibited lower counts (25 and 70, respectively). This resulted in significantly lower carbon and sulfur metabolism capabilities in the HDPE biofilm than in the other two pipes. The stability of wastewater quality during the transmission process in HDPE pipes reduces the metabolic generation of toxic and harmful gases within the pipes, favoring the preservation of carbon sources for sewer systems. This study reveals the variations in carbon and sulfur metabolism in wastewater pipe systems influenced by pipe materials and provides insights for designing future sewers.

Evolution of phosphate scouting in the terrestrial biosphere

Chemistry assigns phosphorus and its most oxidized form, inorganic phosphate, unique roles for propelling bioenergetics and metabolism in all domains of life, possibly since its very origin on prebiotic Earth. For plants, access to the vital mineral nutrient profoundly affects growth, development and vigour, thus constraining net primary productivity in natural ecosystems and crop production in modern agriculture. Unlike other major biogenic elements, the low abundance and uneven distribution of phosphate in Earth's crust result from the peculiarities of phosphorus cosmochemistry and geochemistry. Here, we trace the chemical evolution of the element, the geochemical phosphorus cycle and its acceleration during Earth's history until the present (Anthropocene) as well as during the evolution and rise of terrestrial plants. We highlight the chemical and biological processes of phosphate mobilization and acquisition, first evolved in bacteria, refined in fungi and algae and expanded into powerful phosphate-prospecting strategies during land plant colonization. Furthermore, we review the evolution of the genetic and molecular networks from bacteria to terrestrial plants, which monitor intracellular and extracellular phosphate availabilities and coordinate the appropriate responses and adjustments to fluctuating phosphate supply. Lastly, we discuss the modern global phosphorus cycle deranged by human activity and the challenges imposed ahead. This article is part of the theme issue 'Evolution and diversity of plant metabolism'.

Applications of ancestral sequence reconstruction for understanding the evolution of plant specialized metabolism

Studies of enzymes in modern-day plants have documented the diversity of metabolic activities retained by species today but only provide limited insight into how those properties evolved. Ancestral sequence reconstruction (ASR) is an approach that provides statistical estimates of ancient plant enzyme sequences which can then be resurrected to test hypotheses about the evolution of catalytic activities and pathway assembly. Here, I review the insights that have been obtained using ASR to study plant metabolism and highlight important methodological aspects. Overall, studies of resurrected plant enzymes show that (i) exaptation is widespread such that even low or undetectable levels of ancestral activity with a substrate can later become the apparent primary activity of descendant enzymes, (ii) intramolecular epistasis may or may not limit evolutionary paths towards catalytic or substrate preference switches, and (iii) ancient pathway flux often differs from modern-day metabolic networks. These and other insights gained from ASR would not have been possible using only modern-day sequences. Future ASR studies characterizing entire ancestral metabolic networks as well as those that link ancient structures with enzymatic properties should continue to provide novel insights into how the chemical diversity of plants evolved. This article is part of the theme issue 'The evolution of plant metabolism'.

Evolution of plant metabolism: the state-of-the-art

Immense chemical diversity is one of the hallmark features of plants. This chemo-diversity is mainly underpinned by a highly complex and biodiverse biochemical machinery. Plant metabolic enzymes originated and were inherited from their eukaryotic and prokaryotic ancestors and further diversified by the unprecedentedly high rates of gene duplication and functionalization experienced in land plants. Unlike prokaryotic microbes, which display frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced relatively few gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner using existing networks as a starting point and under various evolutionary constraints. That said, until recently, the evolution of only a handful of metabolic traits had been extensively investigated and as such, the evolution of metabolism has received a fraction of the attention of, the evolution of development, for example. Advances in metabolomics and next-generation sequencing have, however, recently led to a deeper understanding of how a wide range of plant primary and specialized (secondary) metabolic pathways have evolved both as a consequence of natural selection and of domestication and crop improvement processes. This article is part of the theme issue 'The evolution of plant metabolism'.

Harmonizing soil restoration and microbial diversity: Insights from a Two-Year field experiment with Sedum-Rice rotation systems

Phytoremediation coupled with agroproduction (PCA) model contributes to sustainable agriculture and environmental management. This study investigated the impact of continuous cropping early/late season rice (RR) and Sedum alfredii-rice rotation (SR) on soil physical and chemical properties, as well as their relationships with soil microbial community. In 2022, SR treatment significantly increased pH value and organic matter content by 7 % and 17 %, respectively, compared to the levels in 2020, while RR treatment showed no change. RR treatment resulted in a significant decrease in soil concentrations of Ca, Mg, and K by 18.42 %, 29.01 %, and 7.77 %, respectively. Furthermore, SR treatment saw reductions of 29.62 % in total Cd and 38.30 % in DTPA extractable Cd in the soil. Over the two years, both treatments notably influenced the diversity, structure, and network of the rhizosphere bacterial and fungal communities, which are crucial for nutrient cycling and plant health. Notably, SR treatment exhibited a more complex network compared to RR, suggesting a greater impact on the interconnected systems. Therefore, these findings highlight the potential of Sedum rotation system to rehabilitate contaminated soils while supporting agricultural practices, which is essential for food security and environmental sustainability. This research direction holds promise for future exploration and application in the fields of phytoremediation and agroecology.

A critical review of Mnammox coupled with the NDMO for innovative nitrogen removal

In the context of increasing global nitrogen pollution, traditional biological nitrogen removal technologies like nitrification and denitrification are hindered by high energy consumption. Additionally, the deployment of anaerobic ammonium oxidation (Anammox) technology is constrained due to the slow growth rate of Anammox bacteria and there is a bottleneck in nitrogen removal efficiency. To overcome these technical bottlenecks, researchers have discovered a revolutionary nitrogen removal technology that cleverly combines the redox cycling of manganese with nitrification and denitrification reactions. In this new process, manganese dependent anaerobic ammonium oxidation (Mnammox) bacteria can convert NH4+ to N2 under anaerobic conditions, while nitrate/nitrite dependent manganese oxidation (NDMO) bacteria use NO3-/NO2- as electron acceptors to oxidize Mn2+ to Mn4+. Mn4+ acts as an electron acceptor in Mnammox reaction, thereby realizing the autotrophic nitrogen removal process. This innovative method not only simplifies the steps of biological denitrification, but also significantly reduces the consumption of oxygen and organic carbon, providing a more efficient and environmentally friendly solution to the problem of nitrogen pollution. The article initially provides a concise overview of prevalent nitrogen removal technologies and the application of manganese in these processes, and discusses the role of manganese in biogeochemical cycles, including its discovery, mechanism of action, microbial communities involved, and its impact on these key factors in the process. Subsequently, metabolic principles, benefits, advantages, and environmental considerations of Mnammox coupled with the NDMO process are analyzed in detail. Finally, this article summarizes the shortcomings of current research and looks forward to future research directions. The goal of this article is to provide a valuable reference for researchers to fully understand the application of manganese in nitrogen removal processes.

Phylogenetic distribution and characterization of conserved C-di-GMP metabolizing proteins in filamentous cyanobacterium Arthrospira

Cyclic diguanosine monophosphate (c-di-GMP) is a second messenger in bacteria that regulates multiple biological functions, including biofilm formation, virulence, and intercellular communication. However, c-di-GMP signaling is virtually unknown in economically important filamentous cyanobacteria, Arthrospira. In this study, we predicted 31 genes encoding GGDEF-domain proteins from A. platensis NIES39 as potential diguanylate cyclases (DGCs). Phylogenetic distribution analysis showed five genes (RS09460, RS04865, RS26155, M01840, and E02220) with highly conserved distribution across 25 Arthrospira strains. Adc1 encoded by RS09460 was further characterized as a typical DGC. By establishing the genetic transformation system of Arthrospira, we demonstrated that the overexpression of Adc1 promoted the production of extracellular polymeric substances (EPS), which in turn caused the aggregation of filaments. We also confirmed that RS04865 and RS26155 may encode active DGCs, while enzymatic activity assays showed that proteins encoded by M01840 and E02220 have phosphodiesterase (PDE) activity. Meta-analysis revealed that the expression profiles of RS09460 and RS04865 were unaffected under 31 conditions, suggesting that they may function as conserved genes in maintaining the basal level of c-di-GMP in Arthrospira. In summary, this report will provide the basis for further studies of c-di-GMP signal in Arthrospira.

Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer

Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 108 to 1012 particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.

Harnessing the plant microbiome for environmental sustainability: From ecological foundations to novel applications

In plant environments, there exist heterogeneous microbial communities, referred to as the plant microbiota, which are recruited by plants and play crucial roles in promoting plant growth, aiding in resistance against pathogens and environmental stresses, thereby maintaining plant health. These microorganisms, along with their genomes, collectively form the plant microbiome. Research on the plant microbiome can help unravel the intricate interactions between plants and microbes, providing a theoretical foundation to reduce pesticide use, enhance agricultural productivity, and promote environmental sustainability. Despite significant progress in the field of research, unresolved challenges persist due to ongoing technological limitations and the complexities inherent in studying microorganisms at small scales. Recently, synthetic community (SynCom) has emerged as a novel technique for microbiome research, showing promising prospects for applications in the plant microbiome field. This article systematically introduces the origin and distribution of plant microbiota, the processes of their recruitment and colonization, and the mechanisms underlying their beneficial functions for plants, from the aspects of composition, assembly, and function. Furthermore, we discuss the principles, applications, challenges, and prospects of SynCom for promoting plant health.

Contribution of groundwater-borne nutrients to eutrophication potential and the share of benthic algae in a large lowland river

Groundwater inflow can be a significant source of nutrients for riverine ecosystems, which can affect eutrophication i.e., the elevated primary production and the corresponding accumulation of algal biomass. Experimental and modelling work has shown that benthic algae (autotrophic biofilms) in particular benefit, as they have direct access to the inflowing groundwater-borne nutrients. Primarily the supply of phosphorus (P) enhances pelagic algal biomass, as it is the limiting nutrient for primary production in most freshwater systems. In this study, we estimate the effect of groundwater inflow on overall eutrophication of a large, European lowland river and tested its seasonal effect on biofilms in particular. We calculated the effects on overall eutrophication during summer according to the estimated input of groundwater-borne P and the C:P stoichiometry of planktonic algae in the Elbe River. Our model indicated that these diffuse P inputs have the potential to significantly increase eutrophication. Groundwater-P can contribute up to 1.5 t/d PO4 over the investigated 450 km stretch of the Elbe River under low flow conditions. This would result in an additional planktonic load of about 46 t/d of particulate organic carbon, thereby contributing to eutrophication at the regional scale in this river. In contrast, at the local scale, biofilms were collected seasonally from artificial substrata exposed in the river either in hydrogeologically active areas with groundwater inflow, or in areas of varying hydraulic connectivity. Analyses of biofilm macronutrients, structural components and biofilm community composition show distinct effects of season, hydrogeology and groundwater inflow. The dominant predictors were season and the interaction between hydrogeology and groundwater. Benthic eutrophication is most likely to occur in autumn in areas of loose rock with high groundwater inflow. The strong interaction of environmental factors in determining benthic eutrophication highlights the need to assess these factors in combination rather than in isolation.

Transcending antibiotic resistance: The potential of mass Galla chinensis et camelliae Fermentata to Dismantle Helicobacter pylori biofilms and enhance anti-biotic activity

ETHNOPHARMACOLOGICAL RELEVANCE

Helicobacter pylori (H. pylori) infections are on the rise, presenting a significant global health challenge. Mass Galla chinesis et camelliae Fermentata (Chinese gall leaven, CGL), a traditional Chinese medicinal product made from the fermentation of Rhus chinensis Mill., is frequently employed to address digestive system ailments. Contemporary pharmacological research reveals that CGL exhibits anti-inflammatory, anti-diarrheal, and enzyme-inhibitory activities and holds potential as a treatment for H. pylori infections. However, the precise mechanisms underlying CGL's efficacy against H. pylori remain to be fully elucidated.

AIM

The objective of the study is to evaluate CGL's ability to disrupt the H. pylori biofilm and to explore its synergistic potential with antibiotics in targeting the biofilm-efflux pump system, a mechanism implicated in bacterial resistance.

METHORDS

The study determined the Minimum Inhibitory Concentration (MIC) of CGL and metronidazole against H. pylori and evaluated their effects on H. pylori biofilms using an in vitro model. Structural changes induced by drug interventions were compared to those in untreated and antibiotic-treated models through scanning electron microscopy and laser confocal microscopy. The accumulation of H33342 dye in planktonic and biofilm H. pylori before and after drug treatment was assessed to evaluate cell viability and biofilm disruption. The study also involved adding experimental drugs to a biofilm H. pylori medium containing D-glucose, measuring glucose concentrations post-intervention using the glucose oxidase method, and calculating changes in glucose uptake. Finally, the relative expression levels of several genes in planktonic and biofilm H. pylori treated with CGL alone or in combination with antibiotics were measured to understand the impact on the biofilm-efflux pump system.

RESULTS

Both CGL alone and in combination with metronidazole demonstrated effective disruption of H. pylori biofilms. The combination therapy was particularly effective in reducing the biofilm transfer-enhancing effect of metronidazole and decreasing SpoT expression in the 'SpoT-(p)ppGpp' pathway, especially in biofilms. It showed a greater inhibition of the 'σ54-gluP-sugar uptake' pathway, with significant reductions in rpoN and gluP expression under biofilm conditions compared to CGL or metronidazole alone. The treatment also suppressed H. pylori proliferation and may have altered glucose uptake mechanisms. Moreover, it significantly inhibited the 'hp0939/hp0497/hp0471-RND efflux pump' pathway, with a notable reduction in gene expression compared to the 1/2 MIC metronidazole treatment.

CONCLUSION

This study demonstrates that CGL effectively hinders the development of drug resistance in H. pylori by targeting biofilm formation and critical molecular pathways associated with antibiotic resistance. The synergistic effect of combining CGL with metronidazole notably enhances biofilm disruption and inhibits the bacterium's metabolic and reparative mechanisms. Further in vivo studies are needed to confirm these results and to investigate additional mechanisms of CGL's action.

Chitosan coatings on titanium-based implants - From development to characterization and behavior: A systematic review

Chitosan is a promising natural polymer for coatings, it combines intrinsic antibacterial and pro-osteoblastic properties, but the literature still has a gap from the development to behavior of these coatings, so this systematic review aimed to answer, "What is the relationship between the physical and chemical properties of polymeric chitosan coatings on titanium implants on antibacterial activity and osteoblast viability?". PRISMA guidelines was followed, the search was applied into 4 databases and grey literature, without the restriction of time and language. The selection process occurred in 2 blinded steps by the authors. The criteria of eligibility were in vitro studies that evaluated the physical, chemical, microbiological, and biological properties of chitosan coatings on titanium surfaces. The risk of bias was analyzed by the specific tool. Of 734 potential articles 10 were included; all had low risk of bias. The coating was assessed according to the technique of fabrication, FT-IR, thickness, adhesion, roughness, wettability, antibacterial activity, and osteoblast viability. The analyzed coatings showed efficacy on antibacterial activity and cytocompatibility dependent on the class of material incorporated. Thus, this review motivates the development of time-dependent studies to optimize manufacturing and allow for an increase in patents and availability on the market.

Feasibility analysis of reclaimed water reuse based on water quality data and microbial community structure study

The ecological recharge of urban landscapes with reclaimed water plays a crucial role in alleviating urban water shortage. In Yinchuan, we examined the effects of recharging urban rivers with either Yellow River or reclaimed water on the abundance and diversity of microbial communities. This study aimed to support the effective utilization of reclaimed water. We monitored six sites: three in the reclaimed water recharge area (Lucaowa inlet (ZLJ), Lucaowa channel (ZLH), and Lucaowa outlet (ZLC)) and three in the Yellow River water recharge area (Ningcheng lock (FNCZ), Qingfengjie (FQFJ), and Laifosi (FLFS)). Various indicators (pH, turbidity, temperature (T), dissolved oxygen (DO), electrical conductivity (EC), chemical oxygen demand (COD), total phosphorus (TP), total nitrogen (TN), ammonia nitrogen (NH3-N), and nitrate nitrogen (NO3-N)) were used to assess the water quality. The microbial community abundance and diversity were evaluated using 16S rRNA high-throughput sequencing. The results indicated that throughout the monitoring period, the reclaimed water recharge area exhibited increased water transparency and greater microbial community abundance and diversity than the Yellow River water recharge area. However, the reclaimed water recharge area also showed significantly higher levels of nitrogen, phosphorus, organic matter, and electrical conductivity, along with an increase in Firmicutes. Seasonal changes significantly influenced water quality factors, significantly affecting Cyanobacteria and Campylobacter populations, as demonstrated by RDA analysis, which showed a close relationship between microbial communities and environmental factors. Further comparative analysis revealed that erythrocytic bacteria were predominant in the reclaimed water recharge area, whereas Actinobacteria, Planktonia, and Aspergillus spp. were more significant in the Yellow River water recharge area. Predictive analysis of microbial functions suggested that carbon and nitrogen cycle-related functions were more abundant in the reclaimed water recharge area, indicating that reclaimed water recharge could improve the self-purification capacity of the water body.

Genetically engineered bacterial biofilm materials enhances portable whole cell sensing

In recent years, whole-cell biosensors (WCBs) have emerged as a potent approach for environmental monitoring and on-site analyte detection. These biosensors harness the biological apparatus of microorganisms to identify specific analytes, offering advantages in sensitivity, specificity, and real-time monitoring capabilities. A critical hurdle in biosensor development lies in ensuring the robust attachment of cells to surfaces, a crucial step for practical utility. In this study, we present a comprehensive approach to tackle this challenge via engineering Escherichia coli cells for immobilization on paper through the Curli biofilm pathway. Furthermore, incorporating a cellulose-binding peptide domain to the CsgA biofilm protein enhances cell adhesion to paper surfaces, consequently boosting biosensor efficacy. To demonstrate the versatility of this platform, we developed a WCB for copper, optimized to exhibit a discernible response, even with the naked eye. To confirm its suitability for practical field use, we characterized our copper sensor under various environmental conditions-temperature, salinity, and pH-to mimic real-world scenarios. The biosensor-equipped paper discs can be freeze-dried for deployment in on-site applications, providing a practical method for long-term storage without loss of sensitivity paper discs demonstrate sustained functionality and viability even after months of storage with 5 μM limit of detection for copper with visible-to-naked-eye signal levels. Biofilm-mediated surface attachment and analyte sensing can be independently engineered, allowing for flexible utilization of this platform as required. With the implementation of copper sensing as a proof-of-concept study, we underscore the potential of WCBs as a promising avenue for the on-site detection of a multitude of analytes.

Characterization of a novel multifunctional glycoside hydrolase family in the metagenome-assembled genomes of horse gut

The gut microbiota is a treasure trove of carbohydrate-active enzymes (CAZymes). To explore novel and efficient CAZymes, we analyzed the 4,142 metagenome-assembled genomes (MAGs) of the horse gut microbiota and found the MAG117.bin13 genome (Bacteroides fragilis) contains the highest number of polysaccharide utilisation loci sites (PULs), indicating its high capability for carbohydrate degradation. Bioinformatics analysis indicate that the PULs region of the MAG117.bin13 genome encodes many hypothetical proteins, which are important sources for exploring novel CAZymes. Interestingly, we discovered a hypothetical protein (595 amino acids). This protein exhibits potential CAZymes activity and has a lower similarity to CAZymes, we named it BfLac2275. We purified the protein using prokaryotic expression technology and studied its enzymatic function. The hydrolysis experiment of the polysaccharide substrate showed that the BfLac2275 protein has the ability to degrade α-lactose (156.94 U/mg), maltose (92.59 U/mg), raffinose (86.81 U/mg), and hyaluronic acid (5.71 U/mg). The enzyme activity is optimal at pH 5.0 and 30 ℃, indicating that the hypothetical protein BfLac2275 is a novel and multifunctional CAZymes in the glycoside hydrolases (GHs). These properties indicate that BfLac2275 has broad application prospects in many fields such as plant polysaccharide decomposition, food industry, animal feed additives and enzyme preparations. This study not only serves as a reference for exploring novel CAZymes encoded by gut microbiota but also provides an example for further studying the functional annotation of hypothetical genes in metagenomic assembly genomes.

Cobalt effects on prokaryotic communities of river biofilms: Impact on their colonization kinetics, structure and functions

Although cobalt (Co) plays a significant role in the transition to low-carbon technologies, its environmental impact remains largely unknown. This study examines Co impacts on the prokaryotic communities within river biofilms to evaluate their potential use as bioindicators of Co contamination. To this end, biofilms were cultivated in artificial streams enriched with different environmental Co concentrations (0.1, 0.5, and 1 μM Co) over 28 days and examined for prokaryotic abundance and diversity via quantitative PCR and DNA-metabarcoding every 7 days. The prokaryotic community's resilience was further investigated after an additional 35 days without Co contamination. The prokaryotic communities were affected by 0.5 and 1 μM Co from the onset of biofilm colonization. The biofilm biomass was comparable between treatments, but the community composition differed. Control biofilms were dominated by Cyanobacteria and Planctomycetes, whereas Bacteroidetes dominated the Co-contaminated biofilms. Potential functional redundancy was observed through the implementation of carbon fixation alternatives by non-photosynthetic prokaryotes in biofilms exposed to high Co concentrations. No structural resilience was observed in the biofilms after 35 days without Co contamination. Measuring the prokaryotic community structural response using molecular approaches appears to be a promising method for assessing shifts in water quality owing to Co contamination.

Vaccination with OprB porin, and its epitopes offers protection against A. baumannii infections in mice

A. baumannii is a deadly antimicrobial resistance pathogen that acquires drug resistance through different mechanisms. Therefore, it is necessary to investigate all its virulence factors and design effective vaccines against it. For this purpose, OprB, an outer membrane porin, was investigated in this study, and its secondary and tertiary structures, physicochemical properties, and B-T epitopes were determined. The vaccine potential of this protein and its linear, non-continuous, and chimeric epitopes were also in-vivo analyzed. Based on the results, two surface epitopes and one non-continuous epitope were identified. Surface contiguous epitopes were produced recombinantly and non-continuous epitope sequences were synthesized and then produced. The chimeric epitope was also produced via the SOE-PCR technique. Active and passive immunization of mice with the whole OprB protein, non-continuous epitope, contiguous epitopes, two epitopes in chimeric form, as well as the mixture of two purified epitopes showed that the survival level and total IgG titer of the mice compared to non-vaccinated mice or mice that were vaccinated with an internal fragment increased significantly. The bacterial load in the immunized mice's lung, liver, kidney, and spleen was much lower than in the control groups, and the TNF-α, IFN-γ, and IL-6 cytokines levels were also lower in these groups and were similar to the naive mice. On the other hand, subunit vaccines showed acceptable safety and due to their minimal cross-activity, their use is much safer.

Moldy odors in food - a review

Food products are susceptible to mold contamination, releasing moldy odors. These moldy odors not only affect the flavor of food, but also pose a risk to human health. Moldy odors are a mixture of volatile organic compounds (VOCs) released by the fungi themselves, which are the main source of moldy odors in moldy foods. These VOCs are secondary metabolites of fungi and are synthesized through various biosynthetic pathways. Both the fungi themselves and environmental factors affect the release of moldy odors. This review summarized the main components of musty odors in moldy foods and their producing fungi. In addition, this review focused on the functions of moldy volatile organic compounds (MVOCs) and the biosynthetic pathways of the major MVOCs, and summarized the factors affecting the release of MVOCs as well as the detection methods. It expected to provide a basis for ensuring food safety.

Taxonomic characterization and comparative genomic analysis of a novel Devosia species revealed that phenolic acid-degrading traits are ubiquitous in the Devosia genus

Phenolic acids (PAs) are widely distributed allelochemicals in various environments. To better understand the fate of PAs in environments, a halotolerant PAs-degrading bacterium (named strain RR2S18T) isolated from rhizosphere soil was identified as a novel species of Devosia, named Devosia rhizosphaerae sp. nov. The strain initially degraded PAs into central ring-fission intermediates (protocatechuic acid) using the CoA-dependent non-β-oxidation pathway. The produced ring-fission intermediates were then consecutively degraded by an ortho-cleavage reaction and the β-ketoadipic acid pathway. A comparative genomics analysis of 62 Devosia strains revealed that PAs-degrading genes were ubiquitous in their genomes, indicating that PAs degradation is universal among members of this genus. The analysis also suggested that the genes involved in CoA-dependent non-β-oxidation are inherent to Devosia strains, while those involved in ring-fission and β-ketoadipic acid pathways were obtained by horizontal gene transfer.

Grifola frondosa polysaccharide's therapeutic potential in oxazolone-induced ulcerative colitis

Grifola frondosa polysaccharide (GFP) is a consumable fungus recognized for its potential health advantages. The present study aimed to investigate the development and potential etiologies of ulcerative colitis (UC) utilizing oxazolone (OXZ) as an inducer in mice, along with assessing the therapeutic effects of GFP at varying doses in UC mice, with sulfasalazine (SASP) serving as the positive control. The obtained results indicated that OXZ intervention in mice induced numerous physical manifestations of UC, including increased disease activity index (DAI), decreased goblet cell division, enhanced fibrosis, reduced expression of Claudin1 and Zona encludens protein1 (ZO-1), decreased proliferative activity of colonic mucosal epithelial cells, disturbed oxidation balance, and alterations in intestinal flora. Nonetheless, GFP intervention significantly ameliorated or even resolved these abnormal indicators to a considerable extent. Consequently, this study suggests that GFP might serve as a prebiotic to regulate intestinal flora, mitigate enterotoxin production, restore oxidative balance, thereby reducing the generation of inflammatory mediators, restoring the intestinal barrier, and ultimately improving OXZ-induced UC in mice. GFP demonstrates promising potential as a candidate drug for colitis treatment and as a dietary supplement for alleviating intestinal inflammatory issues.

Chromolaena odorata affects soil nitrogen transformations and competition in tropical coral islands by altering soil ammonia oxidizing microbes

Invasive plants can change the community structure of soil ammonia-oxidizing microbes, affect the process of soil nitrogen (N) transformation, and gain a competitive advantage. However, the current researches on competition mechanism of Chromolaena odorata have not involved soil nitrogen transformation. In this study, we compared the microbially mediated soil transformations of invasive C. odorata and natives (Pisonia grandis and Scaevola taccada) of tropical coral islands. We assessed how differences in plant biomass and tissue N contents, soil nutrients, N transformation rates, microbial biomass and activity, and diversity and abundance of ammonia oxidizing microbes associated with these species impact their competitiveness. The results showed that C. odorata outcompeted both native species by allocating more proportionally biomass to aboveground parts in response to interspecific competition (12.92 % and 22.72 % more than P. grandis and S. taccada, respectively). Additionally, when C. odorata was planted with native plants, the available N and net mineralization rates in C. odorata rhizosphere soil were higher than in native plants rhizosphere soils. Higher abundance of ammonia-oxidizing bacteria in C. odorata rhizosphere soil confirmed this, being positively correlated with soil N mineralization rates and available N. Our findings help to understand the soil N acquisition and competition strategies of C. odorata, and contribute to improving evaluations and predictions of invasive plant dynamics and their ecological effects in tropical coral islands.

Copper and cadmium co-contamination increases the risk of nitrogen loss in red paddy soils

The microbiome plays a crucial role in soil nitrogen (N) cycling and in regulating its bioavailability. However, the functional and genomic information of microorganisms encoding N cycling in response to copper (Cu) and cadmium (Cd) contamination is largely unknown. Here, metagenomics and genome binning were used to examine microbial N cycling in Cu and Cd co-contaminated red paddy soils collected from a polluted watershed in southern China. The results showed that soil Cu and Cd concentrations induced more drastic changes in microbial N functional and taxonomic traits than soil general properties. Soil Cu and Cd co-contamination stimulated microbial nitrification, denitrification, and dissimilatory nitrate reduction processes mainly by increasing the abundance of Nitrospira (phylum Nitrospirota), while inhibiting N fixation by decreasing the abundance of Desulfobacca. These contrasting changes in microbial N cycling processes suggested a potential risk of N loss in paddy soils. A high-quality genome was identified as belonging to Nitrospirota with the highest abundance in heavily contaminated soils. This novel Nitrospirota strain possessed metabolic capacities for N transformation and metal resistance. These findings elucidate the genetic mechanisms underlying soil N bioavailability under long-term Cu and Cd contamination, which is essential for maintaining agricultural productivity and controlling heavy metal pollution.

Differentiation of Listeria monocytogenes serotypes using near infrared hyperspectral imaging

Among the severe foodborne illnesses, listeriosis resulting from the pathogen Listeria monocytogenes exhibits one of the highest fatality rates. This study investigated the application of near infrared hyperspectral imaging (NIR-HSI) for the classification of three L. monocytogenes serotypes namely serotype 4b, 1/2a and 1/2c. The bacteria were cultured on Brain Heart Infusion agar, and NIR hyperspectral images were captured in the spectral range 900-2500 nm. Different pre-processing methods were applied to the raw spectra and principal component analysis was used for data exploration. Classification was achieved with partial least squares discriminant analysis (PLS-DA). The PLS-DA results revealed classification accuracies exceeding 80 % for all the bacterial serotypes for both training and test set data. Based on validation data, sensitivity values for L. monocytogenes serotype 4b, 1/2a and 1/2c were 0.69, 0.80 and 0.98, respectively when using full wavelength data. The reduced wavelength model had sensitivity values of 0.65, 0.85 and 0.98 for serotype 4b, 1/2a and 1/2c, respectively. The most relevant bands for serotype discrimination were identified to be around 1490 nm and 1580-1690 nm based on both principal component loadings and variable importance in projection scores. The outcomes of this study demonstrate the feasibility of utilizing NIR-HSI for detecting and classifying L. monocytogenes serotypes on growth media.

Antimicrobial resistance induction potential of grapefruit seed extract on multi-species biofilm of E. coli in food industry

Biofilm formation in natural environments involving complex multi-structural arrangements hinders challenges in antimicrobial resistance. This study investigated the antimicrobial resistance potential of grapefruit seed extract (GSE) by examining the formation of mono-, dual-, and multi-species biofilms. We also explored the counterintuitive effect in response to GSE at various concentrations, including minimum inhibitory concentration (MIC) and sub-MIC (1/2 and 1/4 MIC). The results of the swimming and swarming motility tests revealed increased motility at the sub-MIC of GSE. The crystal violet assay demonstrated increased biofilm formation in multi-species biofilms, highlighting the synergistic effect of Escherichia coli, Salmonella Typhimurium, and Listeria monocytogenes. At the MIC concentration of GSE, field emission scanning electron microscopy (FE-SEM) revealed cell morphology damage, while sub-MIC increased biofilm formation and architectural complexity. Multi-species biofilms demonstrated greater biofilm-forming ability and antimicrobial resistance than mono-species biofilms, indicating synergistic interactions and enhanced resilience. These findings highlight the importance of understanding biofilm dynamics and antimicrobial resistance to ensure environmental safety.

Bacterial membrane vesicles combined with nanoparticles for bacterial vaccines and cancer immunotherapy

Similar to mammalian cells, most bacteria can release nano-sized membrane vesicles (MVs) into the extracellular environment. MVs contain lipids, bioactive proteins, nucleic acids, and metabolites, and play important roles in microbial physiology. MVs have great potential for immunotherapeutic applications, such as bacterial vaccines and cancer immunotherapy. However, because of the diversity in content and heterogeneity in size of MVs, the clinical application of MVs has been limited. Recently, the use of MVs combined with nanoparticles (NPs) has been shown to be effective in improving the homogeneity, stability and function of MVs. In this review, we focus on studies of MVs combined with NPs (MV-NPs) and describe the use of these MV-NPs in biotechnology, especially in bacterial vaccine and cancer immunotherapy.

Possible toxification mechanisms of acute and chronic pentachlorophenol to Montipora digitata: Limitation of energy supply and immunotoxicity

Pentachlorophenol (PCP) is widely found in coastal environments and has various adverse effects, and its potential impact on coral reef ecosystems concerning. The scleractinian coral Montipora digitata was used for PCP stress experiments in this study. Phenotypes, physiological indicators, microbial diversity analysis and RNA sequencing were used to investigate the mechanisms underlying the responses of corals to acute and chronic PCP exposure. After 96 h of acute exposure, coral bleaching occurred at 1000 μg/LPCP and there was a significant decrease in Symbiodiniaceae density, Fv/Fm, and chlorophyll a content. Exposure to different concentrations of PCP significantly increased the content of malondialdehyde (MDA), leading to oxidative stress in corals. Chronic PCP exposure resulted in bleaching at 60 days, with the Fv/Fm significantly reduced to 0.461. Microbial diversity analysis revealed an increase in the abundance of potential pathogens, such as Vibrio, during acute PCP exposure and the emergence of the degrading bacterium Delftia during chronic PCP exposure. Transcriptional analysis showed that PCP exposure caused abnormal carbohydrate and amino acid metabolism in zooxanthella, which affected energy supply, induced immune responses, and disrupted symbiotic relationships. Corals respond to injury by boosting the expression of genes associated with signal transduction and immune response. Additionally, the expression of genes associated with environmental adaptation increased with chronic PCP exposure, which is consistent with the results of the microbial diversity analysis. These results indicate that PCP exposure might affect the balance of coral- zooxanthellae symbiosis in the stony coral M. digitata, impairing coral health and leading to bleaching.

Interspecific cross-talk: The catalyst driving microbial biosynthesis of secondary metabolites

Microorganisms co-exist and co-evolve in nature, forming intricate ecological communities. The interspecies cross-talk within these communities creates and sustains their great biosynthetic potential, making them an important source of natural medicines and high-value-added chemicals. However, conventional investigations into microbial metabolites are typically carried out in pure cultures, resulting in the absence of specific activating factors and consequently causing a substantial number of biosynthetic gene clusters to remain silent. This, in turn, hampers the in-depth exploration of microbial biosynthetic potential and frequently presents researchers with the challenge of rediscovering compounds. In response to this challenge, the coculture strategy has emerged to explore microbial biosynthetic capabilities and has shed light on the study of cross-talk mechanisms. These elucidated mechanisms will contribute to a better understanding of complex biosynthetic regulations and offer valuable insights to guide the mining of secondary metabolites. This review summarizes the research advances in microbial cross-talk mechanisms, with a particular focus on the mechanisms that activate the biosynthesis of secondary metabolites. Additionally, the instructive value of these mechanisms for developing strategies to activate biosynthetic pathways is discussed. Moreover, challenges and recommendations for conducting in-depth studies on the cross-talk mechanisms are presented.

Best Practices in Treatment of Fungal Urinary Tract Infections

Fungal pathogens within the urine, specifically Candida species, are a common finding amongst hospitalized patients. Risk factors for the development of candiduria involve patients with indwelling urinary drainage devices, surgical patients, patients undergoing urologic instrumentation, and diabetic patients. Candiduria often presents with an asymptomatic course but can also be a severe life-threatening process. This article will review the epidemiology and risk factors associated with fungal urinary tract infections, and the diagnosis and categorization of these infections along with a review of current medical and surgical treatments for this condition.

Distinct metabolites affect the phloem fungal communities in ash trees (Fraxinus spp.) native and nonnative to the highly invasive emerald ash borer (AGRILUS PLANIPENNIS)

Emerald ash borer (EAB, Agrilus planipennis) is an invasive killer of ash trees (Fraxinus spp.) in North America and Europe. Ash species co-evolved with EAB in their native range in Asia are mostly resistant, although the precise mechanism(s) remain unclear. Very little is also known about EAB or ash tree microbiomes. We performed the first joint comparison of phloem mycobiome and metabolites between a native and a nonnative ash species, infested and uninfested with EAB, in conjunction with investigation of larval mycobiome. Phloem mycobiome communities differed between the tree species, but both were unaffected by EAB infestation. Several indicator taxa in the larval gut shared a similarly high relative abundance only with the native host trees. Widely targeted metabolomics revealed 24 distinct metabolites in native trees and 53 metabolites in nonnative trees, respectively, that differed in relative content between infested and uninfested trees only in one species. Interestingly, four metabolites shared a strong relationship with the phloem mycobiomes, majority of which affected only the native trees. Collectively, our results demonstrate a complex interplay between host tree chemistry and mycobiome, and suggest the shared relationships between the mycobiomes of the native host tree and EAB may reflect their shared co-evolution.

Detection and characterization of multidrug resistant Escherichia coli carrying virulence gene isolated from broilers in Bangladesh

BACKGROUND

The emergence and dissemination of multidrug resistant (MDR) bacteria pose a severe threat to public health by limiting clinical treatment and prophylactic options.

OBJECTIVES

This study investigates the prevalence of Escherichia coli in broilers, their phenotypic antimicrobial resistance (AMR) profiles and the presence of virulence-associated genes (VAGs) and antimicrobial resistance genes (ARGs) using polymerase chain reaction (PCR).

MATERIALS AND METHODS

A total of 216 pooled cloacal samples were collected from 1080 broilers across six districts of Bangladesh. Each pooled sample comprised randomly selected cloacal swabs from five birds per farm. E. coli isolates were identified using standard bacteriological approach, followed by biochemical assays and PCR. Antimicrobial susceptibility was assessed using the Kirby-Bauer disc diffusion method, and the presence of ARGs and VAGs was determined via PCR. Five selected isolates were partially sequenced for five VAGs using Sanger sequencing.

RESULTS

A total of 177 E. coli isolates (81.94%, 95% confidence interval: 76.24%-86.53%) were identified. The isolates showed the highest resistance to ampicillin (93.79%), followed by tetracycline (91.53%), erythromycin (89.27%) and ciprofloxacin (87%). Conversely, ceftriaxone (80.79%) showed highest susceptibility, followed by gentamicin (37.29%) and neomycin (31.07%). All isolates were MDR, with a multiple antibiotic resistance indexes were <0.3. A significant percentage (16.38%) of E. coli isolates were MDR to five antimicrobial classes and harboured blaTEM, sul1, ere (A), tetA, tetB and tetC genes. The highest prevalent ARGs were blaTEM (88.14%) followed by ere (A) (83.62%) and sul 1 (72.32%). The prevalence of VAGs was astA (56.50%), iucD (31.07%), iss (21.47%), irp2 (15.82%) and cva/cvi (3.39%), respectively.

CONCLUSIONS

This study highlights the presence of ARGs contributing to the development of MDR in E. coli carrying VAGs in broilers. Effective monitoring and surveillance of antimicrobial usage in poultry production systems are urgently required to prevent emergence and dissemination of AMR.

Comparative genomic analysis of ESBL-selected and non-selected Escherichia coli in Australian wastewater: Elucidating differences in diversity, antimicrobial resistance, and virulence profiles

Extended-spectrum β-lactamases (ESBLs)-producing E. coli have been proposed as an indicator bacterium for antimicrobial resistance (AMR) surveillance within a OneHealth framework. However, it is important to understand the effects and potential biases ESBL-selection has on E. coli populations. Utilising whole genome sequencing, this study compared 80 ESBL-selected E. coli isolates with 201 non-selected isolates from Australian wastewater. The findings revealed significant variations between these cohorts in genetic diversity, AMR profiles, and carriage of virulence-associated genes (VAGs), plasmids, and the transmissible Locus of Stress Tolerance (tLST), a genomic island that imparts resistance to extreme heat and chlorination. The study highlights the predominance of certain sequence types (STs), particularly ST131 (75 % clade A), in ESBL-selected isolates (40 % vs 2 %) and overall the ESBL-selected isolates were largely multidrug-resistant (MDR), predominantly carrying genes for resistance to aminoglycosides, extended-spectrum β-lactams, fluoroquinolone, macrolides, sulphonamides/trimethoprim, and tetracyclines. The ESBLs identified were almost exclusively blaCTX-M genes, most commonly blaCTX-M-15 > blaCTX-M-27 > blaCTX-M-14. These were predominately carried on IncF plasmids or chromosomally (always ISEcp1 associated), in equal numbers. In contrast, 80 % of non-selected isolates carried no acquired ARGs, and none carried blaCTX-M genes. In both cohorts, extraintestinal pathogenic E. coli (ExPEC) was the dominate pathotype (35 % total) with few (4 % total) intestinal pathogenic E. coli pathotypes identified (aEPEC > ETEC > EAEC). Nevertheless, some clinically important genes were only identified in the non-selected group, namely tigecycline-resistance gene tet(X4) and AmpC ESBL blaCMY-2. Additionally, the presence of tLST, associated with higher metal resistance gene carriage (Ag, As, Cu, Hg, Ni), in a substantial portion of non-selected isolates (20 % vs 0 %), underscores environmental pressures shaping bacterial populations in wastewater ecosystems. These insights are important for developing comprehensive, less biased genomic surveillance strategies to understand and manage public health threats posed by pathogenic E. coli and AMR.

Is there a role for intestinal sporobiota in the antimicrobial resistance crisis?

Antimicrobial resistance (AMR) is a complex issue requiring specific, multi-sectoral measures to slow its spread. When people are exposed to antimicrobial agents, it can cause resistant bacteria to increase. This means that the use, misuse, and excessive use of antimicrobial agents exert selective pressure on bacteria, which can lead to the development of "silent" reservoirs of antimicrobial resistance genes. These genes can later be mobilized into pathogenic bacteria and contribute to the spread of AMR. Many socioeconomic and environmental factors influence the transmission and dissemination of resistance genes, such as the quality of healthcare systems, water sanitation, hygiene infrastructure, and pollution. The sporobiota is an essential part of the gut microbiota that plays a role in maintaining gut homeostasis. However, because spores are highly transmissible and can spread easily, they can be a vector for AMR. The sporobiota resistome, particularly the mobile resistome, is important for tracking, managing, and limiting the spread of antimicrobial resistance genes among pathogenic and commensal bacterial species.

Decrypting the viral community in aerobic activated sludge reactors treating antibiotic production wastewater

Viruses are the most abundant yet understudied members that may influence microbial metabolism in activated sludge treating antibiotic production wastewater. This study comprehensively investigated virome community characteristics under the selection pressure of nine types and different concentrations of antibiotics using a metagenomics approach. Of the 15,514 total viral operational taxonomic units (tOTUs) recovered, only 37.5 % were annotated. Antibiotics altered the original viral community structure in activated sludge. The proportion of some pathogenic viral families, including Herpesviridae_like, increased significantly in reactors treating erythromycin production wastewater. In total, 16.5 % of the tOTUs were associated with two or more hosts. tOTUs rarely carried antibiotic resistance genes (ARGs), and the ARG types in the tOTUs did not match the ARGs carried by the bacterial hosts. This suggests that transduction contributes little to the horizontal ARG transfer. Auxiliary metabolic genes (AMGs) were prevalent in tOTUs, and those involved in folate biosynthesis were particularly abundant, indicating their potential to mitigate antibiotic-induced host damage. This study provides comprehensive insights into the virome community in activated sludge treating antibiotic production wastewater and sheds light on the potential role of viral AMGs in mitigating antibiotic-induced stress.

Transcriptional regulation of the anaerobic 3-hydroxybenzoate degradation pathway in Aromatoleum sp. CIB

Phenolic compounds are commonly found in anoxic environments, where they serve as both carbon and energy sources for certain anaerobic bacteria. The anaerobic breakdown of m-cresol, catechol, and certain lignin-derived compounds yields the central intermediate 3-hydroxybenzoate/3-hydroxybenzoyl-CoA. In this study, we have characterized the transcription and regulation of the hbd genes responsible for the anaerobic degradation of 3-hydroxybenzoate in the β-proteobacterium Aromatoleum sp. CIB. The hbd cluster is organized in three catabolic operons and a regulatory hbdR gene that encodes a dimeric transcriptional regulator belonging to the TetR family. HbdR suppresses the activity of the three catabolic promoters (PhbdN, PhbdE and PhbdH) by binding to a conserved palindromic operator box (ATGAATGAN4TCATTCAT). 3-Hydroxybenzoyl-CoA, the initial intermediate of the 3-hydroxybenzoate degradation pathway, along with benzoyl-CoA, serve as effector molecules that bind to HbdR inducing the expression of the hbd genes. Moreover, the hbd genes are subject to additional regulation influenced by the presence of non-aromatic carbon sources (carbon catabolite repression), and their expression is induced in oxygen-deprived conditions by the AcpR transcriptional activator. The prevalence of the hbd cluster among members of the Aromatoleum/Thauera bacterial group, coupled with its association with mobile genetic elements, suggests acquisition through horizontal gene transfer. These findings significantly enhance our understanding of the regulatory mechanisms governing the hbd gene cluster in bacteria, paving the way for further exploration into the anaerobic utilization/valorization of phenolic compounds derived from lignin.

Vacuolar recruitment of retromer by a SNARE complex enables infection-related trafficking in rice blast

The retromer complex is a conserved sorting machinery that maintains cellular protein homeostasis by transporting vesicles containing cargo proteins to defined destinations. It is known to sort proteins at the vacuole membranes for retrograde trafficking, preventing their degradation in the vacuole. However, the detailed mechanism of retromer recruitment to the vacuole membrane has not yet been elucidated. Here, we show that the vacuolar SNARE complex MoPep12-MoVti1-MoVam7-MoYkt6 regulates retromer-mediated vesicle trafficking by recruiting the retromer to the vacuole membrane, which promotes host invasion in Magnaporthe oryzae. Such recruitment is also essential for the retrieval of the autophagy regulator MoAtg8 and enables appressorium-mediated host penetration. Furthermore, the vacuolar SNARE subunits are involved in suppressing the host defense response by regulating the deployment of retromer-MoSnc1-mediated effector secretion. Altogether, our results provide insights into the mechanism of vacuolar SNAREs-dependent retromer recruitment which is necessary for pathogenicity-related membrane trafficking events in the rice blast fungus.

WHO elements - A new category of selfish genetic elements at the borderline between homing elements and transposable elements

Homing genetic elements are a form of selfish DNA that inserts into a specific target site in the genome and spreads through the population by a process of biased inheritance. Two well-known types of homing element, called inteins and homing introns, were discovered decades ago. In this review we describe WHO elements, a newly discovered type of homing element that constitutes a distinct third category but is rare, having been found only in a few yeast species so far. WHO elements are inferred to spread using the same molecular homing mechanism as inteins and introns: they encode a site-specific endonuclease that cleaves the genome at the target site, making a DNA break that is subsequently repaired by copying the element. For most WHO elements, the target site is in the glycolytic gene FBA1. WHO elements differ from inteins and homing introns in two fundamental ways: they do not interrupt their host gene (FBA1), and they occur in clusters. The clusters were formed by successive integrations of different WHO elements into the FBA1 locus, the result of an 'arms race' between the endonuclease and its target site. We also describe one family of WHO elements (WHO10) that is no longer specifically associated with the FBA1 locus and instead appears to have become transposable, inserting at random genomic sites in Torulaspora globosa with up to 26 copies per strain. The WHO family of elements is therefore at the borderline between homing genetic elements and transposable elements.

Drug tolerance and persistence in bacteria, fungi and cancer cells: Role of non-genetic heterogeneity

A common feature of bacterial, fungal and cancer cell populations upon treatment is the presence of tolerant and persistent cells able to survive, and sometimes grow, even in the presence of usually inhibitory or lethal drug concentrations, driven by non-genetic differences among individual cells in a population. Here we review and compare data obtained on drug survival in bacteria, fungi and cancer cells to unravel common characteristics and cellular pathways, and to point their singularities. This comparative work also allows to cross-fertilize ideas across fields. We particularly focus on the role of gene expression variability in the emergence of cell-cell non-genetic heterogeneity because it represents a possible common basic molecular process at the origin of most persistence phenomena and could be monitored and tuned to help improve therapeutic interventions.