Peculiarities of biofilm formation by Paracoccus denitrificans

Biofilm Resilience: Molecular Mechanisms Driving Antibiotic Resistance in Clinical Contexts

Healthcare-associated infections pose a significant global health challenge, negatively impacting patient outcomes and burdening healthcare systems. A major contributing factor to healthcare-associated infections is the formation of biofilms, structured microbial communities encased in a self-produced extracellular polymeric substance matrix. Biofilms are critical in disease etiology and antibiotic resistance, complicating treatment and infection control efforts. Their inherent resistance mechanisms enable them to withstand antibiotic therapies, leading to recurrent infections and increased morbidity. This review explores the development of biofilms and their dual roles in health and disease. It highlights the structural and protective functions of the EPS matrix, which shields microbial populations from immune responses and antimicrobial agents. Key molecular mechanisms of biofilm resistance, including restricted antibiotic penetration, persister cell dormancy, and genetic adaptations, are identified as significant barriers to effective management. Biofilms are implicated in various clinical contexts, including chronic wounds, medical device-associated infections, oral health complications, and surgical site infections. Their prevalence in hospital environments exacerbates infection control challenges and underscores the urgent need for innovative preventive and therapeutic strategies. This review evaluates cutting-edge approaches such as DNase-mediated biofilm disruption, RNAIII-inhibiting peptides, DNABII proteins, bacteriophage therapies, antimicrobial peptides, nanoparticle-based solutions, antimicrobial coatings, and antimicrobial lock therapies. It also examines critical challenges associated with biofilm-related healthcare-associated infections, including diagnostic difficulties, disinfectant resistance, and economic implications. This review emphasizes the need for a multidisciplinary approach and underscores the importance of understanding biofilm dynamics, their role in disease pathogenesis, and the advancements in therapeutic strategies to combat biofilm-associated infections effectively in clinical settings. These insights aim to enhance treatment outcomes and reduce the burden of biofilm-related diseases.

Profile of Bacterial Communities in Copper Mine Tailings Revealed through High-Throughput Sequencing

Mine-tailing dumps are one of the leading sources of environmental degradation, often with public health and ecological consequences. Due to the complex ecosystems generated, they are ideal sites for exploring the bacterial diversity of specially adapted microorganisms. We investigated the concentrations of trace metals in solid copper (Cu) mine tailings from the Ovejería Tailings Dam of the National Copper Corporation of Chile and used high-throughput sequencing techniques to determine the microbial community diversity of the tailings using 16S rRNA gene-based amplicon sequence analysis. The concentrations of the detected metals were highest in the following order: iron (Fe) > Cu > manganese (Mn) > molybdenum (Mo) > lead (Pb) > chromium (Cr) > cadmium (Cd). Furthermore, 16S rRNA gene-based sequence analysis identified 12 phyla, 18 classes, 43 orders, 82 families, and 154 genera at the three sampling points. The phylum Proteobacteria was the most dominant, followed by Chlamydiota, Bacteroidetes, Actinobacteria, and Firmicutes. Genera, such as Bradyrhizobium, Aquabacterium, Paracoccus, Caulobacter, Azospira, and Neochlamydia, showed high relative abundance. These genera are known to possess adaptation mechanisms in high concentrations of metals, such as Cd, Cu, and Pb, along with nitrogen-fixation capacity. In addition to their tolerance to various metals, some of these genera may represent pathogens of amoeba or humans, which contributes to the complexity and resilience of bacterial communities in the studied Cu mining tailings. This study highlights the unique microbial diversity in the Ovejería Tailings Dam, including the discovery of the genus Neochlamydia, reported for the first time for heavy metal resistance. This underscores the importance of characterizing mining sites, particularly in Chile, to uncover novel bacterial mechanisms for potential biotechnological applications.

Activating Biocake Communities Retards Jumps of Transmembrane Pressure in Membrane Bioreactors

Sudden jump of transmembrane pressure (TMP) in membrane bioreactors (MBRs), associated with abrupt aggravation of membrane fouling, limits practical applications of MBRs and calls for effective mitigation strategies. While the TMP jump is generally related to the bacterial activity of biocakes, the mechanisms underlying the TMP jump remain unclear. Herein, we conducted various backwash protocols with different nutrient (e.g., nitrate and sodium acetate) loadings on fouled membranes in MBRs to reveal the critical role of bacterial activity of biocakes for the TMP jump. The filtration tests showed a lower TMP jump rate for the membrane backwashed with a nutrient solution (a mixture of 180 mg/L NaNO3 and 200 mg/L NaAc, averaged at 1.40 kPa/d) than that backwashed with tap water (averaged at 3.56 kPa/d), implying that TMP jump could be efficiently mitigated by providing sufficient nutrients to biocake bacteria. The characterization of biocakes showed that high-nutrient solution backwash considerably increased bacterial viability and activity, while considerably reducing biomolecule accumulation on membranes. The keystone taxa (e.g., g_Aeromonas and o_Chitinophagaceae) in the network of nutrient-enriched biocake communities were involved in nitrate reduction and biomolecule degradation. Ecological null model analyses revealed that the deterministic manner mainly shaped biocake communities with high-nutrient availability. Overall, this study highlights the significance of the bacterial activity of biocakes for TMP development and provides potential alternatives for controlling membrane fouling.

Co-application of chitooligosaccharides and arbuscular mycorrhiza fungi reduced greenhouse gas fluxes in saline soil by improving the rhizosphere microecology of soybean

Soil salinization can affect the ecological environment of soil and alter greenhouse gas (GHG) emissions. Chitooligosaccharides and Arbuscular mycorrhizal fungi (AMF) reduced the GHG fluxes of salinized soil, and this reduction was attributed to an alteration in the rhizosphere microecology, including changes in the activities of β-glucosidase, acid phosphatase, N-acetyl-β-D-glucosidase, and Leucine aminopeptidase. Additionally, certain bacteria species such as paracoccus, ensifer, microvirga, and paracyclodium were highly correlated with GHG emissions. Another interesting finding is that foliar spraying of chitooligosaccharides could transport to the soybean root system, and improve soybean tolerance to salt stress. This is achieved by enhancing the activities of antioxidant enzymes, and the changes in amino acid metabolism, lipid metabolism, and membrane transport. Importantly, the Co-application of chitooligosaccharides and Arbuscular mycorrhiza fungi was found to have a greater effect compared to their application alone.

Revealing the roles of chemical communication in restoring the formation and electroactivity of electrogenic biofilm under electrical signaling disruption

Electrogenic biofilms in microbial electrochemical systems have played significant roles in simultaneous wastewater treatment and energy recovery owing to their unique extracellular electron transfer. Their formation has been shown to be regulated by electrical and chemical communication, but the interaction between these signal communication pathways has not been studied. This research investigated the coordination between intracellular c-di-GMP signaling and reinforced quorum sensing with or without exogenous HSL (a common quorum sensing molecule), on the formation of mixed-cultured electrogenic biofilm under electrical signaling disruption by tetraethylammonium (TEA, a broad-range potassium channel blocker). Intracellular c-di-GMP was spontaneously reinforced in response to TEA stress, and metagenomic analysis revealed that the dominant DGC (the genes for producing c-di-GMP) induced the eventual biofilm formation by mediating exopolysaccharide synthesis. Meanwhile, reinforced quorum sensing by exogenous HSL could also benefit the biofilm restoration, however, it alleviated the TEA-induced communication stress, resulting in the weakening of c-di-GMP dominance. Interestingly, suppressing electrical communication with or without HSL addition both induced selective enrichment of Geobacter of 85.5% or 30.1% respectively. Functional contribution analysis revealed the significant roles of Geobacter and Thauera in c-di-GMP signaling, especially Thauera in resistance to TEA stress. This study proposed a potential strategy for electrogenic biofilm regulation from the perspectives of cell-to-cell communication.

The biofilm matrix: multitasking in a shared space

The biofilm matrix can be considered to be a shared space for the encased microbial cells, comprising a wide variety of extracellular polymeric substances (EPS), such as polysaccharides, proteins, amyloids, lipids and extracellular DNA (eDNA), as well as membrane vesicles and humic-like microbially derived refractory substances. EPS are dynamic in space and time and their components interact in complex ways, fulfilling various functions: to stabilize the matrix, acquire nutrients, retain and protect eDNA or exoenzymes, or offer sorption sites for ions and hydrophobic substances. The retention of exoenzymes effectively renders the biofilm matrix an external digestion system influencing the global turnover of biopolymers, considering the ubiquitous relevance of biofilms. Physico-chemical and biological interactions and environmental conditions enable biofilm systems to morph into films, microcolonies and macrocolonies, films, ridges, ripples, columns, pellicles, bubbles, mushrooms and suspended aggregates - in response to the very diverse conditions confronting a particular biofilm community. Assembly and dynamics of the matrix are mostly coordinated by secondary messengers, signalling molecules or small RNAs, in both medically relevant and environmental biofilms. Fully deciphering how bacteria provide structure to the matrix, and thus facilitate and benefit from extracellular reactions, remains the challenge for future biofilm research.

Cryptic Oral Microbiota: What Is Its Role as Obstructive Sleep Apnea-Related Periodontal Pathogens?

Periodontitis has been commonly linked to periodontopathogens categorized in Socransky's microbial complexes; however, there is a lack of knowledge regarding "other microorganisms" or "cryptic microorganisms", which are rarely thought of as significant oral pathogens and have been neither previously categorized nor connected to illnesses in the oral cavity. This study hypothesized that these cryptic microorganisms could contribute to the modulation of oral microbiota present in health or disease (periodontitis and/or obstructive sleep apnea (OSA) patients). For this purpose, the presence and correlation among these cultivable cryptic oral microorganisms were identified, and their possible role in both conditions was determined. Data from oral samples of individuals with or without periodontitis and with or without OSA were obtained from a previous study. Demographic data, clinical oral characteristics, and genera and species of cultivable cryptic oral microorganisms identified by MALDI-TOF were recorded. The data from 75 participants were analyzed to determine the relative frequencies of cultivable cryptic microorganisms' genera and species, and microbial clusters and correlations tests were performed. According to periodontal condition, dental-biofilm-induced gingivitis in reduced periodontium and stage III periodontitis were found to have the highest diversity of cryptic microorganism species. Based on the experimental condition, these findings showed that there are genera related to disease conditions and others related to healthy conditions, with species that could be related to different chronic diseases being highlighted as periodontitis and OSA comorbidities. The cryptic microorganisms within the oral microbiota of patients with periodontitis and OSA are present as potential pathogens, promoting the development of dysbiotic microbiota and the occurrence of chronic diseases, which have been previously proposed to be common risk factors for periodontitis and OSA. Understanding the function of possible pathogens in the oral microbiota will require more research.

Overexpression of pdeR promotes biofilm formation of Paracoccus denitrificans by promoting ATP production and iron acquisition

Bacterial biofilms are ubiquitous in natural environments and play an essential role in bacteria’s environmental adaptability. Quorum sensing (QS), as the main signaling mechanism bacteria used for cell-to-cell communication, plays a key role in bacterial biofilm formation. However, little is known about the role of QS circuit in the N-transformation type strain, Paracoccus denitrificans, especially for the regulatory protein PdeR. In this study, we found the overexpression of pdeR promoted bacterial aggregation and biofilm formation. Through RNA-seq analysis, we demonstrated that PdeR is a global regulator which could regulate 656 genes expression, involved in multiple metabolic pathways. Combined with transcriptome as well as biochemical experiments, we found the overexpressed pdeR mainly promoted the intracellular degradation of amino acids and fatty acids, as well as siderophore biosynthesis and transportation, thus providing cells enough energy and iron for biofilm development. These results revealed the underlying mechanism for PdeR in biofilm formation of P. denitrificans, adding to our understanding of QS regulation in biofilm development.

Microbial fuel cells for bioelectricity production from waste as sustainable prospect of future energy sector

Microbial fuel cell (MFC) is lauded for its potentials to solve both energy crisis and environmental pollution. Technologically, it offers the capability to harness electricity from the chemical energy stored in the organic substrate with no intermediate steps, thereby minimizes the entropic loss due to the inter-conversion of energy. The sciences underneath such MFCs include the electron and proton generation from the metabolic decomposition of the substrate by microbes at the anode, followed by the shuttling of these charges to cathode for electricity generation. While its promising prospects were mutually evinced in the past investigations, the upscaling of MFC in sustaining global energy demands and waste treatments is yet to be put into practice. In this context, the current review summarizes the important knowledge and applications of MFCs, concurrently identifies the technological bottlenecks that restricted its vast implementation. In addition, economic analysis was also performed to provide multiangle perspectives to readers. Succinctly, MFCs are mainly hindered by the slow metabolic kinetics, sluggish transfer of charged particles, and low economic competitiveness when compared to conventional technologies. From these hindering factors, insightful strategies for improved practicality of MFCs were formulated, with potential future research direction being identified too. With proper planning, we are delighted to see the industrialization of MFCs in the near future, which would benefit the entire human race with cleaner energy and the environment.

Response characteristics of nirS-type denitrifier Paracoccus denitrificans under florfenicol stress

Florfenicol (FF) is widely used in aquaculture and can interfere with denitrification when released into natural ecosystems. The aim of this study was to analyze the response characteristics of nirS-type denitrifier Paracoccus denitrificans under FF stress and further mine antibiotic-responsive factors in aquatic environment. Phenotypic analysis revealed that FF delayed the nitrate removal with a maximum inhibition value of 82.4% at exponential growth phase, leading to nitrite accumulation reached to 21.9-fold and biofilm biomass decreased by ~38.6%, which were due to the lower bacterial population count (P < 0.01). RNA-seq transcriptome analyses indicated that FF treatment decreased the expression of nirS, norB, nosD and nosZ genes that encoded enzymes required for NO₂^- to N₂ conversion from 1.02- to 2.21-fold (P < 0.001). Furthermore, gene associated with the flagellar system FlgL was also down-regulated by 1.03-fold (P < 0.001). Moreover, 10 confirmed sRNAs were significantly induced, which regulated a wide range of metabolic pathways and protein expression. Interestingly, different bacteria contained the same sRNAs means that sRNAs can spread between them. Overall, this study suggests that the denitrification of nirS-type denitrifiers can be hampered widely by FF and the key sRNAs have great potential to be antibiotic-responsive factors.