Research in microbiology最新文献

Bacteria are ubiquitous prokaryotes. They are involved in biofilm formation and also have the ability to produce anti-biofilm products for biofilm mitigation. This special issue entitled: “Biofilms- community structure, applications and mitigation” of the journal Research in Microbiology was designed to discuss the flexibility of bacterial biofilms and their products under particular circumstances. Given that quorum sensing (QS) controls biofilm growth in some situations, especially for pathogenic bacteria antibiotic evading strategies. In Gram-negative bacteria, N-acyl homoserine lactones are the major quorum sensing signaling molecules. Another approach to prevent bacterial biofilm formation may be to inhibit the QS-regulated activities using quorum quenching (QQ). In this context, QS inhibitors and QS enzymes are important because they, respectively, interfere with signal creation, perception, or degradation and chemical modification. There have been numerous reports of QQ enzymes from bacteria. Treatment failure and recurrent staphylococcal infections are also brought on by biofilm development, which boosts an organism's ability to withstand antibiotics and is thought to be a virulence factor in patients. However, polyphenol quercetin antibiofilm activity is naturally available against drug-resistant Staphylococcus aureus.

Wastewater often contains an increased amount of mercury and, at the same time, resistant microorganisms. During wastewater treatment, a biofilm of indigenous microorganisms is often unavoidable. Therefore, the objective of this research is to isolate and identify microorganisms from wastewater and investigate their ability to form biofilms for possible application in mercury removal processes.

The resistance of planktonic cells and their biofilms to the effects of mercury was investigated using Minimum Biofilm Eradication Concentration-High Throughput Plates. The formation of biofilms and the degree of resistance to mercury were confirmed in polystyrene microtiter plates with 96 wells. Biofilm on AMB Media carriers (Assisting Moving Bad Media) was quantified using the Bradford protein assay. The removal of mercury ions by biofilms formed on AMB Media carriers of selected isolates and their consortia was determined by a removal test in Erlenmeyer flasks simulating MBBR.

All isolates in planktonic form showed some degree of resistance to mercury. The most resistant microorganisms (Enterobacter cloacae, Klebsiella oxytoca, Serratia odorifera, and Saccharomyces cerevisiae) were tested for their ability to form biofilms in the presence and absence of mercury, both in polystyrene plates and on ABM carriers. The results showed that among planktonic forms, K. oxytoca was the most resistant. A biofilm of the same microorganisms was more than 10-fold resistant. Most consortia biofilms had MBEC values > 100,000 μg/mL. Among individual biofilms, E. cloacae showed the highest mercury removal efficiency (97.81% for 10 days). Biofilm consortia composed of three species showed the best ability to remove mercury (96.64%–99.03% for 10 days).

This study points to the importance of consortia of different types of wastewater microorganisms in the form of biofilms and suggests that they can be used to remove mercury in wastewater treatment bioreactors.

Quorum sensing (QS) is the ability of bacteria to monitor their population density and adjust gene expression accordingly. QS-regulated processes include host–microbe interactions, horizontal gene transfer, and multicellular behaviours (such as the growth and development of biofilm). The creation, transfer, and perception of bacterial chemicals known as autoinducers or QS signals are necessary for QS signalling (e.g. N-acylhomoserine lactones). Quorum quenching (QQ), another name for the disruption of QS signalling, comprises a wide range of events and mechanisms that are described and analysed in this study. In order to better comprehend the targets of the QQ phenomena that organisms have naturally developed and are currently being actively researched from practical perspectives, we first surveyed the diversity of QS-signals and QS-associated responses. Next, the mechanisms, molecular players, and targets related to QS interference are discussed, with a focus on natural QQ enzymes and compounds that function as QS inhibitors. To illustrate the processes and biological functions of QS inhibition in microbe–microbe and host–microbe interactions, a few QQ paradigms are described in detail. Finally, certain QQ techniques are offered as potential instruments in a variety of industries, including agriculture, medical, aquaculture, crop production, and anti-biofouling areas.

Staphylococcus aureus is typically treated with antibiotics, however, due to its widespread and unselective usage, resistant strains of S. aureus have increased to a great extent. Treatment failure and recurring staphylococcal infections are also brought on by biofilm development, which boosts an organism's ability to withstand antibiotics and is thought to be a virulence factor in patients. The present study investigates the antibiofilm activity of naturally available polyphenol Quercetin against drug-resistant S. aureus. Micro dilution plating and tube adhesion methods were performed to evaluate the antibiofilm activity of quercetin against S. aureus. Quercetin treatment resulted in remarkably reduction of biofilm in S. aureus cells. Further we performed a study to investigate binding efficacies of quercetin with genes icaB and icaC from ica locus involved in biofilm formation. 3D structure of icaB, icaC and quercetin were retrieved from Protein data bank and PubChem chemical compound database, respectively. All computational simulation were carried out using AutoDock Vina and AutoDockTools (ADT) v 1.5.4. In silico study demonstrated a strong complex formation, large binding constants (K_b) and low free binding energy (ΔG) between quercetin and icaB (K_b = 1.63 × 10⁻⁵, ΔG = −7.2 k cal/mol) and icaC (K_b = 1.98 × 10⁻⁶, ΔG = −8.7 kcal/mol). This in silico analysis indicates that quercetin is capable of targeting icaB and icaC proteins which are essential for biofilm formation in S. aureus. Our study highlighted the antibiofilm activity of quercetin against drug resistant pathogen S.aureus.

Several species within the Acidithiobacillus (At.) genus can derive energy from oxidizing ferrous iron and sulfur. Two bacterial strains according to their 16S rRNA gene sequences closely related to At. ferridurans and At. ferrivorans were obtained from the industrial sulfide heap leaching process at Minera Escondida (SLH), named D2 and DM, respectively. We applied statistical and data mining analyses to the abundance of At. ferridurans D2 and At. ferrivorans DM taxa in the industrial process over 16 years of operation. In addition, we performed phylogenetic analysis and genome comparison of the type strains, as well as culturing approaches with representative isolates of At. ferridurans D2 and At. ferrivorans DM taxa to understand the differential phenotypic features. Throughout the 16 years, two main operational stages were identified based on the D2 and DM taxa predominance in solution samples. The better suitability of At. ferrivorans DM to grow in a wide range of temperature and in micro-oxic environments, and to oxidize S by reducing Fe(III) revealed through culturing approaches can, in a way, explain the taxa distribution in both operational stages. The isolate At. ferridurans D2 could be considered as a specialist in aerobic sulfur oxidation, while isolate At. ferrivorans DM is a specialist in iron oxidation. In addition, the results from ore samples occasionally obtained from the industrial heap suggest that At. ferridurans D2 abundance was more related to its abundance in the solution samples than At. ferrivorans DM was. This dynamic coincides with previously obtained results in in-lab cell-mineral attaching experiments with both strains. This information increases our knowledge the ecophysiology of Acidithiobacillus and of the importance of diverse physiological traits at industrial bioleaching scales.

Extreme acidophiles thrive in acidic environments, confront a multitude of challenges, and demonstrate remarkable adaptability in their metabolism to cope with the ever-changing environmental fluctuations, which encompass variations in temperature, pH levels, and the availability of electron acceptors and donors. The survival and proliferation of members within the Acidithiobacillia class rely on the deployment of transcriptional regulatory systems linked to essential physiological traits. The study of these transcriptional regulatory systems provides valuable insights into critical processes, such as energy metabolism and nutrient assimilation, and how they integrate into major genetic-metabolic circuits. In this study, we examined the transcriptional regulatory repertoires and potential interactions of forty-three Acidithiobacillia complete and draft genomes, encompassing nine species. To investigate the function and diversity of Transcription Factors (TFs) and their DNA Binding Sites (DBSs), we conducted a genome-wide comparative analysis, which allowed us to identify these regulatory elements in representatives of Acidithiobacillia. We classified TFs into gene families and compared their occurrence among all representatives, revealing conservation patterns across the class. The results identified conserved regulators for several pathways, including iron and sulfur oxidation, the main pathways for energy acquisition, providing new evidence for viable regulatory interactions and branch-specific conservation in Acidithiobacillia. The identification of TFs and DBSs not only corroborates existing experimental information for selected species, but also introduces novel candidates for experimental validation. Moreover, these promising candidates have the potential for further extension to new representatives within the class.

Within the European research project NEMO, a bioleaching strategy was developed for efficient metal extraction from bioleach residue currently heap-leached at Sotkamo (Finland) that still contains sulphidic minerals and valuable metals (Ni, Zn, Co, Cu). The strategy of gradually increasing the solid content with 5% steps allowed the adaptation of the consortium up to 20% (w/w) solid content, with efficient metal dissolution and same dominant bacteria. Largest proportions of Sulfobacillus thermosulfidooxidans while Eh increased suggested it to be most involved in iron oxidation. Acidithiobacillus caldus was rather found when pH stabilized, in line with a production of protons from sulphur oxidation that maintained low pH. ‘Acidithiomicrobium’ P2 was favoured towards the end of the runs and at 20% (w/w) solids possibly due to its tolerance to Ni. The use of gene abundance to evaluate biomass in the pulp provided complementary results to classical cell counts in the liquid phase, and suggested a key role of bacteria associated to mineral particles in iron oxidation. Scaling-up in 21-L stirred-tank reactor at 20% (w/w) solids had no detrimental effect on bioleaching and confirmed metal extraction rates. ‘Acidithiomicrobium’ P2 and Sb. thermosulfidooxidans remained main actors. However, the biological activity was considerably reduced at 30% (w/w) solid concentration, which may be due to a too drastic environmental change for the bacteria to adapt to higher solid concentration. Efficient bioleaching of Sotkamo bioleaching residue at high solid concentration was demonstrated, as well as the robustness of the selected moderately thermophilic consortium, at laboratory and pilot scales.

The sulfur oxidation kinetics of an industrial strain of Acidithiobacillus caldus (At. caldus) cultured on elemental sulfur was explored in batch experiments in the absence and presence of thiocyanate (SCN⁻), a toxin inherent within cyanidation tailings wastewater. The Contois rate expression accurately described At. caldus sulfate generation (R² > 0.93) and microbial growth (R² > 0.87). For a culture maintained at 45 °C a maximum specific growth rate (${\mu }_{\max }$) of 0.105 h⁻¹, sulfate yield from biomass ($Y_{px}$) of 4.8 × 10⁻⁹ mg SO₄²⁻.cell⁻¹, and Contois affinity coefficient ($K_x$) of 1.56 × 10⁻⁸ mg S.cell⁻¹ were established. The presence of SCN⁻ (0 mg/L - 20 mg/L) in the bulk solution inhibited the microbial system competitively. Moreover, SCN⁻ impeded microbial growth differentially; the rate expression was therefore partitioned with respect to SCN⁻ concentration and inhibition constants ($K_i$) were determined for each region. Adaptation to discrete concentrations of SCN⁻ (1 mg/L and 20 mg/L) improved SCN⁻ tolerance in At. caldus; however, adapted strains exhibited reduced sulfur oxidation potential when cultured under thiocyanate-free conditions relative to the non-adapted control strain. To describe the adapted systems accurately, the Contois affinity coefficient ($K_x$) was revised to reflect the suspected metabolic decline. The derived $K_x$ values increased in magnitude and affirmed an innate reduction in microbial substrate affinity or substrate adsorption capacity. Inclusion of these updated $K_x$ constants within the rate equation suitably represented the experimental data for both adapted At. caldus strains with R² > 0.94. Furthermore, the impact of adaptation on the inhibition kinetics and inhibition mechanism associated with SCN⁻ exposure were reviewed. Thiocyanate inhibited sulfur oxidation non-competitively in the adapted strains, and the shift in inhibition mechanism may be attributed to the compromised metabolic state following adaptation.

Bioleaching processes and acid mine drainage (AMD) generation are mainly driven by aerobic microbial iron(II) and inorganic sulfur/compound oxidation. Dissimilatory iron(III) reduction coupled to sulfur/compound oxidation (DIRSO) by acidophilic microorganisms has been described for anaerobic cultures, but iron reduction was observed under aerobic conditions as well. Aim of this study was to explore reaction rates and mechanisms of this process. Cell-specific iron(III) reduction rates for different Acidithiobacillus (At.) strains during batch culture growth or stationary phase with iron(III) (∼40 mM) as electron acceptor and elemental sulfur or tetrathionate as electron donor (1% or 5 mM, respectively) were determined. The rates were highest under anaerobic conditions for the At. ferrooxidans type strain with 6.8 × 10⁶ and 1.1 × 10⁷ reduced iron(III) ions per second per cell for growth on elemental sulfur and tetrathionate, respectively. The iron(III) reduction rates were somehow lower for the anaerobically sulfur grown archaeon Ferroplasma acidiphilum, and lowest for the sulfur grown At. caldus type strain under aerobic conditions (1.7 × 10⁶ and 7.3 × 10⁴ reduced iron(III) ions per second per cell, respectively). The rates for five strains of At. thiooxidans (aerobe) were in between those for At. ferrooxidans (anaerobe) and At. caldus (aerobe). There was no pronounced pH dependence of iron(III) reduction rates in the range of pH 1.0–1.9 for the type strains of all species but rates increased with increasing pH for four other At. thiooxidans strains. Thiosulfate as sulfur intermediate was found for At. ferrooxidans during anaerobic growths on tetrathionate and iron(III) but not during anaerobic growths on elemental sulfur and iron(III), and a small concentration was measured during aerobic growths on tetrathionate without iron(III). For the At. thiooxidans type strain thiosulfate was found with tetrathionate grown cells under aerobic conditions in presence and absence of iron(III), but not with sulfur grown cells. Evidence for hydrogen sulfide production at low pH was found for the At. ferrooxidans as well as the At. thiooxidans type strains during microaerophilic growth on elemental sulfur and for At. ferrooxidans during anaerobic growths on tetrathionate and iron(III). The occurrence of sulfur compound intermediates supports the hypothesis that chemical reduction of iron(III) ions takes place by sulfur compounds released by the microbial cells.

Rare earth element (REE) recovery from waste streams, mine tailings or recyclable components using bioleaching is gaining traction due to the shortage and security of REE supply as well as the environmental problems that occur from processing and refining. Four heterotrophic microbial species with known phosphate solubilizing capabilities were evaluated for their ability to leach REE from a high-grade monazite when provided with either galactose, fructose or maltose. Supplying fructose resulted in the greatest amount of REE leached from the ore due to the largest amount of organic acid produced. Gluconic acid was the dominant organic acid identified produced by the cultures, followed by acetic acid. The monazite proved difficult to leach with the different carbon sources, with preferential release of Ce over La, Nd and Pr.